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Minor binder design tutorial edits
- Fixed cd28_nag.pdb: the F chain NAG molecule did not have a residue number - Updated the example runscript files to remove any system/user-specific information. I also removed the variables as they seemed unnecessary for such a simple runscript. - Added example output files for CD28 and PDF1 - Added a 'Step 3' section for the small molecule example - Corrected noisy and denoised trajectory file descriptions in the tutorial text.
This commit is contained in:
Rachel Clune
@@ -263,8 +263,8 @@ Let's break this down:
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After RFD3 runs, 4 types of files should be generated:
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(In the list below 'n' can be 0 through 7, there should be one of each file for each RFD3 designed binder.)
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- pdl1_test_0_denoised_model_n.cif.gz: A trajectory of the diffusion process for just the designed portion of the model (the binder). If you play through the frames, it will start with the final structure and end with a set of fully diffused atoms.
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- pdl1_test_0_noised_model_n.cif.gz: A trajectory of the diffusion process for the full structure. If you play through the frames, it will start with the final structure and end with a set of fully diffused atoms.
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- pdl1_test_0_denoised_model_n.cif.gz: This trajectory files shows what the diffusion network thinks the final clean structure will be at each timestep. The input [motif](#binder_design_motif_def) is not held fixed in this view. Can be used to see what the model 'learned' at each step as it is easier to watch the secondary structure emerge during the diffusion process.
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- pdl1_test_0_noisy_model_n.cif.gz: A trajectory that shows how the diffusion process actually progressed while the input [motifs](#binder_design_motif_def) are held fixed. Can be used to verify motif integrity.
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- pdl1_test_0_model_n.cif.gz: This file contains the final binder structure generated by RFD3 along with any portions of the input structure that were specified by the configuration file.
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- pdl1_test_0_model_n.json: A JSON file with information about the design including metrics and a map between the input structure and the output structure, when applicable.
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@@ -464,6 +464,19 @@ Atoms on four residues (B42, B64, B87, B98) along with three polar atoms on the
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```{note}
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Fore more details on these settings, see the main text of the tutorial.
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```
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#### Step 3: Running RFD3
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You can run RFD3 to design this binder in the same way that was shown in the main example. Just make sure to change your output directory:
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```bash
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rfd3 design \
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out_dir="./pdf1_sm_binder_outputs" \
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inputs="./pdf1.yaml" \
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n_batches=1 \
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diffusion_batch_size=8 \
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dump_trajectories=True
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```
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(binder_design_glossary)=
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## Glossary
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(binder_design_hotspots_def)=
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@@ -1,5 +1,5 @@
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#!/bin/bash
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#SBATCH --partition=h100
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#SBATCH --partition=<your_partition>
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=6
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@@ -8,18 +8,11 @@
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#SBATCH --time 00:59:00
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#SBATCH --job-name="rfd3"
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source ~/.bashrc
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conda activate rc-foundry
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# Set variables
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INFILE="./cd28.yaml" #or .json
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OUTDIR="./diffusion_outs"
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# Run RFdiffusion3
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rfd3 design \
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out_dir="$OUTDIR" \
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inputs="$INFILE" \
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out_dir="./cd28_nag_binder_outputs" \
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inputs="./cd28.yaml" \
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n_batches=1 \
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diffusion_batch_size=1 \
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diffusion_batch_size=8 \
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dump_trajectories=1 # OPTIONAL, FOR VISUALIZATION PURPOSES
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@@ -1,4 +1,4 @@
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CRYST1 76.874 117.939 145.719 90.00 90.00 90.00 P 21 21 21 8
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CRYST1 76.874 117.939 145.719 90.00 90.00 90.00 P 21 21 21 1
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ATOM 1 N ASN B 1 38.389 -34.092 -9.177 1.00137.25 B N
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ANISOU 1 N ASN B 1 21502 14357 16290 1895 2418 -387 B N
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ATOM 2 CA ASN B 1 38.968 -34.790 -7.994 1.00128.01 B C
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@@ -31,8 +31,8 @@ ATOM 15 CD LYS B 2 34.653 -35.675 -4.782 1.00103.70 B C
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ANISOU 15 CD LYS B 2 16077 11051 12272 1054 904 -737 B C
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ATOM 16 CE LYS B 2 33.396 -36.184 -5.481 1.00104.44 B C
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ANISOU 16 CE LYS B 2 16624 11076 11983 677 623 -863 B C
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ATOM 17 NZ LYS B 2 32.173 -35.844 -4.747 1.00 98.10 B N
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ANISOU 17 NZ LYS B 2 15391 10627 11256 445 170 -892 B N
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ATOM 17 NZ LYS B 2 32.173 -35.844 -4.747 1.00 98.10 B N1+
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ANISOU 17 NZ LYS B 2 15391 10627 11256 445 170 -892 B N1+
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ATOM 18 N ILE B 3 38.280 -34.042 -2.067 1.00 90.16 B N
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ANISOU 18 N ILE B 3 12681 9873 11702 1775 1343 -170 B N
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ATOM 19 CA ILE B 3 39.133 -33.842 -0.907 1.00 84.65 B C
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@@ -95,8 +95,8 @@ ATOM 47 CD LYS B 6 43.427 -37.278 6.420 1.00134.57 B C
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ANISOU 47 CD LYS B 6 15494 16936 18701 2457 1131 1681 B C
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ATOM 48 CE LYS B 6 44.215 -37.293 5.126 1.00123.69 B C
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ANISOU 48 CE LYS B 6 14116 15463 17420 2732 1565 1891 B C
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ATOM 49 NZ LYS B 6 44.040 -36.032 4.387 1.00112.91 B N
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ANISOU 49 NZ LYS B 6 12776 14101 16024 2471 1441 1696 B N
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ATOM 49 NZ LYS B 6 44.040 -36.032 4.387 1.00112.91 B N1+
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ANISOU 49 NZ LYS B 6 12776 14101 16024 2471 1441 1696 B N1+
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ATOM 50 N GLN B 7 39.100 -38.754 10.005 1.00 89.11 B N
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ANISOU 50 N GLN B 7 10656 10843 12357 1844 325 631 B N
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ATOM 51 CA GLN B 7 38.564 -38.444 11.318 1.00 84.60 B C
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@@ -235,8 +235,8 @@ ATOM 117 CG ASP B 15 32.452 -33.897 32.903 1.00143.76 B C
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ANISOU 117 CG ASP B 15 24476 15108 15037 -1176 -1142 -186 B C
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ATOM 118 OD1 ASP B 15 32.523 -35.122 33.223 1.00139.70 B O
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ANISOU 118 OD1 ASP B 15 23701 14731 14648 -1010 -1205 -104 B O
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ATOM 119 OD2 ASP B 15 32.670 -32.969 33.715 1.00161.77 B O
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ANISOU 119 OD2 ASP B 15 27544 17092 16831 -1545 -1238 -197 B O
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ATOM 119 OD2 ASP B 15 32.670 -32.969 33.715 1.00161.77 B O1-
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ANISOU 119 OD2 ASP B 15 27544 17092 16831 -1545 -1238 -197 B O1-
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ATOM 120 N ASN B 16 29.864 -34.792 28.764 1.00 94.68 B N
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ANISOU 120 N ASN B 16 16158 9425 10392 42 -105 -447 B N
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ATOM 121 CA ASN B 16 28.928 -34.428 27.701 1.00 95.89 B C
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@@ -349,8 +349,8 @@ ATOM 174 CD LYS B 23 43.986 -34.665 11.434 1.00110.63 B C
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ANISOU 174 CD LYS B 23 11526 14919 15588 1050 -659 1932 B C
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ATOM 175 CE LYS B 23 43.796 -34.687 12.944 1.00112.30 B C
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ANISOU 175 CE LYS B 23 11790 15227 15652 793 -1032 1941 B C
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ATOM 176 NZ LYS B 23 45.074 -34.483 13.633 1.00113.01 B N
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ANISOU 176 NZ LYS B 23 11395 15718 15827 588 -1325 2431 B N
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ATOM 176 NZ LYS B 23 45.074 -34.483 13.633 1.00113.01 B N1+
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ANISOU 176 NZ LYS B 23 11395 15718 15827 588 -1325 2431 B N1+
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ATOM 177 N TYR B 24 41.447 -32.628 6.442 1.00 90.84 B N
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ANISOU 177 N TYR B 24 10170 11499 12846 1214 116 778 B N
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ATOM 178 CA TYR B 24 41.254 -32.607 5.007 1.00 78.07 B C
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@@ -495,8 +495,8 @@ ATOM 247 NE ARG B 31 42.183 -23.902 -0.762 1.00 97.53 B N
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ANISOU 247 NE ARG B 31 12208 11627 13220 577 811 297 B N
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ATOM 248 CZ ARG B 31 42.551 -23.951 -2.037 1.00109.44 B C
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ANISOU 248 CZ ARG B 31 13819 13019 14746 760 1097 348 B C
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ATOM 249 NH1 ARG B 31 41.746 -23.535 -2.998 1.00115.51 B N
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ANISOU 249 NH1 ARG B 31 14990 13581 15318 897 1172 158 B N
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ATOM 249 NH1 ARG B 31 41.746 -23.535 -2.998 1.00115.51 B N1+
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ANISOU 249 NH1 ARG B 31 14990 13581 15318 897 1172 158 B N1+
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ATOM 250 NH2 ARG B 31 43.733 -24.439 -2.358 1.00115.55 B N
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ANISOU 250 NH2 ARG B 31 14290 13885 15729 826 1325 627 B N
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ATOM 251 N GLU B 32 37.389 -19.845 0.838 1.00 82.18 B N
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@@ -515,8 +515,8 @@ ATOM 257 CD GLU B 32 34.939 -16.654 0.967 1.00 99.30 B C
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ANISOU 257 CD GLU B 32 15149 10684 11898 995 914 -482 B C
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ATOM 258 OE1 GLU B 32 34.446 -15.971 1.898 1.00 99.41 B O
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ANISOU 258 OE1 GLU B 32 15505 10517 11748 1006 1031 -480 B O
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ATOM 259 OE2 GLU B 32 35.973 -16.337 0.333 1.00 98.19 B O
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ANISOU 259 OE2 GLU B 32 15047 10497 11763 786 953 -487 B O
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ATOM 259 OE2 GLU B 32 35.973 -16.337 0.333 1.00 98.19 B O1-
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ANISOU 259 OE2 GLU B 32 15047 10497 11763 786 953 -487 B O1-
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ATOM 260 N PHE B 33 34.987 -21.703 2.255 1.00 80.35 B N
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ANISOU 260 N PHE B 33 11278 9073 10180 920 228 -507 B N
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ATOM 261 CA PHE B 33 34.566 -23.096 2.394 1.00 75.01 B C
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@@ -557,8 +557,8 @@ ATOM 278 NE ARG B 34 26.610 -25.168 3.870 1.00 78.01 B N
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ANISOU 278 NE ARG B 34 9812 9714 10113 1831 -152 -23 B N
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ATOM 279 CZ ARG B 34 25.699 -25.836 4.544 1.00 88.74 B C
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ANISOU 279 CZ ARG B 34 10932 11222 11564 1832 -180 76 B C
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ATOM 280 NH1 ARG B 34 25.995 -26.998 5.100 1.00 85.29 B N
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ANISOU 280 NH1 ARG B 34 10434 10785 11186 1615 -278 -55 B N
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ATOM 280 NH1 ARG B 34 25.995 -26.998 5.100 1.00 85.29 B N1+
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ANISOU 280 NH1 ARG B 34 10434 10785 11186 1615 -278 -55 B N1+
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ATOM 281 NH2 ARG B 34 24.489 -25.319 4.704 1.00112.63 B N
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ANISOU 281 NH2 ARG B 34 13774 14393 14628 2076 -74 339 B N
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ATOM 282 N ALA B 35 32.106 -26.243 5.864 1.00 67.83 B N
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@@ -635,8 +635,8 @@ ATOM 317 CD LYS B 39 22.984 -37.520 15.925 1.00 86.07 B C
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ANISOU 317 CD LYS B 39 10500 10495 11708 560 261 -328 B C
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ATOM 318 CE LYS B 39 21.890 -38.486 16.278 1.00 99.83 B C
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ANISOU 318 CE LYS B 39 12106 12313 13511 382 348 -237 B C
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ATOM 319 NZ LYS B 39 22.235 -39.324 17.432 1.00110.99 B N
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ANISOU 319 NZ LYS B 39 13811 13503 14856 366 469 -334 B N
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ATOM 319 NZ LYS B 39 22.235 -39.324 17.432 1.00110.99 B N1+
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ANISOU 319 NZ LYS B 39 13811 13503 14856 366 469 -334 B N1+
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ATOM 320 N GLY B 40 24.282 -39.795 12.064 1.00 80.87 B N
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ANISOU 320 N GLY B 40 10074 9877 10775 -63 -274 -608 B N
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ATOM 321 CA GLY B 40 23.445 -40.898 11.629 1.00 88.79 B C
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@@ -675,8 +675,8 @@ ATOM 337 CG ASP B 42 19.583 -41.867 8.102 1.00114.66 B C
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ANISOU 337 CG ASP B 42 13877 15062 14626 -1986 -1229 -113 B C
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ATOM 338 OD1 ASP B 42 20.310 -41.416 8.995 1.00114.24 B O
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ANISOU 338 OD1 ASP B 42 13837 14845 14726 -1527 -976 -207 B O
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ATOM 339 OD2 ASP B 42 18.356 -41.939 8.238 1.00105.85 B O
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ANISOU 339 OD2 ASP B 42 12345 14274 13599 -2261 -1362 141 B O
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ATOM 339 OD2 ASP B 42 18.356 -41.939 8.238 1.00105.85 B O1-
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ANISOU 339 OD2 ASP B 42 12345 14274 13599 -2261 -1362 141 B O1-
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ATOM 340 N SER B 43 23.048 -40.163 7.277 1.00127.99 B N
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ANISOU 340 N SER B 43 16153 16188 16288 -942 -935 -533 B N
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ATOM 341 CA SER B 43 23.500 -38.763 7.270 1.00116.71 B C
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@@ -729,8 +729,8 @@ ATOM 364 CD GLU B 46 24.257 -29.305 7.384 1.00112.83 B C
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ANISOU 364 CD GLU B 46 13468 14497 14906 1417 -286 53 B C
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ATOM 365 OE1 GLU B 46 23.322 -28.500 7.110 1.00106.88 B O
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ANISOU 365 OE1 GLU B 46 12540 13889 14180 1631 -207 295 B O
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ATOM 366 OE2 GLU B 46 25.242 -29.587 6.647 1.00110.28 B O
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ANISOU 366 OE2 GLU B 46 13301 14090 14510 1276 -413 -117 B O
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ATOM 366 OE2 GLU B 46 25.242 -29.587 6.647 1.00110.28 B O1-
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ANISOU 366 OE2 GLU B 46 13301 14090 14510 1276 -413 -117 B O1-
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ATOM 367 N VAL B 47 24.351 -31.611 12.133 1.00 71.72 B N
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ANISOU 367 N VAL B 47 8558 8882 9811 1238 81 -166 B N
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ATOM 368 CA VAL B 47 24.644 -31.133 13.477 1.00 83.80 B C
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@@ -1005,8 +1005,8 @@ ATOM 502 CD LYS B 63 21.604 -25.846 9.739 1.00132.54 B C
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ANISOU 502 CD LYS B 63 16044 16827 17487 2594 831 833 B C
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ATOM 503 CE LYS B 63 20.391 -24.967 9.680 1.00126.53 B C
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ANISOU 503 CE LYS B 63 15089 16192 16796 3034 1142 1249 B C
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ATOM 504 NZ LYS B 63 20.106 -24.698 8.278 1.00137.02 B N
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ANISOU 504 NZ LYS B 63 16118 17803 18139 3076 917 1414 B N
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ATOM 504 NZ LYS B 63 20.106 -24.698 8.278 1.00137.02 B N1+
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ANISOU 504 NZ LYS B 63 16118 17803 18139 3076 917 1414 B N1+
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ATOM 505 N THR B 64 20.269 -28.243 14.807 1.00129.31 B N
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ANISOU 505 N THR B 64 15882 16007 17242 2518 1548 837 B N
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ATOM 506 CA THR B 64 19.296 -29.284 15.104 1.00132.92 B C
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@@ -1093,8 +1093,8 @@ ATOM 546 CG ASP B 69 31.514 -22.953 20.593 1.00 96.27 B C
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ANISOU 546 CG ASP B 69 17089 9249 10239 -434 368 -663 B C
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ATOM 547 OD1 ASP B 69 30.365 -22.480 20.321 1.00 91.53 B O
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ANISOU 547 OD1 ASP B 69 16627 8470 9680 10 834 -634 B O
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ATOM 548 OD2 ASP B 69 32.122 -22.668 21.664 1.00 94.05 B O
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ANISOU 548 OD2 ASP B 69 17408 8746 9579 -864 211 -683 B O
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ATOM 548 OD2 ASP B 69 32.122 -22.668 21.664 1.00 94.05 B O1-
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ANISOU 548 OD2 ASP B 69 17408 8746 9579 -864 211 -683 B O1-
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ATOM 549 N GLY B 70 33.254 -23.801 16.536 1.00 83.98 B N
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ANISOU 549 N GLY B 70 13511 8769 9629 -346 -257 -597 B N
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ATOM 550 CA GLY B 70 34.167 -24.144 15.439 1.00 84.84 B C
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@@ -1119,8 +1119,8 @@ ATOM 559 CD LYS B 71 40.454 -23.023 18.027 1.00108.19 B C
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ANISOU 559 CD LYS B 71 16127 12778 12204 -3093 -2275 196 B C
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ATOM 560 CE LYS B 71 39.706 -21.760 18.446 1.00104.14 B C
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ANISOU 560 CE LYS B 71 16575 11742 11250 -3260 -2034 -36 B C
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ATOM 561 NZ LYS B 71 39.695 -21.599 19.904 1.00102.49 B N
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ANISOU 561 NZ LYS B 71 17019 11316 10607 -3669 -2219 -39 B N
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ATOM 561 NZ LYS B 71 39.695 -21.599 19.904 1.00102.49 B N1+
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ANISOU 561 NZ LYS B 71 17019 11316 10607 -3669 -2219 -39 B N1+
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ATOM 562 N LEU B 72 39.345 -23.198 13.195 1.00 99.31 B N
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ANISOU 562 N LEU B 72 13866 11791 12076 -1608 -1309 -49 B N
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ATOM 563 CA LEU B 72 40.009 -23.458 11.917 1.00 95.52 B C
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@@ -1177,8 +1177,8 @@ ATOM 588 CD GLU B 75 47.229 -30.863 6.137 1.00137.88 B C
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ANISOU 588 CD GLU B 75 14147 18618 19624 844 152 2530 B C
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ATOM 589 OE1 GLU B 75 47.551 -30.690 4.937 1.00133.36 B O
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ANISOU 589 OE1 GLU B 75 13590 17938 19143 1034 507 2581 B O
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ATOM 590 OE2 GLU B 75 47.759 -31.774 6.825 1.00138.48 B O
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ANISOU 590 OE2 GLU B 75 13879 18909 19830 1017 129 2872 B O
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ATOM 590 OE2 GLU B 75 47.759 -31.774 6.825 1.00138.48 B O1-
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ANISOU 590 OE2 GLU B 75 13879 18909 19830 1017 129 2872 B O1-
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ATOM 591 N SER B 76 42.317 -28.489 8.422 1.00 84.32 B N
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ANISOU 591 N SER B 76 9265 10996 11776 -47 -739 817 B N
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ATOM 592 CA SER B 76 41.366 -29.091 9.343 1.00 78.08 B C
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@@ -1431,8 +1431,8 @@ ATOM 715 CG ASP B 90 23.981 -41.948 15.576 1.00 77.33 B C
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ANISOU 715 CG ASP B 90 10026 9036 10321 -58 160 -659 B C
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ATOM 716 OD1 ASP B 90 24.446 -42.588 14.631 1.00 82.84 B O
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ANISOU 716 OD1 ASP B 90 10895 9668 10913 -176 91 -733 B O
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ATOM 717 OD2 ASP B 90 22.761 -41.794 15.735 1.00 84.85 B O
|
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ANISOU 717 OD2 ASP B 90 10737 10144 11359 -183 191 -545 B O
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ATOM 717 OD2 ASP B 90 22.761 -41.794 15.735 1.00 84.85 B O1-
|
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ANISOU 717 OD2 ASP B 90 10737 10144 11359 -183 191 -545 B O1-
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ATOM 718 N ILE B 91 27.186 -42.286 14.974 1.00 68.45 B N
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ANISOU 718 N ILE B 91 9333 7622 9051 325 122 -779 B N
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ATOM 719 CA ILE B 91 28.239 -42.035 14.016 1.00 72.26 B C
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@@ -1523,8 +1523,8 @@ ATOM 761 CD LYS B 95 28.476 -31.901 3.197 1.00120.14 B C
|
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ANISOU 761 CD LYS B 95 15209 14992 15448 784 -669 -576 B C
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ATOM 762 CE LYS B 95 28.959 -30.454 3.149 1.00111.18 B C
|
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ANISOU 762 CE LYS B 95 14062 13829 14350 971 -581 -545 B C
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ATOM 763 NZ LYS B 95 27.930 -29.464 2.834 1.00104.74 B N
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ANISOU 763 NZ LYS B 95 13134 13156 13508 1077 -634 -413 B N
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ATOM 763 NZ LYS B 95 27.930 -29.464 2.834 1.00104.74 B N1+
|
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ANISOU 763 NZ LYS B 95 13134 13156 13508 1077 -634 -413 B N1+
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ATOM 764 N ILE B 96 32.743 -31.341 3.602 1.00 91.46 B N
|
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ANISOU 764 N ILE B 96 11733 11002 12014 1015 -256 -625 B N
|
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ATOM 765 CA ILE B 96 33.428 -30.097 3.251 1.00 89.07 B C
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@@ -1557,8 +1557,8 @@ ATOM 778 CD GLU B 97 29.436 -26.818 -0.583 1.00 90.55 B C
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ANISOU 778 CD GLU B 97 11883 11114 11407 1331 -493 -401 B C
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ATOM 779 OE1 GLU B 97 28.846 -25.715 -0.477 1.00119.13 B O
|
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ANISOU 779 OE1 GLU B 97 15463 14787 15015 1503 -453 -287 B O
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ATOM 780 OE2 GLU B 97 29.017 -27.770 -1.281 1.00 76.75 B O
|
||||
ANISOU 780 OE2 GLU B 97 10175 9426 9561 1187 -645 -404 B O
|
||||
ATOM 780 OE2 GLU B 97 29.017 -27.770 -1.281 1.00 76.75 B O1-
|
||||
ANISOU 780 OE2 GLU B 97 10175 9426 9561 1187 -645 -404 B O1-
|
||||
ATOM 781 N VAL B 98 34.887 -26.578 -0.909 1.00 72.02 B N
|
||||
ANISOU 781 N VAL B 98 9800 8247 9319 1229 146 -532 B N
|
||||
ATOM 782 CA VAL B 98 35.661 -25.378 -1.168 1.00 82.02 B C
|
||||
@@ -1709,8 +1709,8 @@ ATOM 854 CG ASP B 106 31.883 -33.033 -3.513 1.00 99.04 B C
|
||||
ANISOU 854 CG ASP B 106 14348 11363 11920 722 -159 -773 B C
|
||||
ATOM 855 OD1 ASP B 106 32.640 -33.201 -4.487 1.00129.87 B O
|
||||
ANISOU 855 OD1 ASP B 106 18629 15025 15691 792 71 -781 B O
|
||||
ATOM 856 OD2 ASP B 106 30.858 -33.725 -3.379 1.00107.00 B O
|
||||
ANISOU 856 OD2 ASP B 106 15401 12451 12801 484 -379 -796 B O
|
||||
ATOM 856 OD2 ASP B 106 30.858 -33.725 -3.379 1.00107.00 B O1-
|
||||
ANISOU 856 OD2 ASP B 106 15401 12451 12801 484 -379 -796 B O1-
|
||||
ATOM 857 N ASN B 107 34.100 -33.447 -0.580 1.00 86.68 B N
|
||||
ANISOU 857 N ASN B 107 12071 9860 11005 1107 236 -647 B N
|
||||
ATOM 858 CA ASN B 107 34.888 -34.519 0.011 1.00 87.05 B C
|
||||
@@ -1743,8 +1743,8 @@ ATOM 871 CD GLU B 108 36.714 -40.922 -2.955 1.00140.17 B C
|
||||
ANISOU 871 CD GLU B 108 21707 14730 16821 1701 2296 -440 B C
|
||||
ATOM 872 OE1 GLU B 108 37.061 -40.024 -3.776 1.00145.77 B O
|
||||
ANISOU 872 OE1 GLU B 108 22368 15466 17553 1761 2322 -412 B O
|
||||
ATOM 873 OE2 GLU B 108 37.004 -42.140 -3.131 1.00128.31 B O
|
||||
ANISOU 873 OE2 GLU B 108 20796 12844 15113 1832 2708 -391 B O
|
||||
ATOM 873 OE2 GLU B 108 37.004 -42.140 -3.131 1.00128.31 B O1-
|
||||
ANISOU 873 OE2 GLU B 108 20796 12844 15113 1832 2708 -391 B O1-
|
||||
ATOM 874 N LYS B 109 33.340 -39.435 0.737 1.00 89.88 B N
|
||||
ANISOU 874 N LYS B 109 13606 9589 10955 859 681 -766 B N
|
||||
ATOM 875 CA LYS B 109 32.698 -39.992 1.922 1.00 95.63 B C
|
||||
@@ -1761,8 +1761,8 @@ ATOM 880 CD LYS B 109 29.870 -40.925 3.109 1.00111.61 B C
|
||||
ANISOU 880 CD LYS B 109 16111 12681 13614 25 16 -968 B C
|
||||
ATOM 881 CE LYS B 109 29.105 -41.602 4.204 1.00116.43 B C
|
||||
ANISOU 881 CE LYS B 109 16624 13354 14261 -140 -54 -985 B C
|
||||
ATOM 882 NZ LYS B 109 28.738 -42.972 3.827 1.00121.31 B N
|
||||
ANISOU 882 NZ LYS B 109 17813 13699 14580 -435 43 -1059 B N
|
||||
ATOM 882 NZ LYS B 109 28.738 -42.972 3.827 1.00121.31 B N1+
|
||||
ANISOU 882 NZ LYS B 109 17813 13699 14580 -435 43 -1059 B N1+
|
||||
ATOM 883 N SER B 110 33.731 -39.905 4.164 1.00 92.61 B N
|
||||
ANISOU 883 N SER B 110 13133 10261 11791 1096 601 -613 B N
|
||||
ATOM 884 CA SER B 110 34.619 -40.364 5.232 1.00 83.37 B C
|
||||
@@ -1895,8 +1895,8 @@ ATOM 947 CD LYS B 118 30.829 -44.068 29.066 1.00112.11 B C
|
||||
ANISOU 947 CD LYS B 118 17220 12088 13289 944 -22 -70 B C
|
||||
ATOM 948 CE LYS B 118 31.688 -44.397 30.254 1.00114.21 B C
|
||||
ANISOU 948 CE LYS B 118 17759 12332 13302 954 -245 128 B C
|
||||
ATOM 949 NZ LYS B 118 33.095 -44.387 29.847 1.00114.70 B N
|
||||
ANISOU 949 NZ LYS B 118 17483 12693 13405 1005 -586 383 B N
|
||||
ATOM 949 NZ LYS B 118 33.095 -44.387 29.847 1.00114.70 B N1+
|
||||
ANISOU 949 NZ LYS B 118 17483 12693 13405 1005 -586 383 B N1+
|
||||
TER
|
||||
HETATM 950 C1 NAG C 1 16.898 -38.892 24.556 1.00125.19 C C
|
||||
ANISOU 950 C1 NAG C 1 15908 14690 16969 1202 2730 636 C C
|
||||
@@ -1982,34 +1982,34 @@ HETATM 990 O7 NAG E 1 49.621 -23.391 6.703 1.00147.29 E O
|
||||
ANISOU 990 O7 NAG E 1 15423 20281 20258 -2323 -1137 2696 E O
|
||||
HETATM 991 C8 NAG E 1 50.639 -24.329 4.757 1.00140.26 E C
|
||||
ANISOU 991 C8 NAG E 1 13824 19540 19926 -1541 -402 3147 E C
|
||||
HETATM 992 C1 NAG F 2 38.446 -46.151 6.083 1.00113.99 F C
|
||||
ANISOU 992 C1 NAG F 2 16924 11888 14498 2958 2733 543 F C
|
||||
HETATM 993 C2 NAG F 2 39.785 -45.486 6.381 1.00122.68 F C
|
||||
ANISOU 993 C2 NAG F 2 17347 13326 15941 3321 2763 942 F C
|
||||
HETATM 994 N2 NAG F 2 39.728 -44.047 6.264 1.00125.14 F N
|
||||
ANISOU 994 N2 NAG F 2 17154 13976 16418 3066 2351 854 F N
|
||||
HETATM 995 C3 NAG F 2 40.855 -46.108 5.502 1.00133.25 F C
|
||||
ANISOU 995 C3 NAG F 2 18954 14406 17270 3817 3386 1269 F C
|
||||
HETATM 996 O3 NAG F 2 42.102 -45.452 5.670 1.00146.14 F O
|
||||
ANISOU 996 O3 NAG F 2 19886 16398 19243 4120 3411 1693 F O
|
||||
HETATM 997 C4 NAG F 2 40.967 -47.571 5.899 1.00137.06 F C
|
||||
ANISOU 997 C4 NAG F 2 19931 14554 17592 4131 3821 1412 F C
|
||||
HETATM 998 O4 NAG F 2 41.972 -48.234 5.137 1.00145.44 F O
|
||||
ANISOU 998 O4 NAG F 2 21305 15324 18630 4678 4503 1768 F O
|
||||
HETATM 999 C5 NAG F 2 39.632 -48.281 5.685 1.00126.26 F C
|
||||
ANISOU 999 C5 NAG F 2 19339 12797 15835 3719 3783 967 F C
|
||||
HETATM 1000 O5 NAG F 2 38.492 -47.571 6.216 1.00112.39 F O
|
||||
ANISOU 1000 O5 NAG F 2 17310 11303 14089 3168 3160 614 F O
|
||||
HETATM 1001 C6 NAG F 2 39.631 -49.609 6.403 1.00131.91 F C
|
||||
ANISOU 1001 C6 NAG F 2 20473 13241 16408 3944 4102 1075 F C
|
||||
HETATM 1002 O6 NAG F 2 39.849 -49.420 7.808 1.00132.15 F O
|
||||
ANISOU 1002 O6 NAG F 2 19849 13666 16694 4023 3786 1245 F O
|
||||
HETATM 1003 C7 NAG F 2 40.363 -43.191 7.068 1.00126.96 F C
|
||||
ANISOU 1003 C7 NAG F 2 16711 14615 16915 3073 2061 1060 F C
|
||||
HETATM 1004 O7 NAG F 2 40.801 -42.141 6.621 1.00109.11 F O
|
||||
ANISOU 1004 O7 NAG F 2 14120 12549 14789 3010 1942 1118 F O
|
||||
HETATM 1005 C8 NAG F 2 40.502 -43.564 8.519 1.00124.23 F C
|
||||
ANISOU 1005 C8 NAG F 2 16094 14455 16652 3119 1880 1213 F C
|
||||
HETATM 992 C1 NAG F 1 38.446 -46.151 6.083 1.00113.99 F C
|
||||
ANISOU 992 C1 NAG F 1 16924 11888 14498 2958 2733 543 F C
|
||||
HETATM 993 C2 NAG F 1 39.785 -45.486 6.381 1.00122.68 F C
|
||||
ANISOU 993 C2 NAG F 1 17347 13326 15941 3321 2763 942 F C
|
||||
HETATM 994 N2 NAG F 1 39.728 -44.047 6.264 1.00125.14 F N
|
||||
ANISOU 994 N2 NAG F 1 17154 13976 16418 3066 2351 854 F N
|
||||
HETATM 995 C3 NAG F 1 40.855 -46.108 5.502 1.00133.25 F C
|
||||
ANISOU 995 C3 NAG F 1 18954 14406 17270 3817 3386 1269 F C
|
||||
HETATM 996 O3 NAG F 1 42.102 -45.452 5.670 1.00146.14 F O
|
||||
ANISOU 996 O3 NAG F 1 19886 16398 19243 4120 3411 1693 F O
|
||||
HETATM 997 C4 NAG F 1 40.967 -47.571 5.899 1.00137.06 F C
|
||||
ANISOU 997 C4 NAG F 1 19931 14554 17592 4131 3821 1412 F C
|
||||
HETATM 998 O4 NAG F 1 41.972 -48.234 5.137 1.00145.44 F O
|
||||
ANISOU 998 O4 NAG F 1 21305 15324 18630 4678 4503 1768 F O
|
||||
HETATM 999 C5 NAG F 1 39.632 -48.281 5.685 1.00126.26 F C
|
||||
ANISOU 999 C5 NAG F 1 19339 12797 15835 3719 3783 967 F C
|
||||
HETATM 1000 O5 NAG F 1 38.492 -47.571 6.216 1.00112.39 F O
|
||||
ANISOU 1000 O5 NAG F 1 17310 11303 14089 3168 3160 614 F O
|
||||
HETATM 1001 C6 NAG F 1 39.631 -49.609 6.403 1.00131.91 F C
|
||||
ANISOU 1001 C6 NAG F 1 20473 13241 16408 3944 4102 1075 F C
|
||||
HETATM 1002 O6 NAG F 1 39.849 -49.420 7.808 1.00132.15 F O
|
||||
ANISOU 1002 O6 NAG F 1 19849 13666 16694 4023 3786 1245 F O
|
||||
HETATM 1003 C7 NAG F 1 40.363 -43.191 7.068 1.00126.96 F C
|
||||
ANISOU 1003 C7 NAG F 1 16711 14615 16915 3073 2061 1060 F C
|
||||
HETATM 1004 O7 NAG F 1 40.801 -42.141 6.621 1.00109.11 F O
|
||||
ANISOU 1004 O7 NAG F 1 14120 12549 14789 3010 1942 1118 F O
|
||||
HETATM 1005 C8 NAG F 1 40.502 -43.564 8.519 1.00124.23 F C
|
||||
ANISOU 1005 C8 NAG F 1 16094 14455 16652 3119 1880 1213 F C
|
||||
HETATM 1006 C1 NAG G 1 37.496 -29.746 23.883 1.00137.62 G C
|
||||
ANISOU 1006 C1 NAG G 1 19994 16404 15890 -1804 -2332 198 G C
|
||||
HETATM 1007 C2 NAG G 1 37.540 -30.296 25.314 1.00150.63 G C
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@@ -0,0 +1,186 @@
|
||||
{
|
||||
"diffused_index_map": {
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
"B28": "B28",
|
||||
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|
||||
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|
||||
"B31": "B31",
|
||||
"B32": "B32",
|
||||
"B33": "B33",
|
||||
"B34": "B34",
|
||||
"B35": "B35",
|
||||
"B36": "B36",
|
||||
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|
||||
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|
||||
"B39": "B39",
|
||||
"B40": "B40",
|
||||
"B41": "B41",
|
||||
"B42": "B42",
|
||||
"B43": "B43",
|
||||
"B44": "B44",
|
||||
"B45": "B45",
|
||||
"B46": "B46",
|
||||
"B47": "B47",
|
||||
"B48": "B48",
|
||||
"B49": "B49",
|
||||
"B50": "B50",
|
||||
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||||
"B52": "B52",
|
||||
"B53": "B53",
|
||||
"B54": "B54",
|
||||
"B55": "B55",
|
||||
"B56": "B56",
|
||||
"B57": "B57",
|
||||
"B58": "B58",
|
||||
"B59": "B59",
|
||||
"B60": "B60",
|
||||
"B61": "B61",
|
||||
"B62": "B62",
|
||||
"B63": "B63",
|
||||
"B64": "B64",
|
||||
"B65": "B65",
|
||||
"B66": "B66",
|
||||
"B67": "B67",
|
||||
"B68": "B68",
|
||||
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|
||||
"B70": "B70",
|
||||
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|
||||
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|
||||
"B73": "B73",
|
||||
"B74": "B74",
|
||||
"B75": "B75",
|
||||
"B76": "B76",
|
||||
"B77": "B77",
|
||||
"B78": "B78",
|
||||
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||||
"B80": "B80",
|
||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
"B106": "B106",
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||||
"B107": "B107",
|
||||
"B108": "B108",
|
||||
"B109": "B109",
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||||
"B110": "B110",
|
||||
"B111": "B111",
|
||||
"B112": "B112",
|
||||
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|
||||
"B114": "B114",
|
||||
"B115": "B115",
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||||
"B116": "B116",
|
||||
"B117": "B117",
|
||||
"B118": "B118"
|
||||
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|
||||
"metrics": {
|
||||
"max_ca_deviation": 0.9557368755340576,
|
||||
"n_chainbreaks": 2,
|
||||
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|
||||
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|
||||
"n_clashing.ligand_clashes": 0,
|
||||
"n_clashing.ligand_min_distance": 6.276482582092285,
|
||||
"non_loop_fraction": 0.8857142857142857,
|
||||
"loop_fraction": 0.11428571428571428,
|
||||
"helix_fraction": 0.8857142857142857,
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||||
"sheet_fraction": 0.0,
|
||||
"num_ss_elements": 3,
|
||||
"radius_of_gyration": 12.544560262410931,
|
||||
"alanine_content": 0.0851063829787234,
|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
"fixed_com": [
|
||||
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||||
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||||
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||||
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|
||||
},
|
||||
"specification": {
|
||||
"input": "/home/rclune/rfd3_tests/binder_design_tutorial/CD28/cd28_nag.pdb",
|
||||
"contig": "55-88,/0,B1-118,C1-1,D1-1,E1-1,F1-1,G1-2",
|
||||
"length": "179-212",
|
||||
"extra": {
|
||||
"example": "test",
|
||||
"task_name": "cd28_test",
|
||||
"sampled_contig": "70,/0,B1,B2,B3,B4,B5,B6,B7,B8,B9,B10,B11,B12,B13,B14,B15,B16,B17,B18,B19,B20,B21,B22,B23,B24,B25,B26,B27,B28,B29,B30,B31,B32,B33,B34,B35,B36,B37,B38,B39,B40,B41,B42,B43,B44,B45,B46,B47,B48,B49,B50,B51,B52,B53,B54,B55,B56,B57,B58,B59,B60,B61,B62,B63,B64,B65,B66,B67,B68,B69,B70,B71,B72,B73,B74,B75,B76,B77,B78,B79,B80,B81,B82,B83,B84,B85,B86,B87,B88,B89,B90,B91,B92,B93,B94,B95,B96,B97,B98,B99,B100,B101,B102,B103,B104,B105,B106,B107,B108,B109,B110,B111,B112,B113,B114,B115,B116,B117,B118,C1,D1,E1,F1,G1,G2",
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||||
"num_tokens_in": 194,
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"example_id": "cd28_test_0"
|
||||
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|
||||
"select_fixed_atoms": true,
|
||||
"select_unfixed_sequence": false,
|
||||
"select_hbond_donor": {
|
||||
"B100": "OH",
|
||||
"B104": "OH",
|
||||
"B31": "NH1,NH2,NE"
|
||||
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|
||||
"select_hotspots": {
|
||||
"B4": "CB,CD1,CD2,CG",
|
||||
"B3": "CG1,CG2,CD1,CB",
|
||||
"B105": "CB,CD1,CD2,CG",
|
||||
"B104": "CD1,CD2,CE1,CE2,CB,CZ,OH",
|
||||
"B100": "CD1,CD2,CE1,CE2,CB,CZ,OH",
|
||||
"B102": "CB,CD,CG,N",
|
||||
"B101": "CB,CD,CG,N",
|
||||
"B31": "CB,CD,CG,CZ,NH1,NH2,NE"
|
||||
},
|
||||
"infer_ori_strategy": "hotspots",
|
||||
"is_non_loopy": true
|
||||
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|
||||
"ckpt_path": "/home/rclune/foundry_weights/rfd3_latest.ckpt",
|
||||
"seed": null
|
||||
}
|
||||
Binary file not shown.
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Binary file not shown.
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||||
{
|
||||
"diffused_index_map": {
|
||||
"B1": "B1",
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"B12": "B12",
|
||||
"B13": "B13",
|
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"B14": "B14",
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"B15": "B15",
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"B16": "B16",
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"B17": "B17",
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"B18": "B18",
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"B19": "B19",
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"B20": "B20",
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"B21": "B21",
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"B22": "B22",
|
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"B23": "B23",
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"B24": "B24",
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"B25": "B25",
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"B26": "B26",
|
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"B27": "B27",
|
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"B28": "B28",
|
||||
"B29": "B29",
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"B30": "B30",
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"B40": "B40",
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"B41": "B41",
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"B42": "B42",
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"B43": "B43",
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"B44": "B44",
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"B45": "B45",
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"B46": "B46",
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"B47": "B47",
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"B48": "B48",
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"B49": "B49",
|
||||
"B50": "B50",
|
||||
"B51": "B51",
|
||||
"B52": "B52",
|
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"B53": "B53",
|
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"B54": "B54",
|
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"B55": "B55",
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"B56": "B56",
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"B57": "B57",
|
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"B58": "B58",
|
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"B59": "B59",
|
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"B60": "B60",
|
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"B61": "B61",
|
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"B62": "B62",
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"B63": "B63",
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"B64": "B64",
|
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"B65": "B65",
|
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"B66": "B66",
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"B67": "B67",
|
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"B68": "B68",
|
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"B69": "B69",
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"B70": "B70",
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"B71": "B71",
|
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"B72": "B72",
|
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"B73": "B73",
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"B74": "B74",
|
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"B75": "B75",
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"B76": "B76",
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"B77": "B77",
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"B78": "B78",
|
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"B79": "B79",
|
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"B80": "B80",
|
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"B81": "B81",
|
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"B82": "B82",
|
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"B83": "B83",
|
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"B84": "B84",
|
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"B85": "B85",
|
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"B86": "B86",
|
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"B87": "B87",
|
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"B88": "B88",
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"B89": "B89",
|
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"B90": "B90",
|
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"B91": "B91",
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"B92": "B92",
|
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"B93": "B93",
|
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"B94": "B94",
|
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"B95": "B95",
|
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"B96": "B96",
|
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"B97": "B97",
|
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"B98": "B98",
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"B99": "B99",
|
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"B100": "B100",
|
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"B101": "B101",
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"B102": "B102",
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"B103": "B103",
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"B104": "B104",
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"B105": "B105",
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"B106": "B106",
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"B109": "B109",
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"B110": "B110",
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"B113": "B113",
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"B115": "B115",
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"B116": "B116",
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"B117": "B117",
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"B119": "B119",
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"B120": "B120",
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"B121": "B121",
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"B122": "B122",
|
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"B123": "B123",
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"B124": "B124",
|
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|
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|
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|
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|
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|
||||
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|
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
"B161": "B161",
|
||||
"B162": "B162",
|
||||
"B163": "B163",
|
||||
"B164": "B164",
|
||||
"B165": "B165",
|
||||
"B166": "B166",
|
||||
"B167": "B167"
|
||||
},
|
||||
"metrics": {
|
||||
"max_ca_deviation": 0.7722530364990234,
|
||||
"n_chainbreaks": 1,
|
||||
"n_clashing.interresidue_clashes_w_sidechain": 2,
|
||||
"n_clashing.interresidue_clashes_w_backbone": 0,
|
||||
"n_clashing.ligand_clashes": 0,
|
||||
"n_clashing.ligand_min_distance": 4.00691556930542,
|
||||
"non_loop_fraction": 0.6727272727272727,
|
||||
"loop_fraction": 0.32727272727272727,
|
||||
"helix_fraction": 0.4909090909090909,
|
||||
"sheet_fraction": 0.18181818181818182,
|
||||
"num_ss_elements": 5,
|
||||
"radius_of_gyration": 18.92053532521758,
|
||||
"alanine_content": 0.07657657657657657,
|
||||
"glycine_content": 0.036036036036036036,
|
||||
"num_residues": 222,
|
||||
"diffused_com": [
|
||||
0.6073246002197266,
|
||||
-0.2350466251373291,
|
||||
-1.219813346862793
|
||||
],
|
||||
"fixed_com": [
|
||||
-0.020551782101392746,
|
||||
0.0038190188352018595,
|
||||
-0.0013108595740050077
|
||||
]
|
||||
},
|
||||
"specification": {
|
||||
"input": "/home/rclune/rfd3_tests/binder_design_tutorial/PDF1/pdf1_sm.pdb",
|
||||
"contig": "55-88,/0,B1-167,C1-1",
|
||||
"extra": {
|
||||
"example": "test",
|
||||
"task_name": "pdf1_test",
|
||||
"sampled_contig": "55,/0,B1,B2,B3,B4,B5,B6,B7,B8,B9,B10,B11,B12,B13,B14,B15,B16,B17,B18,B19,B20,B21,B22,B23,B24,B25,B26,B27,B28,B29,B30,B31,B32,B33,B34,B35,B36,B37,B38,B39,B40,B41,B42,B43,B44,B45,B46,B47,B48,B49,B50,B51,B52,B53,B54,B55,B56,B57,B58,B59,B60,B61,B62,B63,B64,B65,B66,B67,B68,B69,B70,B71,B72,B73,B74,B75,B76,B77,B78,B79,B80,B81,B82,B83,B84,B85,B86,B87,B88,B89,B90,B91,B92,B93,B94,B95,B96,B97,B98,B99,B100,B101,B102,B103,B104,B105,B106,B107,B108,B109,B110,B111,B112,B113,B114,B115,B116,B117,B118,B119,B120,B121,B122,B123,B124,B125,B126,B127,B128,B129,B130,B131,B132,B133,B134,B135,B136,B137,B138,B139,B140,B141,B142,B143,B144,B145,B146,B147,B148,B149,B150,B151,B152,B153,B154,B155,B156,B157,B158,B159,B160,B161,B162,B163,B164,B165,B166,B167,C1",
|
||||
"num_tokens_in": 223,
|
||||
"num_residues_in": 223,
|
||||
"num_chains": 2,
|
||||
"num_atoms": 1653,
|
||||
"num_residues": 170,
|
||||
"example_id": "pdf1_test_0"
|
||||
},
|
||||
"select_fixed_atoms": true,
|
||||
"select_unfixed_sequence": false,
|
||||
"select_hbond_donor": {
|
||||
"B87": "OH",
|
||||
"B98": "OH",
|
||||
"B64": "OE1,OE2",
|
||||
"B42": "N",
|
||||
"C1": "O20,N21,O27"
|
||||
},
|
||||
"select_hotspots": {
|
||||
"B64": "OE1,OE2,CD,CB,CG",
|
||||
"B126": "CB,CD1,CD2,CG",
|
||||
"B87": "CD1,CD2,CE1,CE2,CB,CZ,OH",
|
||||
"B98": "CD1,CD2,CE1,CE2,CB,CZ,OH",
|
||||
"B88": "CB,CG,OE1,NE2",
|
||||
"B42": "CB,CD,CG,N",
|
||||
"B44": "CB,CD1,CG1,CG2",
|
||||
"C1": "C15,C16,C17,C18,O20,N21,C22,C23,C24,C25,O27"
|
||||
},
|
||||
"is_non_loopy": true
|
||||
},
|
||||
"ckpt_path": "/home/rclune/foundry_weights/rfd3_latest.ckpt",
|
||||
"seed": null
|
||||
}
|
||||
Binary file not shown.
@@ -1,5 +1,5 @@
|
||||
#!/bin/bash
|
||||
#SBATCH --partition=h100
|
||||
#SBATCH --partition=<your_partition>
|
||||
#SBATCH --nodes=1
|
||||
#SBATCH --ntasks=1
|
||||
#SBATCH --cpus-per-task=6
|
||||
@@ -8,18 +8,11 @@
|
||||
#SBATCH --time 00:59:00
|
||||
#SBATCH --job-name="rfd3"
|
||||
|
||||
source ~/.bashrc
|
||||
conda activate rc-foundry
|
||||
|
||||
# Set variables
|
||||
INFILE="./pdf1.yaml" #or .json
|
||||
OUTDIR="./diffusion_outs"
|
||||
|
||||
# Run RFdiffusion3
|
||||
rfd3 design \
|
||||
out_dir="$OUTDIR" \
|
||||
inputs="$INFILE" \
|
||||
out_dir="./pdf1_sm_binder_outputs" \
|
||||
inputs="./pdf1.yaml" \
|
||||
n_batches=1 \
|
||||
diffusion_batch_size=1 \
|
||||
diffusion_batch_size=8 \
|
||||
dump_trajectories=1 # OPTIONAL, FOR VISUALIZATION PURPOSES
|
||||
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
#!/bin/bash
|
||||
#SBATCH --partition=h100
|
||||
#SBATCH --partition=<your_partition>
|
||||
#SBATCH --nodes=1
|
||||
#SBATCH --ntasks=1
|
||||
#SBATCH --cpus-per-task=6
|
||||
@@ -8,18 +8,11 @@
|
||||
#SBATCH --time 00:59:00
|
||||
#SBATCH --job-name="rfd3"
|
||||
|
||||
source ~/.bashrc
|
||||
conda activate rc-foundry
|
||||
|
||||
# Set variables
|
||||
INFILE="./pdl1.yaml" #or .json
|
||||
OUTDIR="./diffusion_outs"
|
||||
|
||||
# Run RFdiffusion3
|
||||
rfd3 design \
|
||||
out_dir="$OUTDIR" \
|
||||
inputs="$INFILE" \
|
||||
out_dir= "./pdl1_binder_outputs" \
|
||||
inputs="./pdl1.yaml" \
|
||||
n_batches=1 \
|
||||
diffusion_batch_size=1 \
|
||||
diffusion_batch_size=8 \
|
||||
dump_trajectories=1 # OPTIONAL, FOR VISUALIZATION PURPOSES
|
||||
|
||||
|
||||
Reference in New Issue
Block a user