Inpainting is trying to connect multiple chains #29
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could you email us ***@***.***, ***@***.***, ***@***.***) with the
example inputs and outputs for this?
there could be a bugfix that hasn't made it into the public version of this
yet.
…On Thu, Sep 22, 2022 at 8:49 AM Jared Adolf-Bryfogle < ***@***.***> wrote:
Trying to build in presence of a receptor as such:
contigs='A219-585,5-10,A588-735,0,R144-237'
The 5-10 loop is rebuilt, but RFDesign is trying to build between the
first and second chain. It outputs everything as a single chain with some
residues being moved from the first chain onto the second chain in a way
that would start to connect them. Any advice on this? Thanks.
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Hey Jue, I tried flipping where the other chain was present (to the beginning instead of the end), but the same problem persists. I'm using this on a public structure, so I could send it. The email is blocked by github - if you are on the RC slack, I can also share them there. If the bug fix is in a branch, I could also try that. -Jared |
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Hi there, |
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Send me your inputs and run script? I thought I fixed this on main after Jared's message but I can doublecheck on your case. |
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Hey Dr. Wang,
So my input PDB is "input_1.pdb", the script I am running is "DesignScript.xml" (txt for attachment). The chain break is supposed to occur between A 15 and 1 in this example. I recently converted all chains in the input to A to help with Rosetta rms alignment for post processing. I have tried a variety of different formats including ",0 ,A" ",0A1..." ",0-0,A..." etc in addition to the suggested format of ",0 A...".
…________________________________
From: Jue Wang ***@***.***>
Sent: Tuesday, November 22, 2022 11:05 AM
To: RosettaCommons/RFDesign ***@***.***>
Cc: Cooper Svajda ***@***.***>; Comment ***@***.***>
Subject: Re: [RosettaCommons/RFDesign] Inpainting is trying to connect multiple chains (Issue #29)
Send me your inputs and run script? I thought I fixed this on main after Jared's message but I can doublecheck on your case.
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#!/bin/bash
##NECESSARY JOB SPECIFICATIONS
#SBATCH --time=00:20:00
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=5
#SBATCH --mem=32G
#SBATCH --output=Out.%j
#SBATCH --gres=gpu:1
#SBATCH --partition=gpu
module load Anaconda/3-5.0.0.1
source activate SE3-nvidia
python /scratch/user/cooper1995/protein/dream/RFDesign/inpainting/inpaint.py --pdb="input/input_1.pdb" --contigs="A7-15,0 A1-1,5-15,A6-6,10-15,A2-2,1-1,A3-3,10-30,A4-4,1-1,A5-5,4-5" --out="/scratch/user/cooper1995/protein/dream/RFDesign/inpainting/output/output_1" --num_designs=3 --dump_all --n_cycle=11
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I think you will need to email this to me (jue@uw.edu). Github did not forward your attachments to this thread. |
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Hey Dr. Wang, were you able to receive my emails and open attachments? |
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has this issue been solved? how to add chain break? |
Trying to build in presence of a receptor as such:
contigs='A219-585,5-10,A588-735,0,R144-237'The 5-10 loop is rebuilt, but RFDesign is trying to build between the first and second chain. It outputs everything as a single chain with some residues being moved from the first chain onto the second chain in a way that would start to connect them. Any advice on this? Thanks.
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