Inpainting is trying to connect multiple chains

Question

Inpainting is trying to connect multiple chains

jadolfbr opened this issue 2 years ago · 8 comments

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.

Answer 1 · 2022-09-22T16:22:41.000Z

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.

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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. — Reply to this email directly, view it on GitHub <#29>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABCU5ZYUKA5FHCVJVORE3LV7R5XTANCNFSM6AAAAAAQTGDD2E> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

Answer 2 · 2022-09-22T16:58:52.000Z

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

Answer 3 · 2022-11-22T16:10:33.000Z

Hi there,
I am having the same issue where it is fusing my receptor chain. I tried completely purging my /RFDesign and redownloading, didn't help. I have tried different formats of contig inputs, ex: "B1-10,0 A1-xx / B1-10,0-0,A1-xx / B1-10,0,A1-xx " etc and they all have either same issue or don't run at all.

Answer 4 · 2022-11-22T17:05:18.000Z

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.

Answer 5 · 2022-11-22T17:28:49.000Z

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...".

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________________________________ 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. — Reply to this email directly, view it on GitHub<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FRosettaCommons%2FRFDesign%2Fissues%2F29%23issuecomment-1323991111&data=05%7C01%7Ccooper.svajda%40ag.tamu.edu%7C51457c9b4c3448e435ce08daccabc223%7C9fd7580a64724d9ca142d131d3a7a116%7C0%7C0%7C638047335311715929%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=c5XZtaA%2FKvEthQOHQ3yw1efWKKOf7oRk3WUcRa2Wtvc%3D&reserved=0>, or unsubscribe<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FA2AKQ6WWC6TMDKD3HBUKISTWJT4NRANCNFSM6AAAAAAQTGDD2E&data=05%7C01%7Ccooper.svajda%40ag.tamu.edu%7C51457c9b4c3448e435ce08daccabc223%7C9fd7580a64724d9ca142d131d3a7a116%7C0%7C0%7C638047335311715929%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Qn2RgKK6HFpIKeZ8DhEH6fuL3pC7RaoESdW3QwPMFaI%3D&reserved=0>. You are receiving this because you commented.Message ID: ***@***.***> #!/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

Answer 6 · 2022-11-22T17:31:24.000Z

I think you will need to email this to me (jue@uw.edu). Github did not forward your attachments to this thread.

Answer 7 · 2022-11-23T14:39:14.000Z

Hey Dr. Wang, were you able to receive my emails and open attachments?

Answer 8 · 2023-08-27T16:24:57.000Z

has this issue been solved? how to add chain break?