1.preprocessing.py error

[kimdn]

Thank you for sharing code.

I downloaded 3ztj.pdb

Then, modified it to start with resnum=1 by https://github.com/haddocking/pdb-tools

Then, I ran python ../iNNterfaceDesign_scripts/1.preprocessing.py PepBB.input

Then, I see

Can you upload your/working 3ztj.pdb file?

Maybe, I should have used rosetta tools' residue_renumber (that Riju and others contributed) instead as iNNterfaceDesign's Manual suggested? -> however, extracting rosetta_bin_linux_3.13_bundle.tgz (18 Gb) takes a long time. Rosetta_xxx.tgz used to be much smaller (around 3 Gb in 2011~2016 as I remember).

[rsyrlyb]

Hello, renumbered 3ztj.pdb is attached. I did not try tools for renumbering other than clean_pdb.py, so I cannot tell if your suggestion works or not. As far as I know, clean_pdb.py is in open access: https://github.com/bestlab/GREMLIN_RF/blob/master/preprocessing/rosetta_scripts/clean_pdb.py I hope this helps. 3ztj_ABCDEF.pdb.gz

[kimdn]

@rsyrlyb Thanks for sharing 3ztj_ABCDEF.pdb.gz

I just used

pdb: 3ztj_ABCDEF
anchor_res: 363-365,367

and ran python ../iNNterfaceDesign_scripts/1.preprocessing.py PepBB.input

Then, I see

What pyrosetta ver. did you use?

[kimdn]

The 2nd approach

I ran python /people/kimd999/bin/rosetta_bin_linux_2021.16.61629_bundle/main/tools/protein_tools/scripts/clean_pdb.py 3ztj.pdb ignorechain

Then, I got 3ztj_ignorechain.pdb (that has ATOM only and starts with resnum=1)

Then, I ran the same command with

pdb: 3ztj_ignorechain
anchor_res: 363-365,367

Then, I got a similar error

[rsyrlyb]

Hello, the error is not related with pyrosetta this time. It is related with your input file: the script got error while tried to read keywords. I have run an input with your keywords and it runs smoothly. Could you try to run my input file, I've attached it.

Raulia

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From: Doo Nam Kim @.> Sent: Thursday, March 24, 2022 12:58 PM To: strauchlab/iNNterfaceDesign @.> Cc: Raulia Syrlybaeva @.>; Mention @.> Subject: Re: [strauchlab/iNNterfaceDesign] 1.preprocessing.py error (Issue #3)

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The 2nd approach

I ran python /people/kimd999/bin/rosetta_bin_linux_2021.16.61629_bundle/main/tools/protein_tools/scripts/clean_pdb.py 3ztj.pdb ignorechain

Then, I got 3ztj_ignorechain.pdb (that has ATOM only and starts with resnum=1)

Then, I ran the same command with

pdb: 3ztj_ignorechain anchor_res: 363-365,367

Then, I got a similar error [Screen Shot 2022-03-24 at 9 56 03 AM]https://user-images.githubusercontent.com/3903446/159969531-43324d93-5bc0-4c73-a100-f058065aaa3b.png

— Reply to this email directly, view it on GitHubhttps://github.com/strauchlab/iNNterfaceDesign/issues/3#issuecomment-1077837744, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AG5IWREB6K5UWJLKP4O4MR3VBSNJZANCNFSM5RP5J66A. You are receiving this because you were mentioned.Message ID: @.***>

[kimdn]

For PepSep,,

I ran python ../iNNterfaceDesign_scripts/1.preprocessing_sp.py PepSep.input

PepSep.input is

pdb: pdb_files/3ztj_ABCDEF
res1:363

Message is

Using 3ztj_ignorechain resulted in the same/similar message as well.

[kimdn]

Raulia

Hi Raulia,

Yes, the error message appears to be related to modules.functions.keywords rather than PyRosetta. I can't find your input file. If you mean your input file as 3ztj_ABCDEF.pdb.gz, I already tried it.

[rsyrlyb]

Names of files should not contain names of folders currently. Besides, PepSep1 is for generating sequences for interfaces, but 3ztj_ABCDEF contains residues of target protein only. You should provide ligand: HL chains which are native or backbones generated by PepBB. res1 is first residue of ligand part, not target protein residue.

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From: Doo Nam Kim @.> Sent: Thursday, March 24, 2022 1:18 PM To: strauchlab/iNNterfaceDesign @.> Cc: Raulia Syrlybaeva @.>; Mention @.> Subject: Re: [strauchlab/iNNterfaceDesign] 1.preprocessing.py error (Issue #3)

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For PepSep,,

I ran python ../iNNterfaceDesign_scripts/1.preprocessing_sp.py PepSep.input

PepSep.input is

pdb: pdb_files/3ztj_ABCDEF res1:363

Message is [Screen Shot 2022-03-24 at 10 13 26 AM]https://user-images.githubusercontent.com/3903446/159973086-db963e77-2838-4f4b-be25-a27dda1fd27a.png

Using 3ztj_ignorechain resulted in the same/similar message as well.

— Reply to this email directly, view it on GitHubhttps://github.com/strauchlab/iNNterfaceDesign/issues/3#issuecomment-1077856326, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AG5IWRDVJKTDUM4LMHAAOMDVBSPWBANCNFSM5RP5J66A. You are receiving this because you were mentioned.Message ID: @.***>

[rsyrlyb]

I have attached it to the previous message. I am going to add a new reply in github with that input. Update: I was answering through email, that's why you did not see the input here.

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From: Doo Nam Kim @.> Sent: Thursday, March 24, 2022 1:25 PM To: strauchlab/iNNterfaceDesign @.> Cc: Raulia Syrlybaeva @.>; Mention @.> Subject: Re: [strauchlab/iNNterfaceDesign] 1.preprocessing.py error (Issue #3)

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Raulia

Hi Raulia,

Yes, the error message appears to be related to modules.functions.keywords rather than PyRosetta. I can't find your input file. If you mean your input file as 3ztj_ABCDEF.pdb.gzhttps://github.com/strauchlab/iNNterfaceDesign/files/8342212/3ztj_ABCDEF.pdb.gz, I already tried it.

— Reply to this email directly, view it on GitHubhttps://github.com/strauchlab/iNNterfaceDesign/issues/3#issuecomment-1077862378, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AG5IWRDEDRHK5GHR55LDWSDVBSQPLANCNFSM5RP5J66A. You are receiving this because you were mentioned.Message ID: @.***>

[rsyrlyb]

input.txt

[rsyrlyb]

Is input.txt work? Could you tell which difference between your and my input caused the error (if you got results)?

[kimdn]

Yes input.txt worked (generated 3ztj_ABCDEF/binders/,, pockets,,,). Thanks.

I was gonna share what caused the error anyway.

When I set PepBB.input as

pdb: 3ztj_ABCDEF
#3ztj_ignorechain
#3ztj_ABCDEF failed as well
#3ztj_starts_w_1_by_pdb_tools.pdb failed with s-s

anchor_res: 363-365,367

it failed.

Once I removed # lines like you share input.txt, the error is solved.

[rsyrlyb]

Thanks. Usage of # lines shouldn't cause the problem, such lines should be ignored: text = {a.split(':')[0]: a.split(':')[1].strip() for a in text if (a[0] != '#') and (a.split(':')[1].strip() != '')}. However, empty line could. I'll check it.

[kimdn]

Thanks. Usage of # lines shouldn't cause the problem, such lines should be ignored: text = {a.split(':')[0]: a.split(':')[1].strip() for a in text if (a[0] != '#') and (a.split(':')[1].strip() != '')}. However, empty line could. I'll check it.

Yes, input file that has # starting lines ran well.