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An: pymol-users@lists.sourceforge.net
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Datum: 15.06.2020 22:47
Betreff: PyMOL-users Digest, Vol 169, Issue 20
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Today's Topics:
1. Re: renumber (Mooers, Blaine H.M. (HSC))
2. Re: renumber (Jared Sampson)
----------------------------------------------------------------------
Message: 1
Date: Mon, 15 Jun 2020 20:11:22 +0000
From: "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu>
To: "Oganesyan, Vaheh" <vaheh.oganes...@astrazeneca.com>, Jared
Sampson <jared.samp...@columbia.edu>
Cc: "pymol-users@lists.sourceforge.net"
<pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber
Message-ID:
<87dcc6c40b22804192b6892e6429ec5fdbefd...@countach.hsc.net.ou.edu>
Content-Type: text/plain; charset="Windows-1252"
Hi Vaheh,
I susoect that your issue is an edge case for PyMOL.
The resi variable is limited to integers (see
https://pymolwiki.org/index.php/Property_Selectors).
Atoms with letters in the resi field are invisible to PyMOL.
You could write a python script to preprocess the coordinates, run the script
from within PyMOL, and then reload the modified coordinates into PyMOL.
It might be more expedient to use pdb_set from ccp4,
antibody_numbering_converter.macosclangrelease in rosetta, or biopython.
Best regards,
Blaine
PS Half of our students work in OMRF labs. Our interactions with OMRF are as
close as ever.
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 2:57 PM
To: Jared Sampson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber
Jared,
Are you saying it cannot be done within PyMOL? The ccp4 option is well known.
Thanks.
From: Jared Sampson <jared.samp...@columbia.edu>
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
Hi Vaheh -
Try `pdbset` from the CCP4 suite.
http://www.ccp4.ac.uk/html/pdbset.html#renumber<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ccp4.ac.uk_html_pdbset.html-23renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=GnEFkqUJR4dd1O4W5j6uD5OVSJXvwp_ONuPcl6tUB_I&e=>
```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```
Hope that helps.
Cheers,
Jared
From: Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com><mailto:vaheh.oganes...@astrazeneca.com>
Reply: Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com><mailto:vaheh.oganes...@astrazeneca.com>
Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC)
<blaine-moo...@ouhsc.edu><mailto:blaine-moo...@ouhsc.edu>, Jarrett Johnson
<jarrett.john...@schrodinger.com><mailto:jarrett.john...@schrodinger.com>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
<pymol-users@lists.sourceforge.net><mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber
Blain,
The command will not change the numbering of amino acids starting from #1. But
if you got missing ones, like in my case, it will. Except for those having also
letter in the number field. I mean the numbering used for CDRs of antibodies,
not alternatives. Hence, my question, is there a command that will ignore the
letters in the number field and renumber the amino acids in the order they
appear in the file.
Thank you.
From: Mooers, Blaine H.M. (HSC)
<blaine-moo...@ouhsc.edu<mailto:blaine-moo...@ouhsc.edu>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>>;
Jarrett Johnson
<jarrett.john...@schrodinger.com<mailto:jarrett.john...@schrodinger.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] renumber
Hi Vaheh,
alter vh, resi=str(int(resi)+0)
will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: [EXTERNAL] Re: [PyMOL] renumber
Thank you Jarrett,
Then the command
alter vh, resi=str(int(resi)+0)
should work, right? But it doesn?t because there are residue numbers with
letters. Is there a command that will either remove the letters or won?t pay
attention to them and renumber sequentially.
Regards,
From: Jarrett Johnson
<jarrett.john...@schrodinger.com<mailto:jarrett.john...@schrodinger.com>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>>
Cc: pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber
Hello,
The command shown on this page
https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=YUAB1OMR35mD78DtkN0-jGzM7DXrF2uIqVbgVkypuvQ&s=uEl_YqHefDypoAGkjQR211JPMc8HPqE4NwgLL5ZiZ_4&e=><https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=>
is not one that comes with PyMOL by default. Try downloading the script and
importing it via the `run` command in the PyMOL command-line:
run
renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=>
and then you should be able to use the command as shown on the Wiki page.
Hope that helps,
Jarrett J.
On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com%3cmailto:vaheh.oganes...@astrazeneca.com>>>
wrote:
Hello PyMOLers,
Wiki uses renumber command to alter residue numbers, but PyMOL doesn?t
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?
Regards,
Vaheh
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--
Jarrett Johnson | Senior Developer
[Schrodinger
Logo]<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.schrodinger.com_&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=my7IR5rxG-1yA5AP52htw3MT5MKRSqHAwEmOVfdcSdc&e=>
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------------------------------
Message: 2
Date: Mon, 15 Jun 2020 16:46:34 -0400
From: Jared Sampson <jared.samp...@columbia.edu>
To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Cc: "=?utf-8?Q?pymol-users=40lists.sourceforge.net?="
<pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] renumber
Message-ID: <etpan.5ee7de2f.17152c71.18...@columbia.edu>
Content-Type: text/plain; charset="utf-8"
Hi Vaheh -?
I wasn't saying it can't be done, just that pdbset is my preferred way to
handle renumbering when going in the insertion code --> integer direction.
Within PyMOL, here is one way (you'll have to repeat for each chain you wish to
renumber):
```
# see:?https://pymolwiki.org/index.php/Pymol.stored
from pymol import stored
# store the current residue numbers in a list
stored.oldresi = []
iterate polymer.protein and chain L and n. CA, stored.oldresi.append(resi)
# make a list of the new residue numbers
stored.newresi = list(range(1, len(stored.oldresi)+1))
# zip them together into a lookup dict
stored.hash = dict(zip(stored.oldresi, stored.newresi))
# change the residue numbers for each atom in your chain
alter polymer.protein and chain L, resi=stored.hash[resi]
```
Hope that helps.
Cheers,
Jared
From:?Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Reply:?Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Date:?June 15, 2020 at 3:57:24 PM
To:?Jared Sampson <jared.samp...@columbia.edu>
Cc:?pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net>
Subject:? RE: [PyMOL] renumber
Jared,
?
Are you saying it cannot be done within PyMOL? The ccp4 option is well known.
?
Thanks.
?
From: Jared Sampson <jared.samp...@columbia.edu>
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
?
Hi Vaheh -
?
Try `pdbset` from the CCP4 suite.
?
http://www.ccp4.ac.uk/html/pdbset.html#renumber
?
```
pdbset xyzin in.pdb xyzout out.pdb > pdbset.log << EOF
renum 1 chain H
renum 1 chain L
end
EOF
```
?
Hope that helps.
?
Cheers,
Jared
?
From:?Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Reply:?Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Date:?June 15, 2020 at 1:28:23 PM
To:?Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>, Jarrett Johnson
<jarrett.john...@schrodinger.com>
Cc:?pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net>
Subject:? Re: [PyMOL] renumber
Blain,
?
The command will not change the numbering of amino acids starting from #1. But
if you got missing ones, like in my case, it will. Except for those having also
letter in the number field. I mean the numbering used for CDRs of antibodies,
not alternatives. Hence, my question, is there a command that will ignore the
letters in the number field and renumber the amino acids in the order they
appear in the file.
?
Thank you.
?
From: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>; Jarrett Johnson
<jarrett.john...@schrodinger.com>
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber
?
Hi Vaheh,
alter vh, resi=str(int(resi)+0)
will not change the residue numbers because 0 is being added.
Replace 0 with your desired residue number offset.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Oganesyan, Vaheh [vaheh.oganes...@astrazeneca.com]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] Re: [PyMOL] renumber
Thank you Jarrett,
Then the command
alter vh, resi=str(int(resi)+0)
should work, right? But it doesn?t because there are residue numbers with
letters. Is there a command that will either remove the letters or won?t pay
attention to them and renumber sequentially.
Regards,
From: Jarrett Johnson <jarrett.john...@schrodinger.com>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh <vaheh.oganes...@astrazeneca.com>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
Hello,
The command shown on this page
https://pymolwiki.org/index.php/Renumber<https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php_Renumber&d=DwMGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=ziFhw29qVsmpI-rra_AyanmqFEsNZVmEsXF4VIjUMmI&e=>
is not one that comes with PyMOL by default. Try downloading the script and
importing it via the `run` command in the PyMOL command-line:
run
renumber.py<https://urldefense.proofpoint.com/v2/url?u=http-3A__renumber.py&d=DwQGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=HQhXfRvgQZ3mFRTUuOGKZTZZVlTRi9o87ygYqEDnPog&s=FHmoNz1s1Pj-_paiWCTfneG3RkPiLccu2uI2KNr8ROw&e=>
and then you should be able to use the command as shown on the Wiki page.
Hope that helps,
Jarrett J.
On Mon, Jun 15, 2020 at 11:29 AM Oganesyan, Vaheh
<vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com>> wrote:
Hello PyMOLers,
Wiki uses renumber command to alter residue numbers, but PyMOL doesn?t
recognize it. Is it that Wiki is old, or my PyMOL version is dusty?
Regards,
Vaheh
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