[PyMOL] Antwort: PyMOL-users Digest, Vol 169, Issue 20

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Von: pym...@li...
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)" <Bla...@ou...>
To: "Oganesyan, Vaheh" <vah...@as...>, Jared
	Sampson <jar...@co...>
Cc: "pym...@li..."
	<pym...@li...>
Subject: Re: [PyMOL] renumber
Message-ID:
	<87D...@CO...>
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 [vah...@as...]
Sent: Monday, June 15, 2020 2:57 PM
To: Jared Sampson
Cc: pym...@li...
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 <jar...@co...>
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh <vah...@as...>
Cc: pym...@li...
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 <vah...@as...><mailto:vah...@as...>
Reply: Oganesyan, Vaheh <vah...@as...><mailto:vah...@as...>
Date: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) <bla...@ou...><mailto:bla...@ou...>, Jarrett Johnson <jar...@sc...><mailto:jar...@sc...>
Cc: pym...@li...<mailto:pym...@li...> <pym...@li...><mailto:pym...@li...>
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) <Bla...@ou...<mailto:Bla...@ou...>>
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>; Jarrett Johnson <jar...@sc...<mailto:jar...@sc...>>
Cc: pym...@li...<mailto:pym...@li...>
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 [vah...@as...]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pym...@li...<mailto:pym...@li...>
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 <jar...@sc...<mailto:jar...@sc...>>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>>
Cc: pym...@li...<mailto:pym...@li...>
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 <vah...@as...<mailto:vah...@as...<mailto:vah...@as...%3cmailto:vah...@as...>>> 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 <jar...@co...>
To: Oganesyan, Vaheh <vah...@as...>
Cc: "=?utf-8?Q?pymol-users=40lists.sourceforge.net?="
	<pym...@li...>
Subject: Re: [PyMOL] renumber
Message-ID: <etP...@co...>
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 <vah...@as...>
Reply:?Oganesyan, Vaheh <vah...@as...>
Date:?June 15, 2020 at 3:57:24 PM
To:?Jared Sampson <jar...@co...>
Cc:?pym...@li... <pym...@li...>
Subject:? RE: [PyMOL] renumber  

Jared,

?

Are you saying it cannot be done within PyMOL? The ccp4 option is well known.

?

Thanks.

?

From: Jared Sampson <jar...@co...>  
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh <vah...@as...>
Cc: pym...@li...
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 <vah...@as...>
Reply:?Oganesyan, Vaheh <vah...@as...>
Date:?June 15, 2020 at 1:28:23 PM
To:?Mooers, Blaine H.M. (HSC) <bla...@ou...>, Jarrett Johnson <jar...@sc...>
Cc:?pym...@li... <pym...@li...>
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) <Bla...@ou...>  
Sent: Monday, June 15, 2020 12:06 PM
To: Oganesyan, Vaheh <vah...@as...>; Jarrett Johnson <jar...@sc...>
Cc: pym...@li...
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 [vah...@as...]
Sent: Monday, June 15, 2020 10:49 AM
To: Jarrett Johnson
Cc: pym...@li...
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 <jar...@sc...>
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh <vah...@as...>
Cc: pym...@li...
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 <vah...@as...<mailto:vah...@as...>> 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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End of PyMOL-users Digest, Vol 169, Issue 20
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[PyMOL] Antwort: PyMOL-users Digest, Vol 169, Issue 20

PyMOL is an OpenGL based molecular visualization system

[PyMOL] Antwort: PyMOL-users Digest, Vol 169, Issue 20