t: Tuesday, June 16, 2020 1:42 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Renumber
Hello Vaheh
Antibody structures are a mess to renumber, both due to the many different
numbering schemes used in different structures, and to some older files not
even adhering to pub standards,
Hello Vaheh
Antibody structures are a mess to renumber, both due to the many different
numbering schemes used in different structures, and to some older files not
even adhering to pub standards, using the alternative localisation columns for
the insertion letters specified by Kabat or Chothia
Thank you Jared.
From: Jared Sampson
Sent: Monday, June 15, 2020 4:47 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] renumber
Hi Vaheh -
I wasn't saying it can't be done, just that pdbset is my preferred way to
handle renumbering when go
ate: June 15, 2020 at 3:57:24 PM
To: Jared Sampson
Cc: 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
Sent: Monday, June 15, 2020 2:41 PM
To: Og
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
-
>
> Message: 1
> Date: Mon, 15 Jun 2020 19:57:14 +0000
> From: "Oganesyan, Vaheh"
> To: Jared Sampson
> Cc: "pymol-users@lists.sourceforge.net"
>
> Subject: Re: [PyMOL] renumber
> Message-ID:
>
>
>
>
Jared,
Are you saying it cannot be done within PyMOL? The ccp4 option is well known.
Thanks.
From: Jared Sampson
Sent: Monday, June 15, 2020 2:41 PM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
Hi Vaheh -
Try `pdbset` from the CCP4 suite.
http
: June 15, 2020 at 1:28:23 PM
To: Mooers, Blaine H.M. (HSC) , Jarrett Johnson
Cc: 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
To: Mooers, Blaine H.M. (HSC); Jarrett Johnson
Cc: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] 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
: [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
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
Johnson
Sent: Monday, June 15, 2020 11:38 AM
To: Oganesyan, Vaheh
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] renumber
Hello,
The command shown on this page
https://pymolwiki.org/index.php/Renumber<https://pymolwiki.org/index.php/Renumber>
is not one that comes with Py
Hello,
The command shown on this page https://pymolwiki.org/index.php/Renumber 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*
and then you should be able to use the command as shown on t
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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Hi Jordan,
nice script, but it does not do the same like the renumber script from
the PyMOLWiki (http://pymolwiki.org/index.php/Renumber). Try this: set
all residue numbers to 1, the renumber script will not care because it
walks along the bonds and increases the count whenever it passes a
peptide
Hi Alex,
the renumber script only sets the residue number, it does not reorder
atoms internally. Just type
PyMOL> sort
to sort internally based on the new residue numbers.
See also:
http://pymolwiki.org/index.php/Sort
Cheers,
Thomas
Alex Truong wrote, On 01/21/13 19:21:
> Hi All,
>
> I've
Does it have to be a pymol script. Renumbering pdbs is the bread and butter of
biopython pdb module:
#!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5
import sys
from Bio.PDB import *
from optparse import OptionParser
import warnings
def main():
usage = "%prog input.pdb output.pdb"
parse
Hi All,
I've been having a bit of trouble recently with the renumber script. I have
a pdb file that I'm trying to renumber, but unlike the other times I've
used it, it is renumbering incorrectly. The numbers are usually spaced out
5 residues apart, but I have one number right near the beginning th
Hi Joel,
thanks a lot for the tip! excellent stuff using my loved editor!
andr
2005/6/29, Joel Tyndall :
> Hi andrea,
>
> I have found an excellent add on tool for emacs which does a lot of
> renumbering stuff (on unix/linux)
>
> http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html
>
Hi andrea,
I have found an excellent add on tool for emacs which does a lot of
renumbering stuff (on unix/linux)
http://stein.bioch.dundee.ac.uk/~charlie/scripts/pdb-mode.html
Cheers
Joel
Andrea Spitaleri wrote:
Hi all,
I couldn't find any command in pymol to renumber the segid of a prote
sourceforge.net] On Behalf Of
> Andrea Spitaleri
> Sent: Wednesday, June 29, 2005 12:44 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Renumber protein segid
>
> Hi all,
> I couldn't find any command in pymol to renumber the segid of
&
Hi all,
I couldn't find any command in pymol to renumber the segid of a protein.
Is there any way to do it?
Regards
andrea
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