-pymol-users-requ...@lists.sourceforge.net schrieb: -
An: pymol-users@lists.sourceforge.net
Von: pymol-users-requ...@lists.sourceforge.net
Datum: 15.06.2020 22:47
Betreff: PyMOL-users Digest, Vol 169, Issue 20
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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
Thanks, Dr. Mooers.
I modified a little.
It seems the pdb files need be loaded.
I put all the following lines in a file multifile_hb.pml
run
C:\Users\user\AppData\Local\Programs\Python\Python38\lib\site-packages\pymol\pymol_path\Pymol-script-repo\list_hb.py
import glob
load model.000.*_minimiz
Hi Charles,
Make sure that PyMOL's present working directory is where the pdb files are
stored.
Copy and paste each of the four lines below one at a time on the command line
in PyMOL.
run list_hb.py
import glob
chains = [('A','B'), ('A','C'), ('A','D'), ('A','E'), ('B','C'), ('B','D'),
('B',
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 going in the insertion
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
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 sc
Hi, Pymol users
Could you help me do this in an efficient way?
Let me describe the task I try to do.
I have a series of numerically ordered files, say model00.pdb model.01.pdb ……
model.30.pdb
All the pdb have the same protein composition, chain A, B, C, D, and E. Their
relative position is di
Coot is also an option.
CCP4 is much better/flexible though.
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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://w
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
Reply: Oganesyan, Vaheh
Date: June 15, 2
Hi Vaheh,
Thank you for the clarification.
There are at least five numbering schemes
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198058).
Which one are you following?
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of M
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 co
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
Universi
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 John
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 Pedro,
There is no designated infrastructure for this. Other plugins typically create
their own directory in the user's home folder, like "~/.myplugindata". You
could also create it inside the "~/.pymol" directory (like
"~/.pymol/myplugindata").
This works on all platforms:
os.path.expandus
Hi Mario,
Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to
manually edit the files there as well. For example with PyMOL 2.4.0 on Linux,
the AMBER force field data files can be found like this:
$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.name
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