[Chimera-users] create automatically all alternative protonation states of protein

[Thomas Evangelidis]

Hi Eric,

Thank you very much for the sample code. I am afraid though that recursion
is not the proper solution. There are much more combinations of protonation
states that must be created. I solved this problem by expanding Tree
structures. However the python module for Tree structures named 'ete3' is
not a standard one, hence Chimera's python interpreter cannot find it
although I have installed in on my local Anaconda python distribution. Do
you know how I can make Chimera find it? I can imagine that even if it
finds it, there may be conflicts between my local python version and
Chimera's python version.

Traceback (most recent call last):
>   File "/home/thomas/Programs/Chimera/share/chimeraInit.py", line 698, in
> init
>     midas_text.doRunScript("runscript", script)
>   File "/home/thomas/Programs/Chimera/share/Midas/midas_text.py", line
> 2248, in doRunScript
>     execfile(scriptPath, scriptGlobals)
>   File "/usr/local/bin/protonate_receptor.py", line 12, in <module>
>     from ete3 import Tree
> ImportError: No module named ete3





On Tue, 19 Mar 2019 at 19:04, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> hi Thomas,
> I’m pretty sure this would have to be a Python script.  The general idea
> would be to select residues within a certain distance of the ligand,
> systematically change their names to indicate alternative protonation
> states, delete all protons and then run AddH and write out PDBs.  Since you
> have an indeterminate number of loops needed, I would use recursion, so
> something like:
>
> pdb_num = 1
> from chimera import runCommand as rc
> rc(“sel ligands z<DIST”)
> from chimera.selection import currentResidues
> residues = currentResidues()
>
> def change_protonation(remaining_residues):
> if not remaining_residues:
> global pdb_num
> rc(“del H”)
> rc(“addh”)
> rc(“write %d.pdb” % pdb_num)
> pdb_num += 1
> return
> r = remaining_residues[0]
> if r.type == “GLU”:
> states = [“GLU”, “GLH”]
> elif r.type == “ASP”:
> states = [“ASP”, “ASH”]
> elif r.type == “HIS”:
> etc….
>
> else:
> states = [r.type]
> for state in states:
> r.type = state
> change_protonation(remaining_residues[1:])
>
> change_protonation(residues)
>
> The script is incomplete and I haven’t tested it, but you get the idea.
>
> —Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
>
> On Mar 19, 2019, at 7:59 AM, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>
> Greetings,
>
> I want to write a script that will read a protein-ligand complex, will
> find all residues with alternative protonation states within a radius from
> the ligand, and will write to separate pdb files all combinations of
> alternative protonations or the protein's binding site. Is this possible in
> Chimera? I saw at the documentation of addh command that there is not a way
> to specify explicitly which residues to protonate and how (e.g. I can
> protonate all ASP to ASH but not ASP34 to ASH34 and keep ASP52 as it is).
>
> Thanks in advance.
> Thomas
>
> --
>
> ======================================================================
>
> Dr Thomas Evangelidis
>
> Research Scientist
>
> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech
> Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
> Prague, Czech Republic
>   &
> CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
> Brno, Czech Republic
>
> email: tevang3 at gmail.com
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>
>
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>

-- 

======================================================================

Dr Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
  &
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic

email: tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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