Dear Pymol Users!
In my work dir I have 200 pdb files of GPCRs and one receptor
reference.pdb (it consist of only one GPCR monomer - seven
transmbembrane scaffold).
I need to write a simple script which will do the following things:
1 - allign (in loop) each structure against reference.pdb using
Hi Gleb,
If you have PSICO installed (which provides a TMalign wrapper), then this
script should be sufficient:
loadall *.pdb
import psico.fitting
extra_fit *, reference, method=tmalign, object=aln
remove not (byres aln)
https://pymolwiki.org/index.php/Psico
Cheers,
Thomas
> On Jul 18, 2017
Hi Thomas,
could you also send the same script but just with the Super command
for the superimposition without PSICO?
it's strange I have a problems of PSICO installation on MAC with python 3
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:52:12)
[GCC 4.2.1 Compatible Apple LL
With super instead of tmalign:
loadall *.pdb
extra_fit *, reference, method=super, object=aln
remove not (byres aln)
The PSICO setup.py installation script wasn't Python 3 ready. It's fixed now:
https://github.com/speleo3/pymol-psico/commit/e92f09374cc5ef7b562e5332292cee4f57f168af
Cheers,
Thom
Hi,
I'm using PSICO to write a DCD. Is it possible to retain the original order
for one segment (protein) while sorting by atom ID for another segment
(water).
Thank you,
Kelly
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There were some errors in the executing pymol script with your commands using
@ script.pml
or
run script.pml
probably because of my MAC Pymol which is v 1.74 mb outdated, no?
BTW on the same MAC I just have tried to install updated setup.py and
it was the following error:
Glebs-MacBook-Pro:pymol
if just add strings in pymol's cmd the "Super version" of the script
works fine so the problem is indeed in MAC :)
2017-07-18 20:53 GMT+02:00 James Starlight :
> There were some errors in the executing pymol script with your commands using
> @ script.pml
> or
> run script.pml
>
> probably because
The link wasn't a direct link to the fixed setup.py file. The direct link is:
https://raw.githubusercontent.com/speleo3/pymol-psico/master/setup.py
MacPyMOL 1.7.4 is recent enough for this exercise. However, your MacPyMOL
installation and your Anaconda3 Python are unrelated, so installing PSICO w
Hi Kelly,
With retain_order=1, PyMOL will sort by rank, which is the order of time of
loading the structure. By setting all rank values to the same value, you'll get
segi/chain/resi sorting. So to preserve rank based sorting only for
non-solvent, you can do this:
set retain_order
alter solvent
