Re: [PyMOL] Retain order for select segment and write trajectory

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

Re: [PyMOL] A structural superimposition and further post-processing

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

Re: [PyMOL] A structural superimposition and further post-processing

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

Re: [PyMOL] A structural superimposition and further post-processing

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script with your commands using @ script.pml or run script.pml probably because of my MAC Pymol which is v 1.74 mb outdated, no?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:

[PyMOL] Retain order for select segment and write trajectory

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 -- Check out the vibrant tech community on

Re: [PyMOL] A structural superimposition and further post-processing

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,

Re: [PyMOL] A structural superimposition and further post-processing

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

Re: [PyMOL] A structural superimposition and further post-processing

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,

[PyMOL] A structural superimposition and further post-processing

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