[PyMOL] Export molecule does not keep COLOUR* changes - RESOLVED
Hello, That might also explain why the same molecule loaded in LiteMol gives different colouring. So the conclusion is that the colors are not defined in molecules but instead in programs that displays them. Thank you! Regards, Jesse Sarameri Lähettäjä: Ali Kusay Lähetetty: tiistai 25. kesäkuuta 2019 20.52.33 Vastaanottaja: Sarameri, Jesse Kopio: pymol-users@lists.sourceforge.net Aihe: Re: [PyMOL] Export molecule does not keep changes Hi Jesse, I am not aware of a structure file (i.e. PDB) which can store information such as color and thus when you load a PDB file pymol applies the default colors to it. You can however make it so that all proteins loaded into pymol are automatically assigned the grey colour, this is done by editing the pymolrc. In the menu go: File -> Edit -> pymolrc (will create file) -> type “set cartoon_color, grey80” When you close and reopen pymol, this will ensure that all proteins loaded into pymol are given the grey80 colour, you can make any additional edits to the pymolrc file as you please i.e stick color is still default Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist Supervised by A/Prof Thomas Balle The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 From: "Sarameri, Jesse" Date: Wednesday, 26 June 2019 at 6:34 pm To: "pymol-users@lists.sourceforge.net" Subject: [PyMOL] Export molecule does not keep changes Hello! (English is not my native language; please excuse typing errors.) Goal is to recolor molecule so it stays that way after the edit. This is how I thought it would work: Lets start by opening any molecule (like downloading 5jh0.cif from https://www.rcsb.org/structure/5jh0) Changed the color of the molecule to grey, save as session (.pse file), open it and still grey, great! But if I want to export to molecule (.pdb for example), open the molecule, no changes applied. Tried to change Saved state settings and different formats but no effect. No error messages either. I did RTFM and STFW not able to find answer. (If I missed it, feel free to send pics with red circles and arrows to highlight it.) Software and hardware used: Open source PyMOL version 2.1.0. Windows 10 Lenovo X280 Laptop Many thanks for help incase someone else might encounter this problem. Regards, Jesse Sarameri ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Multi-snapshot superimposition
update:
for the realisation I have tried to use sep_state script with python version
so I modified sep_state adding superimposition
# pymol_save.py#
from pymol import cmd
import glob
import re
def save_sep(prefix=''):
obj_list = cmd.get_names("public_objects")
if obj_list:
for i in range(len(obj_list)):
obj_name = "%s%s.pdb" % (prefix, obj_list[i])
cmd.save(obj_name, obj_list[i])
print "Saving %s" % obj_name
else:
print "No objects found"
cmd.extra_fit('name CA', '*', 'super')
cmd.extend('save_sep', save_sep)
and use it with my pdbs
pymol ${output}/*.pdb -ckqr pymol_save.py > ${output}/!temp/rmsf_fit.log
it align ensemble but did not save the resulted pdbs in separate
files. Finally, the same happenes when I open it in Pymol GUI
pymol-2.2.0 *.pdb pymol_save.py
remarkably when I use in this GUI session just a command 'save_sep' it
saves the files within the same directory (Which is ok!)
however cmd.extend('prefix', save_sep)does not work :(
чт, 27 июн. 2019 г. в 11:48, James Starlight :
>
> Dear Pymol users!
>
> I have a folder with many pdb files. I would like to use pymol in
> no-gui mode in order to i)load all pdb within the pymol; ii)
> superimpose each pdb agains the first (top) pdb; iii) save sperimposed
> pdbs into the new folder under the SAME names of pdbs.
>
> Here is model of my script, which should be modified according to the
> indicated commentaries (mostly on the step of saving results).
>
> ${pymol} -c -d "
> from pymol import cmd
> # we open at once all pdbs which have "B-factors" suffix in its name!
> cmd.load('${output}/!temp/B-factors*')
> # it do almost what I want in terms of the superimposition, however
> not all snapshots are aligned properly
> cmd.extra_fit('name CA', '*', 'super')
> # here the most tricky part that should be modified since I need to
> save snapshots using some command keeping its original names!
> cmd.save('output' + '.pdb')
> "
>
> so the task is that I would like to use it in one command rather then
> to put inside the loop (e.g. opening 2 snapshots for each time to make
> mobile, reference superimposition, which is more easy way).
>
> Thank you in advance!
> James
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[PyMOL] Multi-snapshot superimposition
Dear Pymol users!
I have a folder with many pdb files. I would like to use pymol in
no-gui mode in order to i)load all pdb within the pymol; ii)
superimpose each pdb agains the first (top) pdb; iii) save sperimposed
pdbs into the new folder under the SAME names of pdbs.
Here is model of my script, which should be modified according to the
indicated commentaries (mostly on the step of saving results).
${pymol} -c -d "
from pymol import cmd
# we open at once all pdbs which have "B-factors" suffix in its name!
cmd.load('${output}/!temp/B-factors*')
# it do almost what I want in terms of the superimposition, however
not all snapshots are aligned properly
cmd.extra_fit('name CA', '*', 'super')
# here the most tricky part that should be modified since I need to
save snapshots using some command keeping its original names!
cmd.save('output' + '.pdb')
"
so the task is that I would like to use it in one command rather then
to put inside the loop (e.g. opening 2 snapshots for each time to make
mobile, reference superimposition, which is more easy way).
Thank you in advance!
James
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[PyMOL] `selection` argument in load_traj
Hi Thomas, I see! Is it supposed to work with other formats too? Or at least, is it planned to be expanded? I'm trying to switch to PyMOL to view GROMACS `.xtc` trajectories, and this feature would be a great addition. Cheers, Lorenzo ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
