[PyMOL] Thermal ellipsoid plot
Dear all, The size of isotropic atoms plotted by using "alter all, vdw = sqrt(b/8)/pi" and "show sphere" looks small compared with the size of anisotropic atoms displayed by "show ellipsoid" in PyMOL default setting with 50% probability. How can I plot the isotropic atoms with 50% probability? The data is a pdb file converted from a cif through Mercury software. Thank you very much for your help. Best regards, Koji ___ 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] pymol in no-gui mode
thank you very much, Ali!
I only changed the quotes in your script because I have integrated it
to my shell script in order to use with the varibables:
# run pymol to align the snapshots and save it to the session
pymol -c -d "
from pymol import cmd
cmd.load('${sim}/${simulation}_after_minimization.pdb')
cmd.load('${sim}/${simulation}_after_equilibration.pdb')
cmd.remove('resn WAT')
cmd.super('${simulation}_after_equilibration*','${simulation}_after_minimization*')
cmd.bg_color('white')
cmd.save('${output}/!!!pymol_sessions/${simulation}_superimposed.pse')
"
вс, 23 июн. 2019 г. в 12:05, Ali Kusay :
>
> Hi James,
>
> Just a follow up, I would still recommend you use the script in a file to do
> this as it is less messy but it can be done:
>
> pymol -c -d '
> from pymol import cmd
> cmd.load("A.pdb")
> cmd.load("B.pdb")
> cmd.load("C.pdb")
> cmd.super("C*","A*")
> cmd.super("B*","A*")
> cmd.bg_color("white")
> cmd.save("output.pse")
> '
>
> If you paste the above as is in shell It should work provided you are the
> directory containing the 3 pdb files
>
> Executing pymol with -d flag in shell means you can input pymol commands, to
> get around indentation you can run leave an ' apostrophe at the end to paste
> the scripts in and execute all as a string without needing to save as a file
>
> Just for reference, the -c flag is "batch processing (no GUI)" and the
> commands above can be saved into a python file and ran using:
>
> pymol -c -r "path_to_script"
>
> Hope this helps.
>
> Cheers,
>
> Ali
>
>
> Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
> The University of Sydney School of Pharmacy | Faculty of Medicine and Health
> 424, Brain and Mind Centre | The University of Sydney | NSW 2050
> Email: akus8...@uni.sydney.edu.au
>
>
> On 23/6/19, 7:00 pm, "James Starlight" wrote:
>
> hello there,
>
> As a part of my scripting routine, I would like to use pymol in no-gui
> mode (directly in the linux shell) to do the following things:
> 1) load in pymol 3 conformations of the same protein, which are
> defined as A.pdb B.pdb C.pdb
> 2) superimpose C to A using "super" or alternatively (which is better)
> "alignall" to A
> 3) change background of the session to white :-)
> 4) save the pymol session for the superimposed A B and C as the *.pse
> output file
>
> could you suggest me 1 string command for pymol, which I can directly
> use in shell terminal to do the mentioned routines in no-gui mode?
>
> thanks you!!
>
> James
>
>
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Re: [PyMOL] pymol in no-gui mode
Hi James,
Just a follow up, I would still recommend you use the script in a file to do
this as it is less messy but it can be done:
pymol -c -d '
from pymol import cmd
cmd.load("A.pdb")
cmd.load("B.pdb")
cmd.load("C.pdb")
cmd.super("C*","A*")
cmd.super("B*","A*")
cmd.bg_color("white")
cmd.save("output.pse")
'
If you paste the above as is in shell It should work provided you are the
directory containing the 3 pdb files
Executing pymol with -d flag in shell means you can input pymol commands, to
get around indentation you can run leave an ' apostrophe at the end to paste
the scripts in and execute all as a string without needing to save as a file
Just for reference, the -c flag is "batch processing (no GUI)" and the commands
above can be saved into a python file and ran using:
pymol -c -r "path_to_script"
Hope this helps.
Cheers,
Ali
Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050
Email: akus8...@uni.sydney.edu.au
On 23/6/19, 7:00 pm, "James Starlight" wrote:
hello there,
As a part of my scripting routine, I would like to use pymol in no-gui
mode (directly in the linux shell) to do the following things:
1) load in pymol 3 conformations of the same protein, which are
defined as A.pdb B.pdb C.pdb
2) superimpose C to A using "super" or alternatively (which is better)
"alignall" to A
3) change background of the session to white :-)
4) save the pymol session for the superimposed A B and C as the *.pse
output file
could you suggest me 1 string command for pymol, which I can directly
use in shell terminal to do the mentioned routines in no-gui mode?
thanks you!!
James
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[PyMOL] pymol in no-gui mode
hello there, As a part of my scripting routine, I would like to use pymol in no-gui mode (directly in the linux shell) to do the following things: 1) load in pymol 3 conformations of the same protein, which are defined as A.pdb B.pdb C.pdb 2) superimpose C to A using "super" or alternatively (which is better) "alignall" to A 3) change background of the session to white :-) 4) save the pymol session for the superimposed A B and C as the *.pse output file could you suggest me 1 string command for pymol, which I can directly use in shell terminal to do the mentioned routines in no-gui mode? thanks you!! James ___ 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
