[PyMOL] Performing backend calculations within PyMOL

leave the program. Kin regards, Ali Kusay PhD student ___ 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

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

Re: [PyMOL] set transparency for selected elements of secondary structure

Hi James, I am not sure what the exact cause of your issue is but I think if you make a selection first then apply the transparency to the selection that should work, i.e.: sele ss H+S set cartoon_transparency, 0.5, sele Something to do with selection based transparency settings not enabling n

Re: [PyMOL] Export molecule does not keep changes

le 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 Fr

Re: [PyMOL] The 'select' command for complex residue selection

-95) c. A is equivalent to chain A and this residue selection formats avoid the need of annoying “or” statements 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 |

Re: [PyMOL] Drawing lines between residues

Hi Jorge and Blaine Another was to do this is to take a measurement between the residues and then use the command, “set dash_gap, 0” This will also allow you to control the thickness of the lines using the “set dash_radius” command Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate

Re: [PyMOL] How to see a homotetramer

ombine using: create 6h07_assembly, 6h07_* Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate The University of Sydney School of Pharmacy | Faculty of Medicine and Health 424, Brain and Mind Centre | The University of Sydney | NSW 2050 From: Clelia Canova Date: Tuesday, 14 January 2020 at 7:45

Re: [PyMOL] Assign different color to dash lines

to them i.e. set dash_color, red, measure01 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

Re: [PyMOL] transparent electron density silhouette

dependent (done through menu, can't find command for it): Setting > Transparency > Angle-dependent I have rendered an image of what it looks like, can certainly play around with the surface settings to further clean up the image: https://photos.app.goo.gl/7CGZY1Zyrihjw4D96 Cheers

Re: [PyMOL] Question about python commands in PyMOL

function does not need to need to be extended as it is already built into PyMOL 2. PyMOL already has a load function which may be overwritten using your new load function, call it something else just to be safe Cheers, Ali Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist The Universit