Re: [PyMOL] Generating of Rg for every state in PyMOL

Hi Jessica, It seems in the gyradius psico script, by default it will calculate the radius of gyration for the current state. You can provide a specific state to this argument and generate the list yourself in a script. ``` from psico.querying import gyradius from pymol import cmd obj = "1nmr"

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

Hi Petro, Add the following to your .pymolrc file (pymolrc.pml on Windows) cmd.do("hide cartoon") cmd.do("show sticks") # I also add these lines to my pymolrc set bg_rgb, white set stick_radius, 0.125 set valence, off Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department

[PyMOL] Generating of Rg for every state in PyMOL

Hi all, I am having difficulty in trying to print out a list of the radius of gyration for all states in my PDB file. I have several files of 100 states each and would like to generate a list of the radius of gyration for every individual state. However, I have only been successful at using

Re: [PyMOL] Surface and cartoon transparency together?

Hi Petro, Try "Setting > Transparency > Multi-Layer" or "Multi-Layer (Real-time OIT)" See also: https://pymolwiki.org/index.php/transparency_mode Cheers, Thomas On Wed, May 17, 2023 at 4:51 PM Petro wrote: > > HI., I have tried to use surface and cartoon transparency together but then I >

Re: [PyMOL] Generate electrostatics by Python command

Hi Petro, This should work (example with PDB 1ubq): from pmg_tk.startup.apbs_gui.creating import pdb2pqr_cli from pmg_tk.startup.apbs_gui.electrostatics import map_new_apbs cmd.fetch("1ubq") pdb2pqr_cli("prepared01", "1ubq", options=["--ff", "amber"]) map_new_apbs("apbs_map01", "prepared01")

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

Hi Blaine. Thank you for your reply. I was not clear. I meant the surface which can be generated via action -> generate -> vacuum electrostatic -> protein contact potential (local) Is there a way to access it via Python? Thank you and best regards. Petro. On Wed, 17 May 2023 at 17:32, Mooers,

Re: [PyMOL] Surface and cartoon transparency together?

Thanks. I will try it. Best regards. Petro. On Wed, 17 May 2023 at 19:49, Jarrett Johnson < jarrett.john...@schrodinger.com> wrote: > Hi Petro, > > You might have luck using Order Independent Transparency: > > `set transparency_mode, 3` > > Hope that helps, > Jarrett J > > On Wed, May 17, 2023

Re: [PyMOL] save format for molecule files

Have you tried .mol2 files. I would expect Maestro to recognise that and it should include bond order etc J Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand

Re: [PyMOL] [EXTERNAL] Generate electrostatics by Python command

Hi Petro, APBS is a plugin and not directly part of PyMOL. You can run apbs from the command line via subprocess in Python. https://apbs.readthedocs.io/en/latest/using/index.html Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology,

Re: [PyMOL] Surface and cartoon transparency together?

Hi Petro, You might have luck using Order Independent Transparency: `set transparency_mode, 3` Hope that helps, Jarrett J On Wed, May 17, 2023 at 10:50 AM Petro wrote: > HI., I have tried to use surface and cartoon transparency together but > then I can see only the surface. Cartoon

Re: [PyMOL] save format for molecule files

Hi Xavier, The best option to transfer bond orders from PyMOL to Maestro might be with .mol2 (or .sdf) format. These formats can store aromatic bond orders and Maestro will convert that to meaningful double/single bonds when loading the file. - .pdb format can't store aromatic bonds (and double

Re: [PyMOL] [EXTERNAL] Disable cartoon representation on load

Thank you. I will try that. Best regards. Petro. On Wed, 17 May 2023 at 17:17, Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > Hi Petro, > > Add the following to your .pymolrc file (pymolrc.pml on Windows) > > cmd.do("hide cartoon") > cmd.do("show sticks") > > # I also add these

Re: [PyMOL] Disable cartoon representation on load

Hi Petro, Put this line in your pymolrc file (File > Edit pymolrc): set auto_show_classified, 0 See also: https://pymolwiki.org/index.php/pymolrc https://pymolwiki.org/index.php/auto_show_classified https://sourceforge.net/p/pymol/mailman/message/36155392/ Cheers, Thomas On Wed, May 17,