Re: [PyMOL] Generating of Rg for every state in PyMOL
Hi Jarrett,
Thank you very much for your kind and comprehensive advice, really appreciate
it!
I will try it out.
Kind regards,
Jessica Lim
From: Jarrett Johnson
Sent: Thursday, May 18, 2023 8:32 PM
To: #JESSICA LIM JIAYING#
Cc: pymol-users@lists.sourceforge.net
Subject: 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"
cmd.fetch(obj)
# for loop
for i in range(cmd.count_states(obj)):
print(f"State {i+1}: {gyradius(obj, state=i+1)}")
# list comprehension
gy_list = [gyradius(obj, state=i+1) for i in range(cmd.count_states(obj))]
print(gy_list)
```
Hope that helps,
Jarrett J
On Thu, May 18, 2023 at 8:05 AM #JESSICA LIM JIAYING# via PyMOL-users
mailto:pymol-users@lists.sourceforge.net>>
wrote:
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 the command gyradius as
part of the psico package in PyMOL but it only outputs a single value, and I
would have to click manually to the next state and re-enter the command to get
the next value. Hence, I would like to be able to obtain a list of values
without having to click through 100 different states.
Any advice or suggestions on how this can be done will be greatly appreciated,
thank you!
Kind regards,
Jessica Lim
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[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 the command gyradius as part of the psico package in PyMOL but it only outputs a single value, and I would have to click manually to the next state and re-enter the command to get the next value. Hence, I would like to be able to obtain a list of values without having to click through 100 different states. Any advice or suggestions on how this can be done will be greatly appreciated, thank you! Kind regards, Jessica Lim ___ 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] Recognition and Display of Secondary Structure Cartoon
Dear Joel, Thank you so much for sharing! Totally answered my question, very much appreciated and I will look into the command as well. Thank you very much for your kind guidance and assistance! Jessica Lim From: Joel Tyndall<mailto:joel.tynd...@otago.ac.nz> Sent: Tuesday, 31 August 2021 5:55 am To: #JESSICA LIM JIAYING#<mailto:jessicaj...@e.ntu.edu.sg>; pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net> Subject: RE: [PyMOL] Recognition and Display of Secondary Structure Cartoon Hi Jessica, Generally secondary structure is extracted from a pdb file and PyMol would read this. e.g. HELIX1 1 GLY A 86 THR A 91 1 6 HELIX2 2 GLY B 86 THR B 91 1 6 SHEET1 A 4 GLN A 2 THR A 4 0 SHEET2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET3 A 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN B 98 SHEET4 A 4 GLN B 2 ILE B 3 -1 N ILE B 3 O LEU A 97 Sometimes the pdb file is incomplete or does not display all secondary structure. Using the command dss in Pymol can usually help define/display correct ss. https://www.pymolwiki.org/index.php/Dss Hope this helps J From: #JESSICA LIM JIAYING# Sent: Saturday, 28 August 2021 6:54 pm To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Recognition and Display of Secondary Structure Cartoon Hi all, I am wondering how PyMOL recognises and display secondary structure (like alpha helix) when selecting the ‘Cartoon’ function. I have attached an image of my molecule where only certain regions are displayed in the cartoon representation whereas there is helical propensity throughout my molecule as seen in the image. Hence, how does PyMOL decide on the secondary structure features? Thank you so much! Any suggestions/advice on where to look will be greatly appreciated! Jessica Lim ___ 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
[PyMOL] Recognition and Display of Secondary Structure Cartoon
Hi all, I am wondering how PyMOL recognises and display secondary structure (like alpha helix) when selecting the ‘Cartoon’ function. I have attached an image of my molecule where only certain regions are displayed in the cartoon representation whereas there is helical propensity throughout my molecule as seen in the image. Hence, how does PyMOL decide on the secondary structure features? Thank you so much! Any suggestions/advice on where to look will be greatly appreciated! Jessica Lim ___ 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
