Aquileo | Recent changes to wiki

Aquileo | Discussion for Home page

2025-07-10T18:56:15.722000Z

i need help please We have observed that when performing superpositions, the visual aid links between corresponding atoms are sometimes displayed in yellow and, in other cases, in purple. We have been trying to understand the underlying logic that determines this color difference.
For instance, we've noticed that complex, non-local, or multi-part superpositions sometimes result in purple links, while simpler alignments often result in yellow ones, but this is not always consistent. Our working hypothesis is that the color may be related to the energetic favorability or the complexity of the alignment solution, but this is purely speculation on our part.

understanding what does this conection between atoms is critical for our work please help

Aquileo | Discussion for Home page

2024-11-14T12:28:13.871000Z

It`s interesting.

Aquileo | Discussion for Home page

2022-07-19T14:39:34.921000Z

Hi,

I have troubles with h_add in Pymol. I was modelling some ligand molecules in PDB format and needed to add hydrogens (eg. chlorophyll A). When h_add is used, Pymol is randomly filling up all the valencies of carbon atoms by adding hydrogen without identifying the double and triple bonds. Is there a way to rectify this or is it a bug needs to be solved?

Thanks in advance!

Aquileo | Discussion for Home page

2022-01-07T17:28:02.458000Z

Hi
I have few qauestions related to interface residues script if you could please answer
In interfaceResidue script,def interfaceResidues(cmpx, cA='c. A', cB='c. B', cutoff=1.0, selName="interface"):
here dASA cutoff is 1.0.
How to decide this cutoff value?
My second question is Is it possible to get the values dASA of the complex and individual chains (calculated through the interfaceResidue.py script in PyMol) printed into any txt or excel sheet?

Aquileo | Discussion for Home page

2020-07-20T15:39:19.532000Z

Hi ,
I am using open source pymol to make a movie and I am having a difficult time finding a work around to use the morphing feauture. Is there anyone who knows a way to use morphing/something similar in open source pymol?

Aquileo | Discussion for Home page

2020-06-02T06:40:54.287000Z

Hi Patricia -
Can you ask this question on the pymol-users mailing list? You need to subscribe first at
http://pymol.org/maillist
and then you can send emails to the list.

Aquileo | Discussion for Home page

2020-06-02T03:48:43.359000Z

Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong.

Schrodenger support provided a recommendation. Part of it is to rename the protein chain to something else (e.g., chain F) so that it wouldn't interfere with chain A from the F-Actin chain. I’ve been unable to figure out how to change the name/ID of my chains. I have tried changing to “3 Button Viewing”, selecting “Chains”, clicking on the chain of interest, clicking on the selection “A” action button and selecting “rename selection”, as well as using the "set_name" command, but neither are working.

Can anyone help me figure out what I’m doing wrong?

Thanks so much!

Aquileo | Home modified by Thomas Holder

2019-05-14T07:18:04.753000Z

--- v2
+++ v3
@@ -3,4 +3,7 @@
 **The Open-Source PyMOL repository has been moved to github:**
 https://github.com/schrodinger/pymol-open-source

+**The PyMOL community wiki has its own home:**
+https://pymolwiki.org/
+
 -----

Aquileo | Home modified by Thomas Holder

2018-06-26T08:28:37.793000Z

--- v1
+++ v2
@@ -1,8 +1,6 @@
-Welcome to your wiki!
+-----

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+**The Open-Source PyMOL repository has been moved to github:**
+https://github.com/schrodinger/pymol-open-source

-The wiki uses [Markdown](/p/pymol/wiki/markdown_syntax/) syntax.
-
-[[project_admins]]
-[[download_button]]
+-----

Aquileo | Discussion for Home page

2016-11-17T16:01:10.995000Z

Dear all，
I come across the same problem as the link below, which is that my movie made by pymol can not transit between different representations smoothly. I seems very simple in MovieSchool5 on pymolwiki website. I don't know why it doesn't work for both of us.
Thank you very much!
https://sourceforge.net/p/pymol/mailman/message/35074780/