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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/

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[Patricia Rea]

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!

[Thomas Holder]

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.

[vanessa natera]

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?

[Maryam]

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?

[Pooja Sarngadharan]

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!