[PyMOL] coloring based on alignment

[Oganesyan, Vaheh]

Colleagues,

Was wondering if there is a functionality built  in PyMOL for coloring of the 
molecule based on sequence identity/similarity? This topic was discussed 
briefly in 2007 and the answer was from Robert Campbell suggesting using his 
scripts. Seems to be a good tool to have for anyone.


Regards,

Vaheh Oganesyan
MedImmune, ADPE
www.medimmune.com



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Re: [PyMOL] coloring based on alignment

[Jed Goldstone]

Vaheh,
You can modify the b-factor column, and color by b-factor. I have used
various value-to-bfactor scripts, with different measures of alignment
similarity.

The one problem I've had is extending the Ca color to the rest of the
residue in stick mode.
Jed
On Oct 28, 2015 3:34 PM, "Oganesyan, Vaheh" 
wrote:

> Colleagues,
>
> Was wondering if there is a functionality built  in PyMOL for coloring of
> the molecule based on sequence identity/similarity? This topic was
> discussed briefly in 2007 and the answer was from Robert Campbell
> suggesting using his scripts. Seems to be a good tool to have for anyone.
>
>
> Regards,
>
> Vaheh Oganesyan
> MedImmune, ADPE
> www.medimmune.com
>
>
>
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>
>
> --
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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