[Chimera-users] Sequence-structure associations

[Hernando J Sosa]

Thanks the split workaround  works.

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Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone (718) 430-3456
FAX (718) 430-8819
emai:  hernando.sosa at einsteinmed.org<mailto:hernando.sosa at einsteinmed.org>
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From: Eric Pettersen <pett at cgl.ucsf.edu>
Sent: Wednesday, July 8, 2020 5:52 PM
To: Hernando J Sosa <hernando.sosa at einsteinmed.org>
Cc: chimera-users at cgl.ucsf.edu BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Sequence-structure associations

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Hi Hernando,
Yes, in Chimera you can only associate a single chain of a model with a single sequence in the alignment.  The simplest workaround is to use the 'split' command to split each chain into its own model, each of which can be associated with the alignment.
ChimeraX uses a different paradigm and will associate each chain of a structure to an alignment as appropriate.  However, the alignment viewer in ChimeraX currently only has a fraction of the functionality of its Chimera counterpart, so switching over might not be appropriate, depending on what you were going to do after getting the associations to happen.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Jul 8, 2020, at 11:47 AM, Hernando J Sosa <hernando.sosa at einsteinmed.org<mailto:hernando.sosa at einsteinmed.org>> wrote:

Dear Chimera,

Chimera sequence-structure associations appears to be limited to one association per model. Is this right? and if not how do you modify this?
E.g. with  a model PDB structure containing  3 chains A,B and C  you could  open the multialign viewer   and align the three sequences corresponding to A B and C. However, it appears that only one of the three sequences in the multialign viewer can be associated with their respective chain in the structure. You could change the association but it seem that you cannot add more associations. Here is a view of the associations dialogue windows. Note that it shows only one entry even when there are three sequences in the multialign viewer window. ??

<image.png>


Thanks

Hernando

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