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. ?? [cid:45cbe218-a6f2-4490-be08-b52fbb7a30e2] Thanks Hernando ___________________________________
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@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
___________________________________ <> <> _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Thanks the split workaround works. ___________________________________ 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@einsteinmed.org<mailto:hernando.sosa@einsteinmed.org> ___________________________________ ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, July 8, 2020 5:52 PM To: Hernando J Sosa <hernando.sosa@einsteinmed.org> Cc: chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Sequence-structure associations CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. 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@einsteinmed.org<mailto:hernando.sosa@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 ___________________________________ _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Chernando.sosa%40einsteinmed.org%7C173479b3861d4aba1a9c08d823893f32%7C9c01f0fd65e040c089a82dfd51e62025%7C0%7C0%7C637298419662626997&sdata=A2jBQZb2NGi95xzo6VyWNVNSuRzIVlCk0Y%2F%2B5SauK5Q%3D&reserved=0>
participants (2)
-
Eric Pettersen -
Hernando J Sosa