Modeller using more than 1 template in Chimera Modeller
Hello,
Is it possible to model 3D structure within Chimera using several complementary pdb templates at once? This is possible in the stand alone Modeller but I was unable to find a tutorial/manual instruction how to do it in Chimera.
Thank you
Vladimir
Hi Vladimir, Are you using Chimera or ChimeraX? You sent this question to the ChimeraX list but your description says Chimera. In the future if the question is really about Chimera, please use the chimera-users@cgl.ucsf.edu address.
For both programs, yes, you can use as many templates as you want, but the details are slightly different. In both cases, however, you specify which structures to use as templates by associating them with sequences in your alignment.
ChimeraX Modeller Comparative tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html
ChimeraX sequence-structure association: https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#association
Chimera comparative modeling https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative
...maybe the tricky part is that even if you choose only one sequence as "template" in the Chimera dialog, the sequence can have multiple structures associated to it, but you can also choose multiple sequences. All of the structures associated with the designated sequences will be used as templates.
Chimera sequence-structures association: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 29, 2024, at 10:35 AM, Vladimir Saudek via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
Is it possible to model 3D structure within Chimera using several complementary pdb templates at once? This is possible in the stand alone Modeller but I was unable to find a tutorial/manual instruction how to do it in Chimera.
Thank you
Vladimir
Hi Elaine,
Many thanks. I am using ChimeraX 1.7. The links you sent will be very useful to me.
Best regards
Vladimir
On 29/01/2024 20:17, Elaine Meng wrote:
Hi Vladimir, Are you using Chimera or ChimeraX? You sent this question to the ChimeraX list but your description says Chimera. In the future if the question is really about Chimera, please use the chimera-users@cgl.ucsf.edu address.
For both programs, yes, you can use as many templates as you want, but the details are slightly different. In both cases, however, you specify which structures to use as templates by associating them with sequences in your alignment.
ChimeraX Modeller Comparative tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html
ChimeraX sequence-structure association: https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#association
Chimera comparative modeling https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative
...maybe the tricky part is that even if you choose only one sequence as "template" in the Chimera dialog, the sequence can have multiple structures associated to it, but you can also choose multiple sequences. All of the structures associated with the designated sequences will be used as templates.
Chimera sequence-structures association: https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 29, 2024, at 10:35 AM, Vladimir Saudek via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
Is it possible to model 3D structure within Chimera using several complementary pdb templates at once? This is possible in the stand alone Modeller but I was unable to find a tutorial/manual instruction how to do it in Chimera.
Thank you
Vladimir
participants (2)
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Elaine Meng -
Vladimir Saudek