[Chimera-users] secondary structure restraints and crosslink restraints

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 27 12:42:18 PST 2019

Dear Fränze Müller,
The Modeller interface in Chimera was meant to be simple, which means easy to use, but also not including many things that are possible when using Modeller directly.  The Modeller interface in Chimera just allows specifying template structure(s) and optionally, the distance restraints you mention.  There must be some secondary structure knowledge used at least indirectly via the template secondary structure, but I do not have a detailed understanding of how that works… you’d have to look in the Modeller documentation.  There is no option for additional files/types of restraints in the interface from Chimera, however.

All the options in our interface to Modeller are described in the User Guide:

Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 27, 2019, at 4:50 AM, Fränze Müller <fraenze.mueller at biologie.uni-freiburg.de> wrote:
> Dear Chimera developers,
> I would like to perform homology modelling using Modeller in Chimera. At the moment I am using just distance restraints formatted like in the Chimera documentation (res1 res2 dist stdev). This file only contains crosslinking data. Is there a way to also include secondary structure restraints, that can serve as additional information during homology modelling? Or can I provide some were another file including this information separate from the crosslink information?
> Best wishes and Thanks for your help,
> -- 
> Fränze Müller
> Postdoctoral Researcher

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