[Chimera-users] Modeller Restraints

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 15 10:14:30 PDT 2019

Hello D.B.
The restraints are specified in the (output) target model residue numbering, not in any of the templates.  You are not restraining the templates, only the model that comes out, so there is no need to specify individual templates in the restraints file.


"Distance restraints file (optional) - Specify an input file containing distance restraints (see example file distres.txt). Each line in the file should be of the format:

res1  res2  dist  stdev

where res1 and res2 are residue numbers or ranges of residue numbers in the target sequence, dist is the distance in Å, and stdev is the standard deviation. If a single residue is specified, its Cα will be used to anchor the restraint. If a residue range (e.g. 233-275) is specified, the range's center of mass will be used to anchor the restraint.”

See also the Modeller manual

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

> On Jul 14, 2019, at 5:12 PM, Danilo Boškovic <a01406823 at unet.univie.ac.at> wrote:
> Dear all,
> how  do i add restraints specific to my templates that i use for comparative modelling in chimera? Specifically what are the names assigned to those templates? Do i need the names to specify the template residues that i want to restrain? Are the names same as in the tab when i choose the templates for the run?
> Thanks,
> D. B.

More information about the Chimera-users mailing list