[phenixbb] exclude atoms/regions in real space refinement

Pavel Afonine pafonine at lbl.gov
Thu Jul 4 23:01:40 PDT 2019

Hi Filip,

no, this is not possible in phenix.real_space_refine at the moment. I 
feel the pressure by having this sort of questions multiple times a 
week, on and off list. So implementing this functionality is in my todo 
list. I can't hint you about ETA given I'm booked all the way till 
November, sorry.

A question I ask everyone who requests this feature: why you need to do 
this and why cutting out a piece of model and a map in a box isn't 
working to mimic this?


On 7/4/19 17:15, Filip Van Petegem wrote:
> Dear Phenix users,
> I want to exclude particular regions of a protein model, docked into a 
> cryo-EM map, from real-space refinement. I know this is possible for 
> refinement in reciprocal space, but is this possible for refining a 
> cryo-EM structure against a map? E.g. I want to totally exclude a 
> region with known crystal structure, placed in an area of poor local 
> resolution, from any form of refinement, but want to apply all other 
> options (morphing, simulated annealing, adp, Global minimization) to 
> the remainder of the structure.
> (I didn't see this option in 
> https://www.phenix-online.org/documentation/reference/real_space_refine.html )
> best regards,
> Filip
> -- 
> Filip Van Petegem, PhD
> Professor, Dept. of Biochemistry and Molecular Biology
> The University of British Columbia
> 2350 Health Sciences Mall - Rm 2.356
> Vancouver, V6T 1Z3
> phone: +1 604 827 4267
> email: filip.vanpetegem at gmail.com <mailto:filip.vanpetegem at gmail.com>
> http://crg.ubc.ca/VanPetegem/
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190704/1bbd13bc/attachment.htm>

More information about the phenixbb mailing list