[phenixbb] idealizing structure

Pavel Afonine pafonine at lbl.gov
Mon Apr 27 13:21:50 PDT 2015


GUI analog of command line phenix.geometry_minimization is:

Model tools (from main Phenix GUI window) -> Geometry minimization

The same but with map restraints (which may be more useful, depending on 
context) is phenix.real_space_refine:


This is command line only, at the moment.


On 4/27/15 12:57 PM, Kgosisejo, Oarabile wrote:
> Hi,
> Is there only the command line version of this or the GUI usage is available as well?
> Best Regards,
> Oarabile Kgosisejo
> ________________________________________
> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine [pafonine at lbl.gov]
> Sent: January 20, 2015 1:58 PM
> To: PC; PHENIX list
> Subject: Re: [phenixbb] idealizing structure
>>    Is there a way to "idealize" a structure in Phenix?
>> I mean, ideal omega, all residues within allowed regions of Ramachandran maps, no clashes..etc. I know it won't fit the map well but I would like to see what it looks like.
> Yes, using phenix.geometry_minimization :
> http://phenix-online.org/documentation/reference/geometry_minimization.html
> Pavel

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