[phenixbb] idealizing structure
o.kgosisejo at usask.ca
Mon Apr 27 13:26:09 PDT 2015
Oarabile M. Kgosisejo
From: Pavel Afonine [pafonine at lbl.gov]
Sent: April 27, 2015 2:21 PM
To: Kgosisejo, Oarabile; PC; PHENIX list
Subject: Re: [phenixbb] idealizing structure
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:
> 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 :
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