[phenixbb] idealizing structure

[Pavel Afonine]

Hi,

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:

http://phenix-online.org/documentation/reference/real_space_refine.html
http://phenix-online.org/presentations/real_space_refine.pdf

This is command line only, at the moment.

Pavel


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