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. Thank you. ____________________________________________________________ FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on your desktop! Check it out at http://www.inbox.com/marineaquarium
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
Hi, Is there only the command line version of this or the GUI usage is available as well? Best Regards, Oarabile Kgosisejo ________________________________________ From: [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi,
The GUI version is available under "Model tools" and called "Geometry
minimization".
Best regards,
Oleg Sobolev.
On Mon, Apr 27, 2015 at 12:57 PM, Kgosisejo, Oarabile
Hi,
Is there only the command line version of this or the GUI usage is available as well?
Best Regards,
Oarabile Kgosisejo ________________________________________ From: [email protected] [ [email protected]] on behalf of Pavel Afonine [ [email protected]] 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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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: [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] 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
Thank you Best Regards, Oarabile M. Kgosisejo ________________________________________ From: Pavel Afonine [[email protected]] Sent: April 27, 2015 2:21 PM To: Kgosisejo, Oarabile; PC; PHENIX list Subject: Re: [phenixbb] idealizing structure 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: [email protected] [[email protected]] on behalf of Pavel Afonine [[email protected]] 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
participants (4)
-
Kgosisejo, Oarabile -
Oleg Sobolev -
Pavel Afonine -
PC