Re: [phenixbb] to get dihedral angles for a ligand

Thanks Nigel Moriarty wrote:

Maia

I can add a feature to write all the columns in some simple text format. I'll let you know when its in the release.

Nigel

On Fri, May 14, 2010 at 9:19 AM, Maia Cherney wrote:

...

Hi Nigel,

I have the ADP and methyl-ATP ligands in my complexes. I see that some torsion angles that are common for both ligands are very different. I want to give a table in my paper with the most changed torsion angles. They should be actual angles after refinement, not from the ideal cif files. Right now I just do screen shots (png files) to save the information from different complexes, but it's very inconvenient. If I could get a list of torsions as a table in a text file that would be most convenient.

Maia

Nigel Moriarty wrote:

...

Maia

You can save a CIF file from REEL using a pull-down menu under File. However, I'm a little unclear on what you are trying to achieve. Can you elaborate?

Nigel

On Thu, May 13, 2010 at 9:25 PM, Maia Cherney wrote:

...

Hi Nigel, The phenix.reel worked, even with the error message (Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory).

I got all dihedrals in the reel window, now how can I save them?

Maia

Nigel Moriarty wrote:

...

That should be model.pdb, the final model from the refinement.

Sorry

Nigel

On Thu, May 13, 2010 at 4:32 PM, Maia Cherney wrote:

...

lig.cif is the cif file from elbow (ideal) that I gave in the refinement. How do I get the model.cif?

Maia

Nigel Moriarty wrote:

> As Patrick correctly stated you should look in the .geo. All the > geometry information is written there and it is instructive to look > there. There is, however, an alternative if you wish to get more info > about a ligand. You can type > > phenix.reel lig,cif model.cif > > choose "Geometry transfer". You can then compare the ideal and the > actual values of all of the restraints listed in the CIF restraints > file. You may have to choose the pull-down menu View->List geometry > values depending on your version. > > Nigel > > On Thu, May 13, 2010 at 2:35 PM, Patrick Loll > wrote: > > > > >> ooh ooh ooh--I know this! >> >> Look in the .geo file >> >> On 13 May 2010, at 5:34 PM, Maia Cherney wrote: >> >> >> >> >> >>> Dear phenixbb, >>> how to get listed all dihedral angles from a ligand after >>> refinement. >>> (Not ideal cif files, but actual dihedral angles). >>> >>> Maia >>> _______________________________________________ >>> phenixbb mailing list >>> [email protected] >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >>> >>> >>> >> --------------------------------------------------------------------------------------- >> Patrick J. Loll, Ph. D. >> Professor of Biochemistry & Molecular Biology >> Director, Biochemistry Graduate Program >> Drexel University College of Medicine >> Room 10-102 New College Building >> 245 N. 15th St., Mailstop 497 >> Philadelphia, PA 19102-1192 USA >> >> (215) 762-7706 >> [email protected] >> >> _______________________________________________ >> phenixbb mailing list >> [email protected] >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> >> >> >> > _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb