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

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:

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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:

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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:

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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:

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ooh ooh ooh--I know this!

Look in the .geo file

On 13 May 2010, at 5:34 PM, Maia Cherney wrote:

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Dear phenixbb, how to get listed all dihedral angles from a ligand after refinement. (Not ideal cif files, but actual dihedral angles).

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