Hi,there
I found that the cif file of ligand from ProDRG server is not good for
phenix.refine.
I always got my ligand pdb file using ProDRG, and use the refmac file as the
restraint file of the ligand, but I found that after running the
phenix.refine, the rmsANGLE is very high.
the I followed someone's advice, using phenix.elbow to produce the ligand's
cif file, that really make sense, now I can easily get the refinement value
of the complex structure in a
reasonable level.
Hope it works with your structure too.
Tiantian
On Tue, May 24, 2011 at 3:34 PM, Priit Eek
Thanks Nigel and Yuri! elbow.where_is_that_cif_file gave me the right cif to use in coot. Off to fix that sucrose now...
Priit
On 23.05.2011, at 17:55, Yuri wrote:
All coot needs to run its real-space refinement is a .cif file as Nigel pointed out. You can also get this file from other ligand library websites (proDrg, hic-cup, etc...). The only catch here is. The name of your sucrose atoms must match, exactly, those in the file. Once you have such file go to the the file drop-down menu and click on Import CIF dictionary in coot. That should enable to rotate the rotatable bonds of your ligand
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