Hi, in a nutshell, the problem with CIF files created by PRODRG is that sometimes PRODRG assigns too small sigmas (esds), which in turn means that the corresponding terms in restraint targets become much larger than the others (since they are proportional to 1/sigma**2), and this results in distorting overall geometry during refinement. So, if you do refinement using phenix.refine it is the best to use phenix.ready_set to obtain cif files for your ligands, or if you get them from elsewhere then make sure they are correct. You can use phenix.reel to check your cif files - my recollection is that it will highlight bad esds. Pavel. On 5/25/11 12:09 AM, ChenTiantian wrote:

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 mailto:[email protected]> wrote:

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

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Hi Mark, I'm pretty sure it is possible (and easy) to do in phenix.refine, but syntax to ask phenix.refine to do this may not be obvious... I should probably add more examples to the documentation. Meanwhile, if you send me the portion of your PDB file containing the residues in questions and HEME, then I will send you back a working example. Pavel. On 6/1/11 2:06 AM, Mark Roe wrote:

Hi,

I have a HEME covalently attached to an amino acid side chain. From mass spec, the original sample was around 50/50 covalent attachment or unlinked. I have created a new library file to deal with the covalently linked HEME. Is there a way to refine the occupancy? I need to constrain the new residue B167 to the original amino acid A167 AND the original HEME A350. If I just do the normal occupancy refinement the new B167 gets constrained only to the original side chain A167. Or (since there isn't any large change in atom position) will the occupancy refinement be meaningless anyway? It's not like different orientations - just different bonding.