Re: [phenixbb] General Questions about Joint x-ray/neutron refinement

On 16/06/11 21:36, Nathaniel Echols wrote:

On Thu, Jun 16, 2011 at 1:26 PM, Louis Lazar wrote:

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On Thu, Jun 16, 2011 at 4:18 PM, Nathaniel Echols wrote:

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On Thu, Jun 16, 2011 at 1:07 PM, Louis Lazar wrote:

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Second, when I try to real space refine any of the residues, I get an error message telling me about exploding atoms. What is the cause of this message, and is it possible to real space refine any of these residues and specifically the hydrogen atoms associated with them. Quick question - are the atoms exploding in Phenix, or in Coot?

Coot

Okay, this is a conflict between the monomer library distributed with Coot, which uses the old PDB v2 standard for hydrogen names, and what Phenix does, which is to use PDB v3 hydrogens. I think you can get around this problem by telling Coot to use the newer CCP4 monomer library, which also uses v3. Unfortunately, I'm not sure where to get this or how to configure it, although I'm pretty sure it involves setting an environment variable. Perhaps Paul Emsley (or someone else who has run into the same problem) could comment?

Quite so. The monomer library can be found here: http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental/refmac_dic... You need to install it into a lib/data directory and point the environment variable COOT_REFMAC_LIB_DIR to that directory. PE.