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

[Paul Emsley]

On 16/06/11 21:36, Nathaniel Echols wrote:
> On Thu, Jun 16, 2011 at 1:26 PM, Louis Lazar<louisl at brandeis.edu>  wrote:
>> On Thu, Jun 16, 2011 at 4:18 PM, Nathaniel Echols<nechols at lbl.gov>  wrote:
>>> On Thu, Jun 16, 2011 at 1:07 PM, Louis Lazar<louisl at brandeis.edu>  wrote:
>>>> 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_dictionary_v5.29.tar.gz

You need to install it into a lib/data directory and point the 
environment variable COOT_REFMAC_LIB_DIR to that directory.

PE.