[phenixbb] General Questions about Joint x-ray/neutron refinement
nechols at lbl.gov
Thu Jun 16 13:36:37 PDT 2011
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?
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?
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