[phenixbb] PHENIX-Coot problem

Nathaniel Echols nechols at lbl.gov
Wed May 7 09:57:53 PDT 2014

On Wed, May 7, 2014 at 8:30 AM, Marcelo Carlos Sousa <
Marcelo.Sousa at colorado.edu> wrote:

> I recently updated to CCP4 6.4 including Coot.
> I updated the path in phenix to point to the coot wrapper startup script.
> Phenix then correctly starts Coot and both programs are "connected".
> However regularizations or real space refinement fail with the "Failed to
> find restraints for: …" message as if the dictionaries are not loading.
> This does not happen when starting Coot from the terminal or form CCP4i…
> Any ideas on how to solve this problem?

Not exactly, but I have an idea about how to debug it.  Coot's terminal
output is relatively verbose and should mention something about the monomer
library when it is initialized (and perhaps when you try regularization).
 So, could you please launch it and run a quick regularization, paste the
terminal output to a text file, and send me the file?  You need to do this
twice: once with Coot launched from the terminal, then launch Phenix from
the terminal and start Coot from Phenix.  Hopefully there will be something
missing in the output from the second try.

I will see if I can reproduce the problem here - however I do not believe
we have observed anything like this in the past.  For what it's worth,
Phenix does not override any environment variables or restraints pertaining
to Coot - it will still use the CCP4 monomer library.  (It will load custom
CIF files if you open it from phenix.refine, but I doubt this is the source
of the problem.)


PS. Which OS/Phenix build?
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