Hi Paul,
I seemed to have fixed the amino acid dictionary issue by following Nick's
suggestion to direct Phenix to the new coot.app location in my ccp4
applications folder.
Though I am still having the issue that Phenix is not connecting to Coot, is
this a known/common issue? Would you please
Hi Nick,
Thanks a lot for that advice, directing Phenix to the new coot.app location
appears to have fixed the amino acids restraints issue!
Though still having issue with Phenix not connecting to Coot, perhaps i will
post this issue on the Phenixbb and see what the community has to say.
Hi Dale,
I recently updated Phenix and CCP4 on iOS had a similar issues with
Phenix/Coot.
I fixed the issues with the restraint dictionary by directing Phenix to the
new location for Coot (in the CCP4 program libraries) in the Phenix
settings. This resolved the lack of restraints for every amino
Hi all,
When opening Coot from ccp4 8 in Phenix, there may be an issue with the
restraints since some environment variables may not be set. The terminal
should show something like
/Applications/ccp4-8.0/coot_py2/bin/coot: line 81:
/Applications/ccp4-8.0/coot_py2/bin/ccp4.setup-sh: No such file
On 27/07/2022 01:44, Dale C wrote:
Hi all,
I recently updated my ccp4 package to Program suite v8.0.002 and i have now run
into a few issues with other programs. The issues are highlighted below...
- When i click 'Open in Coot' on any output through Phenix (so far only tested
phenix.refine
:19 am
To: Dale Calleja , CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8
PC, mac or linux?
-Original Message-
From: CCP4 bulletin board On Behalf Of Dale C
Sent: Wednesday, 27 July 2022 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb]
ct: Re: [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing
ccp4 v8
Hi Dale,
Which version of PyMOL are you using?
(PyMOL questions should really be directed to the PyMOL mailing list).
Ancient versions of PyMOL may not accept cif files via fetch unless you include
the type=cif​ keyword.
board on behalf of Dale C
<8378c932659c-dmarc-requ...@jiscmail.ac.uk>
Sent: Tuesday, July 26, 2022 7:44 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4
v8
Hi all,
I recently updated my ccp4 package to Program suite v8
PC, mac or linux?
-Original Message-
From: CCP4 bulletin board On Behalf Of Dale C
Sent: Wednesday, 27 July 2022 12:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8
Hi all,
I recently updated my ccp4 package to Program suite
Hi all,
I recently updated my ccp4 package to Program suite v8.0.002 and i have now run
into a few issues with other programs. The issues are highlighted below...
- When i click 'Open in Coot' on any output through Phenix (so far only tested
phenix.refine and phenix.phaser), i no longer see
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