Hi Blaine, Thanks for your reply, I thought maybe this was related to my issue with ccp4, though I’ll also direct this to the PyMol mailing list as you suggested.
I am currently using version 2.5.0, unfortunately neither type=pdb or type =cif seemed to fix the issue ☹ Dale. Dale Calleja PhD Student, Komander Lab Ubiquitin Signalling Division WEHI 1G Royal Parade Parkville VIC 3052 Australia Email callej...@wehi.edu.au<mailto:callej...@wehi.edu.au> From: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu> Date: Wednesday, 27 July 2022 at 12:04 pm To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>, Dale Calleja <callej...@wehi.edu.au> Subject: 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. To get the pdb file downloaded, try fetch 6wrh type=pdb. I can download 6wrh into a recent incentive version of PyMOL (2.5.2) via fetch 6wrh. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Dale C <00008378c932659c-dmarc-requ...@jiscmail.ac.uk> Sent: Tuesday, July 26, 2022 7:44 PM To: CCP4BB@JISCMAIL.AC.UK <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 v8.0.002 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 anything open. Nor do i see the "Connected to Phenix" button in the toolbar on Coot. - The 'fetch' command in Pymol no longer works either (I have attached a screenshot of the error message here) - Coot also seems to have an issue with not loading the amino acid restraints so when i click real-space refine, i get the error 'unable to find restraints for residue x,y,z'. I feel they may be all related and my first thought is that it has something to do with my Python dependencies however I have no idea how to fix this or reinstall them. Does anyone have an idea if they are all related? Or how i might fix this? fyi I am using - ccp4 program suit v8.0.002 - Coot 0.9.8.3 - Phenix-1.20.1-4487 Thanks in advance. Dale. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
