[phenixbb] GUI reorders file data type in EM validation task

Ashley Pike ashley.pike at sgc.ox.ac.uk
Wed Oct 30 10:04:44 PDT 2019

Hi Billy,
When I add files - individually - the initial data type is automatically set to 'Real map' which I then alter depending on whether maps are full or half maps. Also when I modify the first datatype from Real -> full, the other two maps have their data type set to unknown - which I then change to half map.

Phenix version 1.17-3644
OS: Centos6.6 / 2.6.32-504.el6.x86_64

In contrast if I run phenix 1.16-3549 on a Centos7 system (3.10.0-1062.1.1.el7.x86_64), the gui behaviour for the validate task is different. The first map I add gets a datatype of 'Full map' and the two halfmaps are then assigned to 'Real map' which I then change to 'half map'. Running this job gives expected file assignments and behaviour.


From: Billy Poon <BKPoon at lbl.gov>
Sent: 25 October 2019 17:49
To: Ashley Pike <ashley.pike at sgc.ox.ac.uk>
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] GUI reorders file data type in EM validation task

Hi Ashley,

Can you tell me which operating system and version you're using? Also, when you add the files, do you add them all at once or one at a time? Thanks!

Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Thu, Oct 24, 2019 at 3:23 AM Ashley Pike <ashley.pike at sgc.ox.ac.uk<mailto:ashley.pike at sgc.ox.ac.uk>> wrote:
I am having problems convincing the GUI which EM map is which for halfmap validation. Version is 1.17-3644
Here is input:
[cid:image001.png at 01D58F3E.688E05A0]

and what is written to Summary tab:
[cid:image002.png at 01D58F3E.688E05A0]
Any tricks to getting this to work? Editing the .eff file written by the gui is an option but running phenix.validation_cryoem on the command line doesn’t seem to produce much viewable output.


Dr. Ashley Pike
Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford
Phone: +44 (0)1865 617576 | FAX: +44 (0)1865 617575 | ashley.pike at sgc.ox.ac.uk<mailto:ashley.pike at sgc.ox.ac.uk> | www.thesgc.org<http://www.thesgc.org/>
Address:  Structural Genomics Consortium, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK

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