[ccp4bb] Oddity in CCP4 library signal mtz -error (developers)

[Bernhard Rupp]

Hi Fellows,

 

while reading logs I notice an (apparently inconsequential) error message
using anomalous refinement in Refmac:

 

OPENED INPUT MTZ FILE 

 Logical Name: HKLIN   Filename:
C:/data/Dropbox/Refinements/ABCD\ABCD_anomalous.mtz 

 

>> CCP4 library signal mtz:File column type different from type expected
by program (Error)

raised in ccp4_lrassn <<

   From ccp4_lrassn: expected type F does not match file type G for column
F-obs(+)

>> CCP4 library signal mtz:File column type different from type expected
by program (Error)

raised in ccp4_lrassn <<

   From ccp4_lrassn: expected type Q does not match file type L for column
SIGF-obs(+)

 

 

The GUI has no problem recognizing/understanding these G and L label types,
though, and Refmac does its job properly producing fine anomalous maps.

 

And oddly enough, for F-obs(-) and SIGF-obs(-)the G and L labels are not
considered offending. 

 

So maybe it's not a real error just expecting F and Q .

 

Best, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

All models are wrong

but some are useful.

--

 




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[ccp4bb] Refmac and hydrogens -developers

[Bernhard Rupp]

Hi Fellows,

 

for an experiment, I am running 0.9 A data with unrestrained Refmac (yes I
know should/could use SHELXL, but let's drop that for now).

 

When I select 'ignore even if present in file' in a PDB that has hydrogens,
I get the identical results than with 'use if present' or 'generate all'.

 

The log informs me that the instructions were properly issued, the output
PDB does not have Hs, but Rs and map are exactly the same 

as with selection of if present or generate all H. Does not seem to make
sense.

 

If I cull the hydrogens from the input PDB and 'use if present' or 'ignore',
the stats and map are different and no H in output as requested -  all as
expected.

 

Maybe that can be reproduced and, if it is not a feature, fixed.

 

Best, BR

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Real knowledge is to know 

the extent of one's ignorance 

--

 




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Re: [ccp4bb] QTMG font too small

[Paul Emsley]

On 21/05/2020 01:00, Khushboo Patel wrote:

Hi Everyone,

This is rather a silly question but the font of my QTMG is too small, 
screenshot attached.
I have tried everything from changing display settings on my mac to looking in 
preferences in QTMG software but cant seem to fix the problem.
Did anyone face the same problem? What can i do to make the fonts larger?



Edit -> Preferences -> Display -> Fonts -> Application



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[ccp4bb] Phenix version 1.18 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.18 of Phenix is 
now available (build 1.18.2-3874). Binary installers for Linux, Mac OSX, and 
Windows platforms, and the source installer, are available at the download site:

http://phenix-online.org/download/

Please note that this recent publication should now be used to cite the use of 
Phenix:

Macromolecular structure determination using X-rays, neutrons and electrons: 
recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, 
Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner 
RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, 
Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams 
CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. 
https://doi.org/10.1107/S2059798319011471

Highlights for the 1.18.2 version of Phenix:

1.18.2 Changes

- Fix weighting for iron sulfur clusters

1.18.1 Changes

- General bug fixes

1.18 Changes

- Amber
  - Automatic creation of Amber files in phenix.refine GUI
  - Added AmberPrep GUI

- Restraints
  - Engh & Huber restraints (2001) for cis-peptides now implemented
  - Restraints added for FeS
  - Metal coordination library is default to Zn+2 and FeS clusters

- Rama-Z: New global Ramachandran score for identifying protein structures with 
unlikely stereochemistry 
  in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports).

- Density modification for cryo-EM
  - Includes model-based density modification with automatic model generation
  - Optimized defaults and additional documentation

- Real-space refinement
  - Hydrogen atoms no longer included in map target function, which improves 
fit.
  - Add NQH flip option (enabled by default)

- Other
  - New tool for ordered solvent picking in cryo-EM maps (phenix.douse)
  - New map and model superposition tool (phenix.match_maps)
  - New FindProgram to find any Phenix program with a text search
  - Project details now has a button for opening the README file for tutorials

For a full list of changes see:

http://www.phenix-online.org/documentation/CHANGES

Please note that this new publication should be used to cite the use of Phenix:

Macromolecular structure determination using X-rays, neutrons and electrons: 
recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, 
Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner 
RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, 
Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams 
CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. 
https://doi.org/10.1107/S2059798319011471

Full documentation is available here:

http://www.phenix-online.org/documentation/

There is a Phenix bulletin board:

http://www.phenix-online.org/mailman/listinfo/phenixbb/

Please consult the installer README file or online documentation for 
installation instructions.

Direct questions and problem reports to the bulletin board or:

h...@phenix-online.org and b...@phenix-online.org

Commercial users interested in obtaining access to Phenix should visit the
Phenix website for information about the Phenix Industrial Consortium.

The development of Phenix is principally funded by the National Institute of
General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge
the generous support of the members of the Phenix Industrial Consortium.

--
Paul Adams
Division Director, Molecular Biophysics & Integrated Bioimaging, LBL 
(http://biosciences.lbl.gov/divisions/mbib)
Principal Investigator, Computational Crystallography Initiative, LBL 
(http://cci.lbl.gov)
Vice President for Technology, the Joint BioEnergy Institute 
(http://www.jbei.org)
Principal Investigator, ALS-ENABLE, Advanced Light Source 
(http://als-enable.lbl.gov)
Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov)
Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov)
Adjunct Professor, Department of Bioengineering, U.C. Berkeley 
(http://bioeng.berkeley.edu)
Adjunct Professor, Comparative Biochemistry, U.C. Berkeley 
(http://compbiochem.berkeley.edu)

Building 33, Room 250
Building 978, Room 4126
Building 977, Room 180C
Tel: 1-510-486-4225
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.

Executive Assistant: Ashley Dawn [ ashleyd...@lbl.gov ][ 1-510-486-5455 ]
--



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[ccp4bb] Scientific Data Curation positions at PDBe and EMDB/EMPIAR

[John Berrisford]

Dear CCP4BB

 

There are two curator positions available in the PDBe and EMDB/EMPIAR teams
at the European Bioinformatics Institute (EBI) on the Wellcome Genome Campus
near Cambridge.

 

We are looking to recruit an expert structural biologist to join the PDBe
curation team. The work involves annotating preliminary PDB and EMDB
submissions and extracting relevant biological information.

 

We are also looking for an expert cryo-electron microscopist to join the
EMDB/EMPIAR team. This work would involve biocuration activity in both EMDB
and EMPIAR archives and the integration of this data with other
bioinformatics resources.

 

The closing date for both posts is 30th June 2020. For more information on
the positions, please visit:

 

PDBe:  
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01532

EMDB/EMPIAR:  
https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01622

 

Kind Regards,

 

John

 

--

John Berrisford

PDBe

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD UK

Tel: +44 1223 492529

 

  http://www.pdbe.org

 
http://www.facebook.com/proteindatabank

  http://twitter.com/PDBeurope

 




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