Re: [ccp4bb] PDB redo R free

[Tim Grüne]

Dear Qixu Cai,
the sets do not have to be identical, as long as refinement reaches a 
steady state.

Best regards,
Tim

Am 28.04.2023 04:51, schrieb Qixu Cai:

Dear all,

I'm using the PDB-REDO server to refine my structure. I found that
PDB-REDO said that 5% R-free set is too small and it created a new
R-free set.

Is possible for the PDB-REDO server to keep the original R-free set to
make final Rfree value comparable?

Best regards,

Qixu Cai
Email: caiq...@gmail.com

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Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

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[ccp4bb] PDB redo R free

[Qixu Cai]

Dear all,

I'm using the PDB-REDO server to refine my structure. I found that PDB-REDO
said that 5% R-free set is too small and it created a new R-free set.

Is possible for the PDB-REDO server to keep the original R-free set to make
final Rfree value comparable?

Best regards,

Qixu Cai
Email: caiq...@gmail.com



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Re: [ccp4bb] Installing older version ccp4 7.0

[Nicholas Pearce]

Hi,

You no longer need to install the old version of ccp4 to run pandda.

You can now install pandda into ccp4-8.0:

  *   Load your ccp4 version (load the bin/ccp4.setup-sh as you would normally)
  *   Download pandda from the bitbucket: 
https://bitbucket.org/pandda/pandda/src/master/
  *   Run the pandda.setup script (in the bin folder)

You may need to install some additional software onto your computer: watch out 
for error messages raised during the pandda.setup script. You should then try 
to run the tutorial data.

Note that in the tutorial there is an error and you will need to run
pandda.analyse data_dirs='data/*' pdb_style='*.dimple.pdb' cpus=X
and NOT

pandda.analyse data_dirs='./data/*' pdb_style='*.dimple.pdb' cpus=X

Thanks,
Nick

———

Nicholas Pearce
Assistant Professor in Bioinformatics
SciLifeLab | Data-Driven Life Sciences (DDLS) Fellow
Linköping University
Sweden

From: CCP4 bulletin board  on behalf of Ashima Chopra 
<9ef63a1c3715-dmarc-requ...@jiscmail.ac.uk>
Date: Friday, 21 April 2023 at 21:47
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Installing older version ccp4 7.0
Hi all,

I am unable to download legacy versions of ccp4, especially ccp4 7.0.72 for 
running PanDDA. Does anyone have advice on how to do that?

Thanks for your help,
Ashima


Ashima Chopra (she/her), PhD

Postdoctoral Associate, Eddy Arnold Laboratory

Department of Chemistry and Chemical Biology/ Center for Advanced Biotechnology 
and Medicine

Rutgers University, New Brunswick





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