[ccp4bb] [mc3h@cms.mail.virginia.edu: Re: Checking for gremlins in deposited diffraction data] (fwd)

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: missing carboxyl oxygen
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-03-07

Next message:
Subject: Postdoctoral position - plant protein crystallography at Umea University, Sweden
From: Uwe Sauer uwe {- dot -} sauer {- at -} CHEM {- dot -} UMU {- dot -} SE
Date: 2009-03-08

Subject: [mc3h@cms.mail.virginia.edu: Re: Checking for gremlins in deposited diffraction data] (fwd)
From: Gerard Bricogne gb10 {- at -} GLOBALPHASING {- dot -} COM
Date: 2009-03-08

Dear all,

I am forwarding to the BB this message from Maksymilian Chruszcz (with
his permission), given that his own attempt at posting it directly was not
successful.

With best wishes,

Gerard.

----- Forwarded message from Maksymilian Chruszcz -----

Date: Sat, 07 Mar 2009 11:56:55 -0500
From: Maksymilian Chruszcz
Subject: Re: Checking for gremlins in deposited diffraction data
To: gb10@GLOBALPHASING.COM, ccp4bb@jiscmail.ac.uk
Cc: "Dauter, Zbigniew" ,
Zbyszek Otwinowski ,
Wladek Minor
X-Mailer: CommuniGate Pro WebUser v5.1.14

Dear Gerard,

Thank you very much for turning our attention to structure factors deposited
for 3FTT. Preliminary check of our data confirmed your suggestion about
F_calc and ph_calc being reported instead of F_meas_au and F_meas_sigma_au
respectively. This error was introduced during the conversion from MTZ to
CIF file. We are currently discussing with PDB source of such error.
Currently I do not know why these particular column were extracted, and I am
guessing that maybe PDB scripts handling new mtz files have problems. From:
http://pdb-extract.rcsb.org/auto-check/help/checksform.html#conversions 'An
automatic conversion is used to convert one standardized SF format to
another. If you are using one of the accepted formats (column labels, etc.),
and you have made no manual changes to the structure file format yourself,
then this method will work for you. Our tool is programmed to recognize
which columns correspond to each parameter (depending on the program's
format) and "automatically" converts the data to the new format
accordingly.' Looks that automatic conversion by PDB was broken by recent
change in CCP4 default naming of mtz columns. Please note that authors of a
deposit do not get file with structure factors converted from mtz to cif
format. They are asked if pdb and mmcif files with coordinates are correct,
but this is not a case for structure factors. Maybe it is worth to change
PDB policy and ask PDB to send structure factors together with coordinates
for authors’ approval. I will let you know what was source of the error
when it will be clarified with PDB. Your suggestion to deposit diffraction
images is very good. Actually CSGID puts the server that will make
accessible all diffraction images for PDB deposits. You (and all intrested
persons) will get access to 3ftt diffraction images next week. Best regards,
Maks Chruszcz

I do not know if it will be posted on CCP4BB. I have problem with
authorization.

----- End forwarded message -----

--

===============================================================
* *
* Gerard Bricogne gb10@GlobalPhasing.com *
* *
* Global Phasing Ltd. *
* Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
* Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
* *
===============================================================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: missing carboxyl oxygen
From: James Stroud xtald00d {- at -} GMAIL {- dot -} COM
Date: 2009-03-07