I am not sure what is meant by "recent change in CCP4 default naming of
mtz columns". The point of the LABIN mechanism is that mtz columns can
have any user-defined labels. Yes there are conventions, but since
"CCP4" consists of many different programs written by many different
authors with many different opinions, it seems highly dangerous to make
assumptions about column naming. This has been true throughout the
history of MTZ and I believe also for LCF (before my time!).
Following the link below below, through to the online conversion tool
http://pdb-extract.rcsb.org/auto-check/index-ext.html
there is an option "Semi-automatic MTZ Conversion to mmCIF" which allows
you to select the correct MTZ column. This seems a safer way to go, and
it seems to work fine on one MTZ file with "non-standard" naming.
Cheers
Martyn
P.S. posting problems are invariably due to subscribing and posting from
different email addresses
On Sun, 2009-03-08 at 16:04 +0000, Gerard Bricogne wrote:
> 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 <[log in to unmask]> -----
>
> Date: Sat, 07 Mar 2009 11:56:55 -0500
> From: Maksymilian Chruszcz <[log in to unmask]>
> Subject: Re: Checking for gremlins in deposited diffraction data
> To: [log in to unmask], [log in to unmask]
> Cc: "Dauter, Zbigniew" <[log in to unmask]>,
> Zbyszek Otwinowski <[log in to unmask]>,
> Wladek Minor <[log in to unmask]>
> 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 -----
>
--
***********************************************************************
* *
* Dr. Martyn Winn *
* *
* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. *
* Tel: +44 1925 603455 E-mail: [log in to unmask] *
* Fax: +44 1925 603825 Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
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