Re: [ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients

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Subject: Re: How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients
From: martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK martyn {- dot -} winn {- at -} STFC {- dot -} AC {- dot -} UK
Date: 2011-12-21

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Subject: Re: MERGING THREE DATASETS
From: arka chakraborty arko {- dot -} chakraborty88 {- at -} GMAIL {- dot -} COM
Date: 2011-12-21

Subject: Re: How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients
From: Peter Keller pkeller {- at -} GLOBALPHASING {- dot -} COM
Date: 2011-12-21

Hi Martyn,

On Wed, 21 Dec 2011, martyn.winn@STFC.AC.UK wrote:

> Thanks for this. I have recently updated the CCP4-supplied dictionary to
> include standard mmCIF, exchange dictionary, plus extra CCP4 items. This
> will be in the next release. I was about to update cif2mtz to recognise
> these extra columns. Will look at what you have done, may save me a job.
>
> cif2mtz is based on the ccif library, which complains if you try to load a
> cif file which contains a non-dictionary item. I'm sure in the past I
> tried to find a way round this, and failed.

This can be done, at least to the extent that the non-dictionary item can be
ignored by the application rather than causing it to crash. (Reading data
values from the mmCIF does absolutely require the item to have been defined
in the dictionary though.) If you look at our suggested patch to cif2mtz to
allow reading the map coefficient data you will get a hint about how to do
this, or I can send details to you off-list or to ccp4-dev.

> From the user point of view, the mmcif file is ascii and you can hand-edit
> the column item names. This is the get-out method if cif2mtz fails. Edit
> the item name to something that is recognised.

This is not ideal (says he, not having forgotten his own involvement here
:-)), and it is possible to imagine cases where this is not trivial to do
because of conflicting requirements of different dictionaries. That is not
intrinsic to the way that cif2mtz is written though, and could be fixed.

Regards,
Peter.

--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
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Cambridge CB3 0AX
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: MERGING THREE DATASETS
From: arka chakraborty arko {- dot -} chakraborty88 {- at -} GMAIL {- dot -} COM
Date: 2011-12-21