Re: [ccp4bb] remediated pdb and coordinate formates ...

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

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

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From: "Fan, Hai-fu" fanhf {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-05-04

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Subject: Re: remediated pdb and coordinate formates ...
From: Chris Putnam cdputnam {- at -} UCSD {- dot -} EDU
Date: 2007-05-04

On Friday 04 May 2007 01:10 am, Ingo P. Korndoerfer wrote:
> but i think i would be willing to put up with having to add another 10
> lines to my scripts to process mmcif, if
> that allows me to take home all the other advantages.
>
> the biggest problem at this point is, as far as i know (and this is also
> what the above website states), that my favourite refinement program
> does not really work with anything but pdb, so i am not really sure
> whether it is the users who are reluctant to use mmcif (as above website
> states) ...
>
> wouldn't it be nice to try and teach our favourite refinement programs
> mmcif ?

Yes it would. With this in mind, I'd like to donate the mmCIF parsing code
that I had written to integrate mmCIF parsing into XtalView into the general
community. The code is written in C and can be downloaded at:

http://www.scripps.edu/~cdputnam/software/mmcif/

The core library is program agnostic and operates like a lot of XML
parsers to build a document object model (DOM) using a finite state
machine. Glue code (like the XtalView examples) can then browse
the DOM for the appropriate mmCIF datablocks/entries/lists and extract
the values into the appropriate structures for the program of interest.

Chris.

--
Christopher Putnam, Ph.D.
Ludwig Institute For Cancer Research
Cellular and Molecular Medicine East, Room 3019
9500 Gilman Drive
La Jolla, CA 92093-0660 USA

CCP4bb navigation

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

Previous message:
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From: "Fan, Hai-fu" fanhf {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-05-04

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From: Alejandro Buschiazzo alebus {- at -} PASTEUR {- dot -} FR
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