From hyang@rcsb.rutgers.edu Wed Mar 15 15:14:12 2006
Date: Tue, 14 Mar 2006 12:38:24 -0500
From: Huanwang Yang <hyang@rcsb.rutgers.edu>
To: Alexei Vagin <alexei@ysbl.york.ac.uk>
Cc: P.J.Briggs <P.J.Briggs@dl.ac.uk>
Subject: Re: Problems/fixes for SFCHECK with CIF coordinate input

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Dear Alexei
Thank you so much for your message.  I tested the command and it worked.
I have a question about the cif tokens generated by the command 'sfcheck 
-f file.mtz -m file.pdb -r':

_shift
_shift_side_chain
_dcorr
_dcorr_side_chain

Do the tokens correspond to the values of  the whole residue and side 
chain only. I noticed that in the PS file, they are main chain and side 
chain. 

As you know, there is a difference between macromolecular cif  and the 
small molecular cif format.  Your export used small molecular cif tokens.

We have defined all the macromolecular cif items according to your paper 
(1999) Acta Cryst. D55.  The link is 
http://rcsb-mmcif-local.rutgers.edu/dictionaries/mmcif_pdbx.dic/Categories/pdbx_refine_component.html
I wonder if you can export the cif items according to the dictionary, so 
that we can directly use them without further modification. 

By the way, if the item definitions are not correct or not accurate, 
please let me know.  Thanks a lot.


Best regards,
Huanwang

Alexei Vagin wrote:

> Dear Peter and Huanwang Yang
>
> 8. At the RCSB they are also interested in writing out to CIF some of
>    the data (for example the density correlations for each residue) that
>    is currently only output to the final postscript file. In order to do
>    this Huanwang has extended the SFCHECK 6.0.5 code, and is now
>    migrating the changes to 7.1.01, however he would be interested in
>    having the changes incorporated into your version of SFCHECK in
>    future if that is possible. Is this something that you would
>    consider?
>
> if we use sfcheck by command string with option "-r" :
>
> sfcheck -f file.mtz -m file.pdb -r
>
> or
>
> sfcheck -f file.cif -m file.pdb -r
>
> or
>
> sfcheck -f file.map -m file.pdb -r
>
> program creates "CIF" output: sfcheck.dst
> with information about dens.coor,index,... for each residue.
>
> I think it is good idea to have one unique version in York.
>
> Best regards
> Alexei
>
>
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*                Huanwang Yang  Ph.D.                      *
* RCSB Protein Data Bank                                   *
* Dep. of Chemistry & Chemical Biology, Rutgers University *  
* 610 Taylor Road, Piscataway, NJ 08854-8087               *
* Phone: (732)-445-0103 (ext 240);  Fax: (732)-445-4320    * 
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