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CCP4BB  January 2007

CCP4BB January 2007

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Subject:

Re: 3 letter code for the Ligand

From:

Gerard DVD Kleywegt <[log in to unmask]>

Reply-To:

Gerard DVD Kleywegt <[log in to unmask]>

Date:

Thu, 25 Jan 2007 17:38:09 +0100

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (37 lines)

> 1) I am working with two ligands, cyclopropanemethanol
> and cyclobutanemethanol. The 3 letter code for them
> CPM and CBM (i thought of using) were assigned to
> other ligands. Is there any standard procedurre to
> name them. I would like them to use in Refmac and
> coot.

while you refine your structure you can call them whatever you like (XXX, ABC, 
WTF, USA, NSW, ...) as long as it's not already used in the refinement 
program's dictionary. when you deposit, you have to contact the deposition 
centre and they will assign a three-letter code

> 2) How do I convert mtz file to dsn6 (O) format. The
> google search took me to
> http://www.imsb.au.dk/~mok/o/o-info/1994/Jan/msg00056.html
> but there is no answer.

an mtz file contains reflections; dsn6 is a format for electron-density maps. 
so you will need to calculate a map first and then, if you really want to, you 
can convert it to dsn6 format (e.g. with mapman or, if you have an ASCII CNS 
map for instance, using the mapman server, 
http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl)

--dvd

******************************************************************
                         Gerard J.  Kleywegt
     [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                 Biomedical Centre  Box 596
                 SE-751 24 Uppsala  SWEDEN

     http://xray.bmc.uu.se/gerard/  mailto:[log in to unmask]
******************************************************************
    The opinions in this message are fictional.  Any similarity
    to actual opinions, living or dead, is purely coincidental.
******************************************************************

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