Hi Rex -
You can usually get the three-letter code from the PDB itself. At top
of the PDB home page, you can see that one of the options for the search
bar is "Ligand". If you put in a (mostly) correct name for the ligand,
you will get back the three-letter code that the PDB is using. This
should match exactly with the Refmac ligand dictionary that Joel mentioned.
Another place to look for ligand names is Gerard Kleywegt's HIC-UP site
( http://xray.bmc.uu.se/hicup/ ). I find that their search function
isn't so great, so I get the entire 7870-compound list by name here:
http://xray.bmc.uu.se/hicup/xname.html
and do a text search for something resembling my compound. You can then
download coordinates (real and idealized), ligand dictionaries, etc.
Furthermore, if the compound you're working with isn't in this list,
it's new to the PDB, and you get to give it your own three-letter code!
(All the good ones are already taken, unfortunately.)
Hope that helps,
Matt
On 10/7/12 5:43 PM, Joel Tyndall wrote:
Hi Rex,
In Coot, under the file menu, “Get Fragment” and the type LBT (upper
case).
This (LBT) is the three letter code for alpha-lactose. Unfortunately
it is not that easy to find the codes. However on my windows machine
the list is here:
C:\CCP4\6.3\lib\data\monomers\list
Hope this helps
Joel
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
Of *Rex Palmer
*Sent:* Monday, 8 October 2012 9:12 a.m.
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] OFF TOPIC
Can anyone please tell me how to extract the pdb for a ligand, eg
alpha lactose, from the COOT library, prior to fitting into difference
density.
Thanks in advance.
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
