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Hi Debanu,
I think coot might be asking for the name as defined in the monomer library.
You can find that in
<coot directory>/share/coot/lib/data/monomers/mon_lib.list
<coot directory>/share/coot/lib/data/monomers/mon_lib.html
These are basically identical to refmac's mon_lib. There are a LOT of monomers
in there, so paging through every monomer one at a time will take forever.
Instead, as you say, I would use your knowledge of things like crystallization
condition, protein cofactors, etc. to make a shorter list of candidates and then
examine those carefully. For example, if you crystallized in AmOAc and your
mystery density is a planar "Y" shape, then you're probably seeing acetate.
HIC-UP (http://alpha2.bmc.uu.se/hicup/) is also a great searchable resource for
working with heterocompounds. From HIC-UP you can download both ideal and
experimental coordinates.
Jacob
Debanu Das wrote:
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Hi,
A clarification to my question about using COOT's ligand library:
I do not know what the ligand is. All I see is some density near the
proposed ligand binding site.
What I would like to do is to read in some kind of library with ligands
and then try to fit them into the density one at a time to see how they
fit and to try to deduce what the ligand may be. I was hoping to do this
by reading in the COOT library and trying out the ligands one by one.
Also, I'm not quite sure how to use the COOT library. It asks for a 3
letter code for a desired ligand to be read in and I can find no list of
3 letter codes for all the ligands it may have in its library, so even
if I wanted to try out a particular ligand based on known molecular
properties of the protein or purification/crystallization conditions, I
would not know its particular 3 letter code and hence cannot read it in.
Any help will be much appreciated.
Thanks in advance.
Debanu.
--
Jacob Corn
The Berger Lab
UC Berkeley - Molecular and Cell Biology
[EMAIL PROTECTED]
phone: 510-643-8893
fax: 510-643-9290
