Hi Arti,
Another way of generating coordinates for your molecule of interest is
by Chemdraw and Chem3d if you have the program. I find it easier
compared to sketcher since the chirality of an atom can be defined while
drawing the molecule in Chemdraw.

Once I get the 3D coordinates from Chem3D, I follow the procedure which
Matt described below.

Madhavi

-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
[log in to unmask]
Sent: Friday, February 23, 2007 12:28 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] previous message monomer library

CCP4 bulletin board <[log in to unmask]> wrote on 02/23/2007 11:22:04
AM:

> Hello all,
> Kindly disregard my message about monomer libraries. The problem (
atoms
> blowing apart) seems to be due to something (yet undetermined) else.
Thank
> you for clearing up ones about COM_COM.
> However, I still wonder if I can add my own ligand libraries to the
> default one, like you can do for ONO.
> Arti Pandey
>
>

Hi Arti -

You absolutely can.  I used to do this all the time when I was working
on
small-molecule drug complexes.

If all you want to do is take an existing library file (e.g. from
HIC-UP)
and use it, skip to the last paragraph of this email.  If you want to
make
a library file, read on.

The simplest way to do this is to create a pdb file containing the
idealized, energy-minimized coordinates of your molecule of interest.
How
you make this file is a little more complicated - I used InsightII from
Accelrys, but that's a very expensive program that you probably don't
have
access to.  Sketcher, in CCP4, will also do this but I never got it to
work
for me.  Even PyMOL will build molecules for you but it won't
energy-minimize them so bond lengths and angles can be distorted.

The CCP4 site suggests these programs (I've never used them):
http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/editor-links.html

Make sure that your new molecule has a unique 3-letter residue code so
that
Refmac won't be confused and think it's one of the entries in its
monomer
library.  There is a file called 'mon_lib.list' in
$CCP4_HOME/lib/data/monomers that gives the codes of everything in the
monomer library.  If you have a number in your residue code you'll
probably
avoid conflicts.

The next step is to run a short Refmac job on this coordinate file,
using a
simple script like the one here:
http://www.ccp4.ac.uk/dist/html/refmac5/dictionary/coord-dict.html

Refmac will generate a library file for your new molecule, then stop.
You
can then open up the new library file (which will have 'lib' in the
filename) and check through it with a text editor.  You'll see a long
list
of topology, bond lengths, angles, etc.  I find that the auto-generation
over-constrains torsion angles, so I delete the ones that aren't fixed
at 0
or 180 degrees.  Also watch out for incorrect planarity restraints - you
get this a lot with linked aromatic ring systems.

Then take your new library file and feed it to Refmac (using the LIBIN
keyword for a script file or the "Library" line in ccp4i.  Your new
definitions will supplement the default library.

Hope that helps,

Matt


--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116   fax:(212)645-2054


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