Re: [ccp4bb] I have my bound ligand (I think), now what?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Narayanasami Sukumar sukumar {- at -} LILITH {- dot -} NEC {- dot -} APS {- dot -} ANL {- dot -} GOV
Date: 2007-12-04

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Subject: Re: I have my bound ligand (I think), now what?
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2007-12-04

Hi Brenda,

you'll need a cif description file for your ligand which you will read
in either Coot or Refmac so that it will also refine correctly.
I usually get my cif's from the Dundee PRODRG server, you can either
paste your current coordinates as ATOMS in the provided field or sketch
your molecule as indicated on the website.
Here's the link:
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/
Then once the cif file is generated you will need to include this in
your refmac script with the following command:
#!/bin/tcsh -f
refmac5
HKLIN $hklin HKLOUT $hklot
LIBIN YOUR_SMALL_MOLECULE.cif
XYZIN my_current.pdb XYZOUT $xyzot
< $log
YOUR REFINEMENT PROTOCOL
EOF

Brenda Patterson wrote:

> Hello all,
>
> right, I think I have found a ligand bound to my protein.
>
> I used the COOT utility to find the ligands after reading in a model
> and library
> file generated by sketcher of my ligand. Now I am a bit unsure as to
> how to
> proceed? How can I 'accept' a state and/or refine it?
>
> Maybe there is a better way to model my ligand into the electron
> density not
> accounted for by my protein?
>
>
> Any general suggestions or comments would be appreciated as I am very
> inexperienced.
>
> cheers
>
> Brenda
>

--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: PEG MW vs. cryoprotectivity
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Date: 2007-12-04