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 \
EOF $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
