Perhaps you could try to use JLigand. It may do a better job. it is
available from:
www.ysbl.york.ac.uk/mxstat/
In the jligand session there are two tutorials also. they may help you
to run and generate your ligand description.
If any problem please let me know.
In general refmac is not the best way of generating ligand. In any
case you have to check you ligand after it has been generated. One
tiny electron or proton can change chemistry completely.
regards
Garib
On 9 Jun 2010, at 12:23, Matthias Zebisch wrote:
Hi Yahui!
I am having this problem as well again and agin. Most problematic is
it, if you have non-standard atoms in your compound.
I don't really know whrere the problem lies, but here is what I do:
Do not use sketcher!
Simply generate your ligand using coot by placing atoms into the
density (you may start from standard compounds if available).
Save your ligand in a pdb file and make sure (text editor), that all
atoms belong to the same compound indicated by the same 3 letter
identfier (e.g. LIG).
Merge this PDB file with your protein in Coot and save.
Run Refmac.
Refmac will abort but before stopping it will put out a library file
with recommended bonds and angles and so on.
This file you should manually edit putting in your chemical knowlege
of the ligand.
Use this cif file in a second run for refmac and for all coot real
space refinements.
Have fun,
Matthias
PS: sometimes (no non-standard atoms) a simpler way is to leave the
field "Regularize with Refmac" unchecked, when you create your final
library file.
Am 6/9/2010 12:23 PM, schrieb Yahui Yan:
Hello,
Could you please help me with the sketcher?
I'm trying to use ccp4 sketcher to generate a new ligand and then
complex it with a protein in coot. I've drawn the ligand, numbered
each atom and defined each bond type. Then I ran save file, create
library description. The pdb file was loaded to coot and worked
fine. Then I imported cif file. However, when I tried to refine the
ligand, a message popped out, saying 'No restrains'. I double
checked the numbering, I think it's Ok. Did I do anything wrong?
I'm really struggling on this. If you need more information, please
let me know. Thanks very much.
Best regards,
Yahui
--
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Dr. Matthias Zebisch
Universität Leipzig
Biotechnologisch-Biomedizinisches Zentrum
Strukturanalytik von Biopolymeren
Deutscher Platz 5
04103 Leipzig
Germany
Phone: 0049-341-97-31323 (lab) -31312 (office)
Fax : 0049-341-97-31319
email: [email protected]
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