I suggest using the PRODRG Server: http://davapc1.bioch.dundee.ac.uk/prodrg/
On Wed, Jun 9, 2010 at 7:22 AM, Matthias Zebisch < matthias.zebi...@bbz.uni-leipzig.de> 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 >> > > > -- > **************************************************** > 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: matthias.zebi...@bbz.uni-leipzig.de > **************************************************** > -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: fairman....@gmail.com james.fair...@nih.gov
