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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: [log in to unmask] ****************************************************