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Dear All can people confirm that the failing cif files only have one monomer description in them. I have one example, but that contains two monomer descriptions. Remove one of the and coot successfully reads the file. Charles Ballard CCP4 On 9 Jun 2010, at 14:34, Yahui Yan wrote: > Hello Garib, > > I just tried JLigand. It's amazing. I opened the pdb file which was made by sketcher and save lib file and coordinate file. Then load these files to coot. Everything works fine now. I think I need to double check the ligand as you advised. > > Thanks a lot to you all. > > Regards, > Yahui > > On Wed, Jun 9, 2010 at 12:28 PM, Garib Murshudov <[log in to unmask]> wrote: > 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 > > > -- > **************************************************** > 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] > **************************************************** >