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 <[email protected]> > 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: [email protected] > **************************************************** >
