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] >> **************************************************** >> >
