Re: [ccp4bb] A quick question - monomer lib cif
On Thu, 2011-01-06 at 11:30 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote: how can I obtain a monomer library CIF (_lib.cif) of a new small molecule that could be recognized by Refmac5? http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Servers_for_ligand_topologies/parameters -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] A quick question - monomer lib cif
Dear all experts, Just a simple question, how can I obtain a monomer library CIF (_lib.cif) of a new small molecule that could be recognized by Refmac5? If i have a CCDC cif file. many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
Re: [ccp4bb] A quick question - monomer lib cif
Dear Stephen, First you change cife file to pdb file of your structure using CCDC mercury program. It's freely available in the CCDC site. Then use CCP4 Sketcher program to create the monomer library file with the pdb file of your structure. Wishes, Sampath N 2011/1/5 Dr. STEPHEN SIN-YIN, CHUI chui...@hkucc.hku.hk Dear all experts, Just a simple question, how can I obtain a monomer library CIF (_lib.cif) of a new small molecule that could be recognized by Refmac5? If i have a CCDC cif file. many thanks stephen -- Dr. Stephen Sin-Yin Chui (徐先賢) Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory) -- Dr. N.Sampath Assistant Professor Dept. of Advanced Technology Fusion Konkuk University 1 Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Korea Tel: 82-2-450-4151 Fax: 82-2-444-6707 E-mail: samp...@konkuk.ac.kr
Re: [ccp4bb] A quick question - monomer lib cif
Dear Stephen, a cif from CCDC is something totally different from a refmac CIF. You need to convert to PDB (you can also use MOE software if available). When you have built in your small molecule PDB into your whole model you just run refmac. Refmac will fail but write out a suggestion for a molecular description cif file. You simply edit this cif file using bond lengths and angles from the CCDC structure (i use pymol for analysis). Through out wrong or weird info (often torsion restraints and stereoisomer info) and use the edited cif file as library input in a new Refmac run. Good luck, Matthias Am 06.01.2011 04:30, schrieb Dr. STEPHEN SIN-YIN, CHUI: Dear all experts, Just a simple question, how can I obtain a monomer library CIF (_lib.cif) of a new small molecule that could be recognized by Refmac5? If i have a CCDC cif file. many thanks stephen -- 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
