Hi Thiyaga, Rather than compounds, you should define LINKs. You can do this in the CCP4 program jligand. You may also want to define angle restraints depending on your resolution. In Refmac you can do that as external restraints. A similar situation is described in this (http://journals.iucr.org/d/issues/2016/10/00/rr5124/rr5124.pdf) paper about zinc coordination.
Cheers, Robbie Sent from my Windows 10 phone Van: S. Thiyagarajan<mailto:0000106fa43264dc-dmarc-requ...@jiscmail.ac.uk> Verzonden: zaterdag 11 maart 2017 06:19 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: [ccp4bb] one metalloid making multiple covalent bonds - generating library Dear Experts, I have a metalloid complex in a structure I am solving, where a single ion makes 3 covalent bonds to 3 different cysteine residues, at a bond length of 1.8 A. How to generate the monomer library for refinement? Leaving it without the bonds makes the SG atoms go farther than the required bond length, building up positive density in the difference map at the right locations. Even if I create one monomer with the metalloid bound to cysteine, other 2 cysteines will have problems as the ion is shared by 3 residues. Any help is appreciated. regards Thiyaga ====================================================== Dr. S. Thiyagarajan Faculty Scientist Institute of Bioinformatics and Applied Biotechnology Behind 3M and next to Arvind Mills Electronics City Phase I Bangalore 560100 Karnataka Ph: +91-80-28528900 ext 124 Fax: +91-80-28528904 =======================================================
