I am using Refmac_5.7.0029 in CCP4ThanksSDY Date: Fri, 9 Nov 2012 20:35:48 +0200 From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc To: CCP4BB@JISCMAIL.AC.UK
What program do you use for refinement?FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 9, 2012, at 20:09 , SD Y <ccp4...@hotmail.com> wrote:Dear All, Thanks for all the suggestions on low resolution, SG and Zn and I learned a lot. I am not done yet. I am trying model co-ordinated ZN+2. I got lot of help from Prof. Roger Rowlett. Also an excellent protocol is available at http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement. Protocol seems to be very straight forward. I am not getting the result I wanted. 1. When ever I generate cif file, its not writing any for ZN-SG links at all. 2. After refmac refinement it only draw in LINK for His-ZN. Please see the imageshttps://www.dropbox.com/s/7sl01pcdmxxcu2z/ZN-cpoordination-1.pnghttps://www.dropbox.com/s/cxlp2m2stbple02/ZN-cpoordination-2.png 3. I get this His-Zn link without using .cif file, so what stage do I use this .cif file? 4. Though cysteines were placed around 2.2 - 2.5 A from ZN, its not writing LINK in PDB. I only see LINKR ZN ZN H 1 SG CYS A 83 ZN-CYS I dont know what is missing, I also attached the log file which generated the ZN-His coordination. Any help is highly appreciated. ThanksSDY Date: Thu, 8 Nov 2012 14:36:59 +0200 From: mbfro...@post.tau.ac.il Subject: Re: [ccp4bb] low-resolution and zinc To: CCP4BB@JISCMAIL.AC.UK The experiment should be very problematic if I can't determine point group on the base of the symmetry merging statistics.Watch CHI2 :-) Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 8, 2012, at 14:29 , herman.schreu...@sanofi.com wrote:Then we agree. I got confused because you mentioned"space group" and not "point group" in your phrase about PHASER and MOLREP and was afraid others might have gotten confused as well. Also, in case of twinning or almost crystallographic non-crystallographic symmetry, determining the point group on the basis of processing statistics alone can be inconclusive or even misleading. If I recall correctly, there has recently been a thread about this in the bulletin board.Herman <74_refmac5_1.log>
