[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. regardsThiyaga == 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 ===
[ccp4bb] image of worn out rotating anode
Dear All Does anybody have a picture of a worn out rotating anode pulled out from your home source. If yes, please send me a copy. I would like to use it for a classroom lecture, to show what electrons do to the copper target. Thanks and with regards Thiyaga -- S. Thiyagarajan Institute of Bioinformatics and Applied Biotechnology Electronics City Phase I Bangalore 560100 KA - India --
[ccp4bb] process data from two crystals in-house data
Dear all I have two data sets, 75 frames each from crystals of the same protein - same cell parameters/space group (P4). I could process them seperately each yielding 90% completeness but with poor multiplicity ( 2 ) If I merge the data sets using CAD, I loose the data reduction statistics of the combined data set. I do not have HKL2000. Which (free) tool can handle two different diffraction data sets, process them together to give a single final data statistics. Thanks and regards Thiyaga S. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University Madurai - 625021 Ph: +91-9159224881 (cell)
[ccp4bb] Nvidia 3D Vision 2 - Centos5 - Coot
Dear CCP4 users Has anybody successfully configured NVIDIA 3D VISION-2 kit in CentOS-5.x and used COOT hardware stereo. I am currently having Quadro 4000 graphics card and a 3D compatible Alienware monitor. I could configure these easily in windows but not getting much clues for CentOS-5.x. Please point me to the right pages if this has been discussed already. Thanks for your help regards Thiyaga S. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University Madurai - 625021 Ph: +91-9159224881 (cell)
[ccp4bb] peak height at mouse click
Dear CCP4 users Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot. Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot. I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. The asymmetric unit has about 425 residues and the data resolution is 1.5A. Thanks and regards S. Thiyagarajan Department of Cell and Organism Biology Lund University Sölvegatan 35 Lund, Sweden
[ccp4bb] Summary: log tools for crystallization conditions
Thanks all for your inputs. Most sophisticated ones are those using database servers. 1.Xtrack http://xray.bmc.uu.se/xtrack uses PostgreSQL and PHP 2. CLIMS http://sourceforge.net/projects/clims/ uses MySQL server. To install the database servers and to keep it running, creating users, granting privileges for users ... requires good deal of DB knowledge. At the student level, this is not good as the boss may not be conversant with these SQL servers and may loose data in the absence of technical assistance. Simple JAVA based tools 1. http://www.pageforaday.com/xtalwizard/ To design plates 2. http://www.ibs.fr/content/ibs_eng/presentation/Platform/plateform_Xtallo/ I would prefer excel sheets as there is more room to improvise Finally, what I think is feasible for everyone is the MS-Access file created by Victor Khangulov. https://jshare.johnshopkins.edu/xythoswfs/webui/_xy-2846190_1-t_CF606nvb Access being a Microsoft product, it is more likely to be present in many computers. This can generate paper reports for logging and there is room for improving it to our needs. Thanks again for your inputs. Comments on the various tools are my personal opinion and are to be re-evaluated by the individual users (A disclaimer of course ) regards S. Thiyagarajan == S. Thiyagarajan== == #5344 Scott Hall == == Department of Biochemistry and Molecular Biology == == School of Medicine, Wayne State University == == 540 E. Canfield St.== == Detroit, MI 48201 U.S.A== == Phone: +1-313-577-0618 (lab) == +1-248-412-3758 (Cell) == --- On Thu, 9/11/08, S. Thiyagarajan [EMAIL PROTECTED] wrote: From: S. Thiyagarajan [EMAIL PROTECTED] Subject: [ccp4bb] log tools for crystallization conditions To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, September 11, 2008, 11:16 AM Hello Everyone I wonder whether somebody knows a good software to log the crystallization conditions. Excel sheets become too clumsy as the crystallization plates pile up. we generally need to record the results after a day, two days, a week, 2 weeks, a month etc. We need to summarize at regular intervals and keep log of our rationales in designing the new set of conditions. When moving on, somebody else taking up the project should be able to follow everything done by the previous researcher. The software supplied by Hauptman-Woodward screen (Buffalo, NY) is good, but we cannot integrate our in-house custom results. Also, that does not give options for summary at regular intervals and an overall summary. any inputs will be highly useful regards S. Thiyagarajan Wayne State University Detroit, MI USA
