Re: [ccp4bb] On the rotamer of Arg
If you want to test this, set the ARG atom occupancies to 0.0 - calculate another map, and see what the density looks like - you can flip through the aRG rotamers using coot. Eleanor On 13 February 2015 at 06:12, Dialing Pretty 03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk wrote: Dear All, I have a set of data, in which there are very nice electron density for several Arg residues. However MolProbity analysis demonstrated that the percentage of the Arg rotamer in my data is 0%. Although there is the possibility that the Arg rotamer in my data is 0%, I still wonder is any possibility that to correct the Arg rotamer in my data so that it would belong to the scope of commonly observed Arg rotamer. I am looking forward to getting a reply from you on it. Dialing
[ccp4bb] Macromolecular Crystallography School in Madrid
Dear colleagues, We are pleased to announce the Sixth edition of the Macromolecular Crystallography School 2015, to be held at the Institute Química-Física Rocasolano- CSIC (Madrid, Spain). Dates: May 18 - 23, 2015 Invited speakers and tutors: Paul Adams, Berkeley, USA Pavel Afonine, Berkeley, USA Armando Albert, Madrid, Spain Jose Maria Carazo, Madrid, Spain Kay Diederichs, Konstanz, Germany Paul Emsley, Cambridge, UK Carmelo Giacovazzo, Bari, Italy Xavier Gomis-Ruth, Barcelona, Spain Juan Hermoso, Madrid, Spain Eugene Krissinel, Oxford, UK Rob Nicholls, Cambridge, UK Maria Solá, Barcelona, Spain Isabel Usón, Barcelona, Spain Please find the program of the Workshop, the application form and further information, at http://www.xtal.iqfr.csic.es/MCS2015/ Applicants: The workshop has been designed for postgraduate, postdoctoral and research scientists that deal with macromolecular crystallography but need further knowledge on the routine uses and fundamentals that underlie the modern techniques for macromolecular crystallography. The topics will cover crystallographic computing and fundamentals using XDS, CCP4 and Phenix, as well as the state of the art on topics such as the strategies for protein production, phasing with ARCCIMBOLDO, SHELX and SIR2014, modeling with COOT and low resolution techniques. MCS2015 will provide five days and a half of lectures and workshops. The course is designed for 25 highly motivated students. Requests to participate must be sent by a free-formated E-mail, before March 21, 2015 to the following address: cur...@fgua.es, indicating the motivation to participate and including a letter of recommendation from PhD Director (only for PhD students). Accepted participants will be notified by e-mail before April 4, 2015. Organizers: Armando Albert (xalb...@iqfr.csic.es ), Juan Hermoso (xj...@iqfr.csic.es) and Xavier Gomis-Rüth (xgr...@ibmb.csic.es ) Prof. Dr. Juan A. Hermoso Dept. Crystallography Structural Biology Inst. Quimica-Fisica Rocasolano CSIC (Spanish National Research Council) Serrano 119, 28006-Madrid, Spain Phone: +34 917459538 Fax: +34 915642431 xj...@iqfr.csic.es http://www.xtal.iqfr.csic.es/grupo/xjuan/
[ccp4bb] OT: PyMOL default opening file type
Dear all, Sorry for this off topic question. When I started PyMOL (Windows 1.6.0.0), it is defaulted to file type ACNT maps. Is there any way that I can set the program to default to PDB? Thanks. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
[ccp4bb] CCP4-6.5 Update 003
Dear CCP4 Users An update for the CCP4-6.5 series has just been released, consisting of the following changes * refmac (all) - bug fix for occupancy refinement * imosflm/mosflm - update to 7.1.2 - bug fix update * pointless (all platforms) - update to 1.9.25 - Some fixes for Saint files. Fix to long-standing but rare bug in hash table - Improvements to analysis of 6-fold screws (though still needs further work), including avoiding an occasional crash * aimless (all) - update to 0.5.2 - bug fix for already merged data * feckless (all) - update to 0.0.5 - correction to hash * ctruncate (all) - update to 1.16.9 - fix for sigma=0 * molrep (all) - improved multi-copy search * sfcheck (all) - bug fixes * monomer library (all) - added missing components * ccp4i (all) - mrSHELXE renamed to shelxe4mr * ccp4.setup (linux, osx) - fixed setup scripts for MANPATH issues Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team
[ccp4bb] Can nucleoprotein complex inhibit EtBr binding?
Dear Community, Sorry for this off topic question. I am dealing with a non specific DNA binding protein. In a non radio-labelled EMSA DNA:protein titration experiment when I EtBr stained the 5% native acrylamide gel, I could see the DNA control (101 bps) but as the amount of my protein increases I saw the free DNA band getting thinner and thinner but I could not see any band shift and probably all the complex stuck at wells. But, even if I assume the whole DNA length is occupied by my protein (I determined the ratio to be 1:15 ish) the molecular weight should not reach the molecular weight of the highest DNA marker band (20kbps = 13,200 kDa). Then why I could not see a retarded band in the gel? Or is it forming a EtBr resistant nucleoprotein filament? Could you guys please give me an idea/suggestions? Many thanks in advance...!!! My best regards, Sudipta.
Re: [ccp4bb] Can nucleoprotein complex inhibit EtBr binding?
Sudipta, the link for the cyanin dyes are at the following link http://www.lifetechnologies.com/us/en/home/references/molecular-probes-the-handbook/nucleic-acid-detection-and-genomics-technology/nucleic-acid-stains.html Sorry for the wrong link P On Fri, Feb 13, 2015 at 1:50 PM, Sudipta Bhattacharyya sudiptabhattacharyya.iit...@gmail.com wrote: Dear Community, Sorry for this off topic question. I am dealing with a non specific DNA binding protein. In a non radio-labelled EMSA DNA:protein titration experiment when I EtBr stained the 5% native acrylamide gel, I could see the DNA control (101 bps) but as the amount of my protein increases I saw the free DNA band getting thinner and thinner but I could not see any band shift and probably all the complex stuck at wells. But, even if I assume the whole DNA length is occupied by my protein (I determined the ratio to be 1:15 ish) the molecular weight should not reach the molecular weight of the highest DNA marker band (20kbps = 13,200 kDa). Then why I could not see a retarded band in the gel? Or is it forming a EtBr resistant nucleoprotein filament? Could you guys please give me an idea/suggestions? Many thanks in advance...!!! My best regards, Sudipta. -- P
Re: [ccp4bb] OT: PyMOL default opening file type
Hi, On 13 Feb 2015, at 12:31, Yu Wai Chen yu-wai.c...@kcl.ac.uk wrote: Dear all, Sorry for this off topic question. When I started PyMOL (Windows 1.6.0.0), it is defaulted to file type ACNT maps. Is there any way that I can set the program to default to PDB? Thanks. Check this link: http://www.thewindowsclub.com/change-file-associations-windows http://www.thewindowsclub.com/change-file-associations-windows Cheers, Ioan
Re: [ccp4bb] Can nucleoprotein complex inhibit EtBr binding?
What is the charge on your protein? If it is a very positively charged protein it may not enter the gel. I have found this before in EMSAs but normally at low protein concentrations it still enters the gel only at the higher concs it does not. I had to change protein to DNA ratio and also the percentage of the gel. There was quite a bit of optimization that had to be done. Sent from my iPhone On 13 Feb 2015, at 11:50 PM, Sudipta Bhattacharyya sudiptabhattacharyya.iit...@gmail.com wrote: Dear Community, Sorry for this off topic question. I am dealing with a non specific DNA binding protein. In a non radio-labelled EMSA DNA:protein titration experiment when I EtBr stained the 5% native acrylamide gel, I could see the DNA control (101 bps) but as the amount of my protein increases I saw the free DNA band getting thinner and thinner but I could not see any band shift and probably all the complex stuck at wells. But, even if I assume the whole DNA length is occupied by my protein (I determined the ratio to be 1:15 ish) the molecular weight should not reach the molecular weight of the highest DNA marker band (20kbps = 13,200 kDa). Then why I could not see a retarded band in the gel? Or is it forming a EtBr resistant nucleoprotein filament? Could you guys please give me an idea/suggestions? Many thanks in advance...!!! My best regards, Sudipta. table width=100% border=0 cellspacing=0 cellpadding=0 style=width:100%; tr td align=left style=text-align:justify;font face=arial,sans-serif size=1 color=#99span style=font-size:11px;This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorised signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary. /span/font/td /tr /table
