Re: [ccp4bb] Plastic and glass plates
Also, plastic plates are suitable for in-situ diffraction tests where glass ones cannot be used due to the high absorption of X-rays by glass. Best wishes, Tadeusz From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim Fairman Sent: 29 August 2012 21:19 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Plastic and glass plates Theresa, The major advantage of the plastic plates is indeed ease of harvest. However, the plastic plates also tend to have some evaporation issues and eventually dry out after a few months, where as the glass plates basically last forever. On the other hand, protein crystals in LCP tend to form in the first several weeks after an experiment is set up so this usually isn't a problem. Some people prefer to set up initial screening experiments in the glass plates and then optimize and set up farm trays using the plastic plates where it's easier to harvest from (and cheaper). I've also set up everything in plastic trays from the start of a project to finish without any problems. If you're looking to perform LCP FRAP experiments, glass is the best way to go. Cheers, Jim On Wed, Aug 29, 2012 at 12:24 PM, Theresa Hsu theresah...@live.commailto:theresah...@live.com wrote: Dear all Is there any pros and cons of using plastic plates for LCP crystallization? The glass is clearer but it is very difficult to open. Thank you. -- Jim Fairman, Ph D. Crystal Core Leader I Emerald BioStructureshttp://www.emeraldbiostructures.com/ Tel: 206-780-8914 Cell: 240-479-6575 E-mail: fairman@gmail.commailto:fairman@gmail.com jfair...@embios.commailto:jfair...@embios.com
Re: [ccp4bb] Phaser Fatal runtime error.
Dear Steve, The mtz file produced by the current version of CrysAlisPro is scaled but unmerged and requires SCALA to produce the merged data set. The new version of CrysAlisPro (currently under testing) will generate the merged mtz file as well. With regards, Tadeusz Agilent Technologies From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jan Dohnalek Sent: 27 June 2012 07:30 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Phaser Fatal runtime error. Data from Crysalis in mtz format are not merged I think - you have to go through the scale and merge step in Scala first ... Jan Dohnalek On Tue, Jun 26, 2012 at 11:21 PM, Steiner, Roberto roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk wrote: Don't know where the exact problem is. However, it is definitely possible to use a Crysalis-Scala-Truncate-Phaser pipeline without runtime errors. I have done a few times. I am sure you will be able to get help from Agilent people. If not, feel free to get back to me. Best Roberto On 26 Jun 2012, at 18:34, Stephen Carr wrote: Dear CCP4bb I have collected a data-set using the supernova x-ray generator from Agilent and taken the mtz file generated by the data processing software in crysalis pro forward for structure solution. The data collection was straight forward and the software seemingly processed the data successfully - space-group P2221, overall Rmerge 9%, I/sigmaI 11, redundancy 4.5 etc. Truncate converted the intensities to structure factors with no problems, but when I tried to use the data for molecular replacement with Phaser it produced the following error: FATAL RUNTIME ERROR: Reflections are not a unique set by symmetry I'm not sure how to proceed from here as other programs in the suite do not seem to detect this problem. Also when this error has been mentioned in the past on the bb it was with a data set collected on a Bruker home source and the data processed with Denzo/scalepack, and the suggested solution was to use the Bruker software to process the data. I am currently attempting to reprocess the data with mosflm, but that is likely to be the subject of another post! Any suggestions will be gratefully received. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.c...@rc-harwell.ac.ukmailto:stephen.c...@rc-harwell.ac.uk tel 01235 567717 Roberto Steiner, PhD Group Leader Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk -- Jan Dohnalek, Ph.D Institute of Macromolecular Chemistry Academy of Sciences of the Czech Republic Heyrovskeho nam. 2 16206 Praha 6 Czech Republic Tel: +420 296 809 340 Fax: +420 296 809 410
[ccp4bb] Application Scientist position at Agilent Technologies (formerly Oxford Diffraction), Yarnton, UK
The Agilent Technologies' X-ray Diffraction department, located in Yarnton near Oxford, is looking for an Application Scientist to join a small team of highly-skilled chemical and macromolecular crystallographers. Your principle activities within the team will include macromolecular X-ray data-collection and data-processing demonstrations to potential customers at our Yarnton lab and at external sites. You will also visit our new customers to provide user training to help them to get the most out of our X-ray equipment and software. You will also use your problem solving skills to solve their experimental and data-processing issues. You will be expected to carry out experiments to test new technologies and methods in the macromolecular X-ray data collection area in support of the Agilent Research and Development effort. You will be also involved in pre-sales and marketing activities, including demos and presentation at crystallographic conferences, and at potential customer sites. Extensive travelling within Europe and world-wide is an essential part of the job. Preference will be given to scientists who have hands-on experience in the use of X-ray systems and a high level of understanding of data collection and processing methods. Ph.D. in the field of chemical or macromolecular crystallography and a few years of experience involving X-ray data collection and processing are required. In addition to a solid scientific background, excellent communication and presentations skills as well as the ability to work efficiently with a team to tight schedules are essential. Interested? Send your CV to emma_dubaniew...@non.agilent.commailto:emma_dubaniew...@non.agilent.com. For informal enquiries contact tadeusz.skarzyn...@agilent.commailto:tadeusz.skarzyn...@agilent.com To find out more about Agilent X-ray products google: agilent crystallography Tadeusz Skarzynski Product Manager - Protein Crystallography Agilent Technologies Yarnton
Re: [ccp4bb] Finding Chlorine =)
Dear Elisabetta, Which program did you use for refinement? If you used REFMAC, the atomic scattering factors are internally coded for copper radiation, and the resulting electron density map after refinement may be much lower for halide atoms than it should be! It is a known REFMAC issue. Tadeusz Sabini, Elisabetta [EMAIL PROTECTED] Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 29-Nov-2007 21:40 Please respond to Sabini, Elisabetta [EMAIL PROTECTED] To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] Finding Chlorine =) Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] --- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ---
