Re: [ccp4bb] PDB SEGID Case Sensitivity
James Stroud wrote: 1. Gee, I thought that it was specified to be case sensitive. 2. Well, someone once told me that it was specified to be case insensitive but I can't remember who that was. 3. I thought it was specified to be something too but most programs largely ignore specifications in my experience. 4. Specifications are for sissies, real crystallographers don't depend on them. Hi James 2 answers from me. Personal answer: 4. Practical answer: 5. And 5 is Some programs do care about what's present in these columns, so I adapt and place there whatever is required by the program I am using. Fred. PS And what I find really annoying is the atom type specified in columns 77-78, since the information is already present in the same line, as CA, N, HG etc. Sometimes I just forget to check what's present in these 2 columns and I have problems with some programs that refuse to run.
Re: [ccp4bb] PDB SEGID Case Sensitivity
Dear James, When reading and writing SEGIDs, why bother making it case unsensitive? Most programming/scripting languages read text case sensitive anyway. Assuming people don't type SEGIDs by hand, differences in capitalization may be significant. When you are generating SEGIDs from scratch, stick to the set you proposed (0-9, A-Z). That way it is more likely that other programs support your SEGIDs. Cheers, Robbie Date: Wed, 3 Feb 2010 16:15:54 -0800 From: merr...@u.washington.edu Subject: Re: [ccp4bb] PDB SEGID Case Sensitivity To: CCP4BB@JISCMAIL.AC.UK On Wednesday 03 February 2010 15:59:26 James Stroud wrote: Hello All, In typically comical fashion, the PDB specification 3.2 at http://www.wwpdb.org/documentation/format32/sect9.html leaves out columns 67-76 for ATOM and HETATM records. Since I can only conclude that SEGIDs must be one of those grey areas, I thought I'd make a multiple choice survey and go with the quorum opinion. Please respond with the most correct answer so I know how to proceed: What is the general status of case sensitivity of SEGID in PDB file formats? Don't ask; don't tell PDB sanction of SEGID has been an on-again off-again thing. In 1999 they said: ] We propose to discontinue support for this identifier in files ] that are processed and released into the archive. No format ] changes are proposed here, we will simply place blanks in any ] SEGID fields. So far as I know, the PDB/RCSB folks do not even look at these columns. So it comes down to a question of individual non-PDB programs. Which program were you wondering about? 1. Gee, I thought that it was specified to be case sensitive. 2. Well, someone once told me that it was specified to be case insensitive but I can't remember who that was. 3. I thought it was specified to be something too but most programs largely ignore specifications in my experience. 4. Specifications are for sissies, real crystallographers don't depend on them. Thank you in advance for taking the time to participate. James -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742 _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop
Re: [ccp4bb] PDB SEGID Case Sensitivity [OT]
Hi Fred, PS And what I find really annoying is the atom type specified in columns 77-78, since the information is already present in the same line, as CA, N, HG etc. Sometimes I just forget to check what's present in these 2 columns and I have problems with some programs that refuse to run. The atomid columns cannot be trusted, especially in (new) hetero compounds. When you try to auto-generate restraints, you need a clear description of the chemical elements involved. Hydrogens are another problem because every other (NMR) program had another 'standard' for hydrogen names. Column 77-78 is much more reliable because there is only one type of information in there. Lets just hope nobody tries to use ununtrium for phasing. Cheers, Robbie _ New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop
[ccp4bb] Scientific programmer to work on iMosflm at MRC LMB, Cambridge UK
Scientific Programmer £20,074 - £27,271 per annum A two year position is available for a programmer to continue the development of iMosflm, the Graphical User Interface for the MOSFLM program package to process X-ray diffraction data from crystals of biological macromolecules. The interface is written in Tcl/Tk and C. Experience in scientific programming is essential, and familiarity with Tcl/Tk and C would be a distinct advantage. It would also be helpful to have some familiarity with crystallographic data processing. Applicants should have a degree in a relevant area. For informal enquiries please contact Andrew Leslie and...@mrc-lmb.cam.ac.uk Your salary will be supported by a flexible pay and reward policy, 30 days annual leave entitlement, an optional MRC final salary pension scheme and excellent on-site sports and social facilities. This position is subject to pre-employment screening. If you would like to receive this advert in large print, Braille, audio, or electronic format/ hard copy, please contact the Recruitment team at the MRC Shared Service Centre on the telephone number below or recruitm...@ssc.mrc.ac.uk Applications for this role must now be made online at http://jobs.mrc.ac.uk inputting reference LMB10/040. If you do not have internet access or experience technical difficulties please call 01793 301280. Closing date: 3rd March 2010. For further information about the MRC please visit www.mrc.ac.uk. The Medical Research Council is an Equal Opportunities Employer
[ccp4bb] Freezing under oil
Dear list, I'm trying to freeze crystals in cryoconditions containing the following: 0.1 M Sodium acetate pH 4.4 2.15-2.3 M Ammonium sulphate 7% n-butanol 15% glycerol The problem is that the crystals (beautiful hexagonal prisms) seem to shatter in a random fashion: some are unaffected, some, coming from the same drop, disgregate miserably. One even split into three parts, of which two disgregated and one survived perfectly well. I've tried both by moving the crystals directly in the cryocondition and by progressively increasing the glycerol concentration to no avail. Shall I just select those that survive? I was wondering if anybody has ever had this same problem and if freezing under oil could be an alternative. If yes: any suggestions on how to fish the crystals? I tried it in the past, but I found it very difficult... Experiences and suggestions are welcome. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969
Re: [ccp4bb] Freezing under oil
Salve Claudia, Glycerol is not the only cryo-protectant that is available. Have you tried with ethylene glycol for example? HTH (spero che aiuta), Fred. Claudia Scotti wrote: Dear list, I'm trying to freeze crystals in cryoconditions containing the following: 0.1 M Sodium acetate pH 4.4 2.15-2.3 M Ammonium sulphate 7% n-butanol 15% glycerol The problem is that the crystals (beautiful hexagonal prisms) seem to shatter in a random fashion: some are unaffected, some, coming from the same drop, disgregate miserably. One even split into three parts, of which two disgregated and one survived perfectly well. I've tried both by moving the crystals directly in the cryocondition and by progressively increasing the glycerol concentration to no avail. Shall I just select those that survive? I was wondering if anybody has ever had this same problem and if freezing under oil could be an alternative. If yes: any suggestions on how to fish the crystals? I tried it in the past, but I found it very difficult... Experiences and suggestions are welcome. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969
Re: [ccp4bb] Zalman LCD availability
Hey, we just got 6 beautiful 24 (1920x1200) monitors from Zalman - it's a limited edition of a prototype Zalman produces (I contacted Zalman directly) We use both, Linux and Macs having NVIDIA cards. Steffen On Jan 16, 2010, at 05:13 , Ben Ammar Youssef wrote: Hi Francois, Zalman LCD (21) is available in Japan. We already bought 2 sets one month ago and both are working perfectly with mac pro, windows and Linux. For William: I think the best way to get extra glasses is to go, in the weekend (or late night show if you like), to the nearest movie theater with 3D projection. Personally I did this way, and I got two pairs of glasses just for ~3US$ extra/pair and of course enjoyed the 3D movie. Youssef Francois Berenger wrote: Hello, By the way, does anyone got this LCD in Japan? My team is interested to know the model's exact reference as well as from where you ordered it. Thanks a lot, Francois. smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Freezing under oil
Hello Claudia, Under what conditions did the crystals grow? If its sodium acetate and ammonium sulphate I would try adding sodium malonate as a cryo protectant (with 2-2.3M ammonium sulphate adding 0.6-0.8M Na malonate should be sufficient) or increasing the ammonium sulphate concentration. Sabine Claudia Scotti wrote: Dear list, I'm trying to freeze crystals in cryoconditions containing the following: 0.1 M Sodium acetate pH 4.4 2.15-2.3 M Ammonium sulphate 7% n-butanol 15% glycerol The problem is that the crystals (beautiful hexagonal prisms) seem to shatter in a random fashion: some are unaffected, some, coming from the same drop, disgregate miserably. One even split into three parts, of which two disgregated and one survived perfectly well. I've tried both by moving the crystals directly in the cryocondition and by progressively increasing the glycerol concentration to no avail. Shall I just select those that survive? I was wondering if anybody has ever had this same problem and if freezing under oil could be an alternative. If yes: any suggestions on how to fish the crystals? I tried it in the past, but I found it very difficult... Experiences and suggestions are welcome. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969 -- -- Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77752 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
[ccp4bb] EMBO Conference Series: Catalytic mechanisms by biological systems: at the interface between chemistry and biology
Registration is open for: EMBO Conference Series Catalytic mechanisms by biological systems: at the interface between chemistry and biology EMBL Hamburg, Germany Wednesday 5 May - Friday 7 May 2010 Recent developments of in vitro, in vivo and in silico research on biocatalytic reaction mechanisms are continuously advancing our insight of the chemistry and biochemistry of catalytic mechanisms by biological systems. The structural and dynamical properties of the proteins are of key importance in this respect. At this conference advanced methodological approaches will be covered, ranging from high resolution kinetic protein crystallography, neutron crystallography, NMR, and mass spectroscopy to single molecule spectroscopy and enzymology. The importance of stability, regulatory, substrate-binding and kinetic properties of enzymes in the context of cellular processes will be highlighted. New emerging technologies important for biocatalysis research for example using transition state analogues and directed evolution methods allow for more insight into the biocatalytic mechanisms. Also bioinformatics and biocomputational approaches are very important in this respect. The conference is aimed at bringing together experts working at the interface of this multidisciplinary research field to facilitate stimulating discussions on this fascinating topic, which is also of key importance for the development of biotech related applications. The multidisciplinary program will provide an ideal framework for getting to know the experts as well as the latest developments in this research field. There will be approximately 25 invited speakers. Participants are encouraged to bring posters, which will be on display during the whole length of the meeting in the lecture hall. Selected poster topics can be included for a general talk. The number of participants is limited to 120. Application deadline is 8th March 2010. For more information and to register please go to www.embl.de/events/2010/CMS10-01
Re: [ccp4bb] What is an aceptable spread in ADP values?
Pavel Afonine wrote: Dear Ed, Tightly restrained refinement will be equivalent to torsion angle parametrization, since bonds and angles are essentially fixed (but dihedrals are not). Simply not true. Think why -:) Hint: in restrained refinement the weight applies to all terms - bonds, angles, torsions, etc... So if you choose tight weight in such refinement the torsions will be restrained as tightly as other terms (at least as it would be in CNS or phenix.refine). In torsion angle refinement (which is, in fact, a constrained rigid-body refinement) you still have weights, and you can make your torsion angle refinement as tight as you like. However, many refinement programs allow you to adjust the weights of different terms differently. So, if you were to make the bond length and angle terms sufficiently tight, but leave the torsion restraints loose, you can indeed end up with something very similar to torsion angle refinement. So why use torsion angle refinement? Because in the scheme I've outlined above the target function can have vastly different curvatures along different directions in parameter space. This presents a problem for the minimiser - without a good deal of second order information the refinement steps have to be incredibly small (step size related to the sharpest curvature) and minimisation process becomes impossibly slow. However, it is seems possible to me that a sufficiently good minimiser with a carefully constructed sparse curvature matrix may be able to deliver the same benefits as torsion refinement while working in Cartesian space. Kevin
[ccp4bb] DLS
Dear Fellow Crystallographers We are going to buy a DLS instrument to help us assess crystallizability of our proteins. I would be grateful for any opinions - either on this BB or in my mail box (in which case I'll keep them to myself, naturally). We have looked more closely at two instruments: DynaPro NanoStar from Wyatt and Zetasizer Micro V from Malvern and both seem to be rather similar in terms of parameters and price. I would appreciate user opinions as to the reliability, ease of use or any features that make a given instrument particularly suited for assessing biological samples. Many thanks, Wojtek -- -- Prof. dr hab. Wojciech Rypniewski tel: +48-61-8528503 Institute of Bioorganic Chemistry fax: +48-61-8520532 Polish Academy of Sciences e-mail: wojt...@ibch.poznan.pl Noskowskiego 12/14 www: www.man.poznan.pl/~wojtekr/ 61-704 Poznan, Poland --
[ccp4bb] Freezing under oil - Thanks and summary
Dear All, Here are the main suggestions I received. I'm going to try them all. Many many thanks for your help. Yours, Claudia Possible solutions: 1. Maybe adding the cryo to the crystallization already? 2. 2R3R-Butandiol is the best cryo as being used in very low amounts. 10% are typically enough. 3. Put a small droplet of paratone-N next to your drop such that they touch and then drag the crystal into the oil and take care to remove the water from around it (the buble aorund it within the oil) and freeze. When draggin into oil go loop first such that the loop plows the way a bit (or some part of it) mechanical sress can be a problem due to the viscosity, but otherwise it often works, though not always.. 4. 2M amm sulfate might be quite enough if you do the transfer and dipping quickly. 5. other option is to add salt. e.g LiSO4 should be good cryoprotectant (see cryosalts) at high conc. 6. Have you tried with ethylene glycol for example? 7. Maybe you do not need any cryoprotectant and crystals mountd in small loops will freeze just fine straight out of your drops... 8. Under what conditions did the crystals grow? If its sodium acetate and ammonium sulphate I would try adding sodium malonate as a cryo protectant (with 2-2.3M ammonium sulphate adding 0.6-0.8M Na malonate should be sufficient) or increasing the ammonium sulphate concentration. Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 From: lp...@cam.ac.uk To: claudiasco...@hotmail.com Subject: Re: [ccp4bb] Freezing under oil Date: Thu, 4 Feb 2010 11:52:03 + Could you try using ammonium sulfate as your cryoprotectant? What happens if you slowly increase the concentration over time to 3M, followed by flash freezing? What about other cryos, like ethylene glycol? lpj Lauren Jackson, PhD lp...@cam.ac.uk On 4 Feb 2010, at 09:54, Claudia Scotti wrote: Dear list, I'm trying to freeze crystals in cryoconditions containing the following: 0.1 M Sodium acetate pH 4.4 2.15-2.3 M Ammonium sulphate 7% n-butanol 15% glycerol The problem is that the crystals (beautiful hexagonal prisms) seem to shatter in a random fashion: some are unaffected, some, coming from the same drop, disgregate miserably. One even split into three parts, of which two disgregated and one survived perfectly well. I've tried both by moving the crystals directly in the cryocondition and by progressively increasing the glycerol concentration to no avail. Shall I just select those that survive? I was wondering if anybody has ever had this same problem and if freezing under oil could be an alternative. If yes: any suggestions on how to fish the crystals? I tried it in the past, but I found it very difficult... Experiences and suggestions are welcome. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Trusted email with powerful SPAM protection. Sign up now. _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969
Re: [ccp4bb] DLS
Hiya. My two penneth on the Malvern Zetasizer. Simple, idiot-proof operation. Software is easy and intuative. Reports are customisable to give you what information you want. Problems easy to trouble shoot IMHO. Does DLS, SLS, melting point determination. After-care support is good from Malvern. Not used the Wyatt instrument. HTH, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk Internetz: http://xtaldave.posterous.com/ Twitter: @xtaldave Skype: DocDCB On 4 February 2010 13:36, Wojciech Rypniewski wojt...@ibch.poznan.pl wrote: Dear Fellow Crystallographers We are going to buy a DLS instrument to help us assess crystallizability of our proteins. I would be grateful for any opinions - either on this BB or in my mail box (in which case I'll keep them to myself, naturally). We have looked more closely at two instruments: DynaPro NanoStar from Wyatt and Zetasizer Micro V from Malvern and both seem to be rather similar in terms of parameters and price. I would appreciate user opinions as to the reliability, ease of use or any features that make a given instrument particularly suited for assessing biological samples. Many thanks, Wojtek -- -- Prof. dr hab. Wojciech Rypniewski tel: +48-61-8528503 Institute of Bioorganic Chemistry fax: +48-61-8520532 Polish Academy of Sciences e-mail: wojt...@ibch.poznan.pl Noskowskiego 12/14 www: www.man.poznan.pl/~wojtekr/ 61-704 Poznan, Poland --
Re: [ccp4bb] DLS
Hi Wojtek I can easily second Dave's comment! Best Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Ph. +32 (0)472 928 519 http://www.LProBE.ugent.be/xray.html On 04/02/10 14:54, David Briggs drdavidcbri...@gmail.com wrote: Hiya. My two penneth on the Malvern Zetasizer. Simple, idiot-proof operation. Software is easy and intuative. Reports are customisable to give you what information you want. Problems easy to trouble shoot IMHO. Does DLS, SLS, melting point determination. After-care support is good from Malvern. Not used the Wyatt instrument. HTH, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk Internetz: http://xtaldave.posterous.com/ Twitter: @xtaldave Skype: DocDCB On 4 February 2010 13:36, Wojciech Rypniewski wojt...@ibch.poznan.pl wrote: Dear Fellow Crystallographers We are going to buy a DLS instrument to help us assess crystallizability of our proteins. I would be grateful for any opinions - either on this BB or in my mail box (in which case I'll keep them to myself, naturally). We have looked more closely at two instruments: DynaPro NanoStar from Wyatt and Zetasizer Micro V from Malvern and both seem to be rather similar in terms of parameters and price. I would appreciate user opinions as to the reliability, ease of use or any features that make a given instrument particularly suited for assessing biological samples. Many thanks, Wojtek -- -- Prof. dr hab. Wojciech Rypniewski tel: +48-61-8528503 Institute of Bioorganic Chemistry fax: +48-61-8520532 Polish Academy of Sciences e-mail: wojt...@ibch.poznan.pl Noskowskiego 12/14 www: www.man.poznan.pl/~wojtekr/ 61-704 Poznan, Poland --
Re: [ccp4bb] Freezing under oil
Rigaku has a couple of Webinars on cryocrystallography that you may wish to view: http://www.rigaku.com/protein/webinars.html Jim _ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Claudia Scotti Sent: Thursday, February 04, 2010 3:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Freezing under oil Dear list, I'm trying to freeze crystals in cryoconditions containing the following: ...
Re: [ccp4bb] Freezing under oil
Sometimes glucose works when glycerol or ethylene glycol does not. We have also had very good success with a gradual, in-the-drop cryo method: see http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Mounting+Protein+Crystals#No_fail_cryoprotection . You may want to consider that it may not be the cryo that is causing fracturing, but drop evaporation. (It's always worst this time of year, when it's cold and dry.) In this case, the "no-fail" method (in which the drops are left in the well as much as possible) or working in the cold room (which raises humidity and slows evaporation) may be good options. Cheers, Roger Rowlett On 2/4/2010 4:29 AM, Vellieux Frederic wrote: Salve Claudia, Glycerol is not the only cryo-protectant that is available. Have you tried with ethylene glycol for example? HTH (spero che aiuta), Fred. Claudia Scotti wrote: Dear list, I'm trying to freeze crystals in cryoconditions containing the following: 0.1 M Sodium acetate pH 4.4 2.15-2.3 M Ammonium sulphate 7% n-butanol 15% glycerol The problem is that the crystals (beautiful hexagonal prisms) seem to shatter in a random fashion: some are unaffected, some, coming from the same drop, disgregate miserably. One even split into three parts, of which two disgregated and one survived perfectly well. I've tried both by moving the crystals directly in the cryocondition and by progressively increasing the glycerol concentration to no avail. Shall I just select those that survive? I was wondering if anybody has ever had this same problem and if freezing under oil could be an alternative. If yes: any suggestions on how to fish the crystals? I tried it in the past, but I found it very difficult... Experiences and suggestions are welcome. Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Trusted email with powerful SPAM protection. Sign up now. https://signup.live.com/signup.aspx?id=60969
[ccp4bb] EMBO Course on Macromolecular Complexes: Grenoble, 31 May- 5 June 2010
Dear colleagues, We are organizing an EMBO Practical Course on the Structural Characterization of Macromolecular Complexes. The course is primarily intended for Ph.D. students and postdocs engaged in challenging structural projects involving macromolecular complexes. WHEN: 31 May - 5 June, 2010 WHERE: Grenoble, France TOPICS INCLUDE: - expression purification of multi-subunit complexes - biophysical biochemical characterization of complexes - bioinformatic experimental analysis of interaction networks - combining different structural methods (EM, NMR, SAXS, crystallography) SPEAKERS INCLUDE: Radu Aricescu (Oxford U.) Imre Berger (EMBL Grenoble) Martin Blackledge (IBS Grenoble) John Briggs (EMBL Heidelberg) Gianni Cesareni (U. Rome) Kai Johnsson (EPFL Lausanne) Par Nordlund (Karolinska Institute, Stockholm) Andreas Plückthun (U. Zurich) Vladimir Rybin (EMBL Heidelberg) Christophe Romier (IGBMC Illkirch) Patrick Schulz (IGBMC Illkirch) Montserrat Soler-López (IRB Barcelona) Michael Sattler (Tech. U. Munich) Christiane Schaffitzel (EMBL Grenoble) Bertrand Séraphin (IGBMC Illkirch) Song Tan (Pennsylvania State U.) APPLICATION DEADLINE: 15 March 2010 A maximum of 20 participants will be selected to attend the course. For more details please visit: http://cwp.embo.org/pc10-20/index.html Best regards, Carlo Petosa, Darren Hart, Elspeth Gordon, Guy Schoehn, Winfried Weissenhorn Carlo Petosa, Ph.D. Institut de Biologie Structurale 41 rue Jules Horowitz 38027 Grenoble Cedex 1, France Tel. +33 438 78 40 24 Fax +33 438 78 54 94
Re: [ccp4bb] DLS
The Malvern is indeed very nice. The only issue I have with ours is that it doesn't do plates. This makes buffer screening a very laborious busy that is best left to graduate students. Andreas On 04/02/2010 2:22, Savvas Savvides wrote: Hi Wojtek I can easily second Dave's comment! Best Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Ph. +32 (0)472 928 519 http://www.LProBE.ugent.be/xray.html On 04/02/10 14:54, David Briggsdrdavidcbri...@gmail.com wrote: Hiya. My two penneth on the Malvern Zetasizer. Simple, idiot-proof operation. Software is easy and intuative. Reports are customisable to give you what information you want. Problems easy to trouble shoot IMHO. Does DLS, SLS, melting point determination. After-care support is good from Malvern. Not used the Wyatt instrument. HTH, Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk Internetz: http://xtaldave.posterous.com/ Twitter: @xtaldave Skype: DocDCB On 4 February 2010 13:36, Wojciech Rypniewskiwojt...@ibch.poznan.pl wrote: Dear Fellow Crystallographers We are going to buy a DLS instrument to help us assess crystallizability of our proteins. I would be grateful for any opinions - either on this BB or in my mail box (in which case I'll keep them to myself, naturally). We have looked more closely at two instruments: DynaPro NanoStar from Wyatt and Zetasizer Micro V from Malvern and both seem to be rather similar in terms of parameters and price. I would appreciate user opinions as to the reliability, ease of use or any features that make a given instrument particularly suited for assessing biological samples. Many thanks, Wojtek -- -- Prof. dr hab. Wojciech Rypniewski tel: +48-61-8528503 Institute of Bioorganic Chemistry fax: +48-61-8520532 Polish Academy of Sciences e-mail: wojt...@ibch.poznan.pl Noskowskiego 12/14 www: www.man.poznan.pl/~wojtekr/ 61-704 Poznan, Poland -- -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] Vapor diffusion calculator
Jacob and CCP4bb It's not exactly what you're looking for, but my colleague Peter Baldock wrote a program called VD to MB a few years ago that does part of the job. It was a program to convert vapor diffusion crystallization conditions into microbatch-under-oil conditions. I tried it back then with several published and unpublished examples where crystallization had been optimized in both vapor diffusion and microbatch. I was originally sceptical, but it seemed to work remarkably well, generally getting the numbers right to within 5 or 10%. The program uses a parameter called 1/e equilibration time for 1M salt (days). I originally used a value of 1, but I think we changed it to 0.5 for 96-well plates. Obviously the value will depend on the geometry of the plates. Does anyone have any practical information about equilibration times? Different salts have very different effects on vapor pressure. I found a list in an old Rubber Book (CRC Handbook of Physics and Chemistry) part of which I have pasted below. I tried quite hard to make sense of this list - hoping that it would also shed light on the protein-precipitating effect of salts - but concluded that the numbers are pretty random apart from obvious valence effects. (Someone here may be able to explain them, though!) You can download the program from http://www.douglas.co.uk/tipsntech.htm near the middle of the page. There's also an equivalent Excel spreadsheet for playing around with. See also http://www.douglas.co.uk/convert.htm for some (very old but still valid!) examples and comments. Also bear in mind that - with many proteins - roughly half of the protein is lost on the surface of VD drops for 100 + 100 nl drops. Peter also wrote an algorithm - now in our optimization software - that calculates the pH of a solution with any number of buffers in it, where the buffers can be at different concentrations too. A sort of super Henderson-Hasselbalch. If anyone is interested I'm sure Peter could show you the maths or pass on the code (it took him about a month of lunch-breaks!) Best wishes Patrick _ Reduction of vapor pressure in mmHg due to the presence of 1M salt at 100C (at which temperature the vapor pressure of water is 760 mmHg) From Handbook of Physics and Chemistry, 76th Ed CdSO4 8.9 ZnSO4 10.4 MnSO4 10.5 FeSO4 10.7 MgSO4 12 CdI2 14.8 CdBr2 17.8 ZnCl2 18.7 CdCl2 18.8 KNO3 21.1 NH4NO3 22 NaNO3 22.5 NH4Cl 23.7 NH4Br 23.9 NH42SO4 24 KCl 24.4 Na2SO4 25 NaCl 25.2 KI 25.3 LiCl 25.5 LiNO3 25.9 NaBr 25.9 LiBr 26.2 BaNO32 27 Li2SO4 28.1 LiI 28.6 K2CrO4 29.5 Na3PO4 30 Li2CrO4 32.6 MnCl2 34 CaNO32 34.8 CoCl2 34.8 Al2S043 36.5 BaCl2 36.7 NiCl2 37 NiNO32 37.3 BaBr2 38.8 MgCl2 39 CaCl2 39.8 MgNO32 42 MgBr2 44 CaBr2 44.2 AlCl3 61 StDev 10.7 Av 27.7 CV 0.4 -- For information and discussion about protein crystallization and automation, please join our bulletin board at http://groups-beta.google.com/group/oryx_group?hl=en patr...@douglas.co.ukDouglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk/ Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: 02 February 2010 22:34 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Vapor diffusion calculator Dear Crystallographers, Is anybody aware of a calculator for vapor diffusion experiments to plot concentrations of various solvent components as a function of time? For a simple example, what happens when I mix a protein solution containing 50mM NaCl 1:1 with a reservoir containing 50% MPD but no salt? Where is the vapor diffusion equilibrium, and how does the drop composition change as a function of time? More complicated would be experiments involving volatile components other than water, as I think, for example, ethanol would almost instantly equilibrate, then the water diffusion would kick in over a longer time scale. Even more complicated would be pH-dependent volatilities such as acetate. I don't think this would be impossible to figure out, but it would be nice if there were a pre-existing tool/server to do such. Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] Dynamics Software for DynaPro DLS?
Hi All, Our group is still running an older DynaPro DLS. The hardware is in great shape and the system is operating smoothly. Unfortunately, we have to reformat the computer currently containing the DLS data acquisition software and our original installation CD is damaged. I have contacted the manufacturer, but they are unwilling to provide the installation software unless we agree to purchase a new system with the next funding cycle. Is anyone still in possession of the setup.exe file for any versions (ideally V5 or V6) of the Dynamics software for this system? Would you be willing to send it along? Many Thanks,Melanie
Re: [ccp4bb] Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors
On Thursday 04 February 2010 05:14:24 hari jayaram wrote: Hi I just installed a fresh ccp4-6.1.3 installation on my 64 bit ubuntu box. After the install my first job was a regular ccp4 sortmtz job using ccp4i gui . The sortmtz job fails with the following NX - related errors in the log file ( see below and snapshot above). Also the GUI says the job failed , even though the output files seems well in order. mtzdump also gives an error popup saying problem in mtzdump and then goes ahead and displays the mtzdump information just fine. sortmtz and mtzdump work just fine from the command line so the error seems NX client / ccp4i related. I will try and run it directly on the machine without NX once I get in. But thought I would report this rather strange non ccp4 related error in the ccp4 log file. Thanks Hari * Resolution Range : 0.000190.13717 ( 73.369 - 2.700 A ) * Sort Order : 1 2 3 0 0 * Space group = 'P3' (number 143) 3179776 records output BFONT COLOR=#FF!--SUMMARY_BEGIN-- SORTMTZ: Normal termination Times: User: 13.0s System:1.2s Elapsed: 0:22 /pre /html !--SUMMARY_END--/FONT/B *** * Information from CCP4Interface script *** The program run with command: /mega/ccp4-6.1.3/ccp4-6.1.3/bin/sortmtz HKLOUT /mega/hj-8-2-1/hjbr5-1/hjbr5-1_sorted_mosflm.mtz has failed with error message ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. My guess is that your machine configuration includes a file that initializes LD_PRELOAD for NX on login. But it should not do this. The LD_PRELOAD setting applies to all programs, so it should not be set blindly to include program-specific libraries. What you see, I think, is that ccp4 is trying to load the NX initialization libraries because they are present in LD_PRELOAD. If you clear LD_PRELOAD from your environment (actually from ccp4's environment, which may not be the same thing if run by script from ccp4i) I think this problem will go away. Ethan ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot be preloaded: ignored. *** #CCP4I TERMINATION STATUS 0 ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot be preloaded: ignored. #CCP4I TERMINATION TIME 04 Feb 2010 07:59:30 #CCP4I MESSAGE Task failed #CCP4I TERMINATION STATUS 0 ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. ERROR: ld.so: object '/usr/NX/lib/libesd.so.0' from LD_PRELOAD cannot be preloaded: ignored.Error from script /mega/ccp4-6.1.3/ccp4-6.1.3/ccp4i/scripts/sortmtz.script: invalid command name CreateAnnotatedLogfile #CCP4I TERMINATION TIME 04 Feb 2010 07:59:30 #CCP4I MESSAGE Task failed -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
[ccp4bb] DLS installation Files Found
Many thanks to all who have responded with the setup files for our DynaPro DLS from Protein Solutions. Please let me know if any of you are in a similar situation and require the installation files for the data acquisition software. BestMelanie
Re: [ccp4bb] What is an aceptable spread in ADP values?
Pavel, Simply not true. Think why -:) Hint: in restrained refinement the weight applies to all terms - bonds, angles, torsions, etc... So if you choose tight weight in such refinement the torsions will be restrained as tightly as other terms (at least as it would be in CNS or phenix.refine). In torsion angle refinement (which is, in fact, a constrained rigid-body refinement) you still have weights, and you can make your torsion angle refinement as tight as you like. I may be wrong, but here are relevant lines from $CNS_TOPPAR/protein.top and $CNS_TOPPAR/protein_rep.param: ATOM NTYPE=NH1 CHARge=-0.35 END ATOM CA TYPE=CH1E CHARge= 0.10 END ATOM CTYPE=C CHARge= 0.55 END ... ADD DIHEdral -C +N +CA +C ... dihe XCH1E NH1 X 0.0 3 0.0 ! phi angle The last line is from the parameter file section labeled free dihedrals. Here is from ener_lib.cif (CCP4) torsions section .CH1 NH1 .. 0.0000.000 3 # AMBER .CCH1 .. 0.000 180.000 3 # AMBER .CH2 NH1 .. 0.0000.000 3 # AMBER .CCH2 .. 0.000 180.000 3 # AMBER .CH1 N.. 0.0000.000 3 # AMBER Which suggests that (0.000 means that Edihe is always 0) phi/psi angles are never restrained by refmac either. There is of course TRANS and CIS in standard links, but I am confused if they are applied by default (CONNECTIVITY No seems to imply that it's not the case). What I understand from this http://www.phenix-online.org/pipermail/phenixbb/2007-July/000355.html is that (default is discard_psi_phi=True) phenix doesn't restrain them by default. Which it shouldn't as it was argued many times that restraining phi/psi would make ramachandran map useless as validation tool. So unless you purposefully deviate from default behavior, phi/psi will not be restrained (chi angles will though). Also, at least in my understanding, tightly restrained doesn't mean constrained. Which it should be to make it equivalent to rigid body. I guess the point you were trying to make is that infinitely strong restraints are equivalent to constraints. If that was your point, you are absolutely right. However, I did not suggest that individual B-factors should be infinitely restrained at low resolution. Again, tightly restrained is not constrained. My point was (and is) that with properly chosen restraints individual B-factor refinement is applicable at 3.1A resolution and, as it appears from results shown by Jose Antonio, may be better than two-adp-groups-per-residue refinement. I don't see why two-B per residue wouldn't capture this distribution throughout the structure (it definitely wouldn't throughout the residue). Because it generates discontinuity. I hope most reasonable people could agree that in a lysine NZ would have higher B-factor than CB (most of the time, there could be some exceptions with salt bridges combined with severe backbone disorder). two-B-per-residue forces both of these atoms to have the same B-factor, underestimating NZ and overestimating CB. I think at any resolution gradual increase along the sidechain could be better description of disorder. You are right to point out that grouped B-factor can capture some of the B-factor variation, but just not as well as properly restrained individual B-factors. I think the example that Jose Antonio originally provided (at 3.1A, not 4A) clearly demonstrates that it makes more sense to do properly restrained individual B-factor refinement than two-adp-groups-per-residue refinement. Do you disagree specifically on this issue? Of course no. Thank you. This is why when I reply on bb to questions like this: which B-factor, group or individual, do I need to refine at say 3.1A resolution, I always suggest to run these refinement jobs and see which one gives the best result: ... This will give the conclusive, rock solid answer about which ADP parameterization and refinement protocol is good for given model and data. An alternative is an endless speculation. See, I am not sure. The R/Rfree for some of the options may be indistinguishable (which was the case with Jose Antonio's example). In which case endless speculation turns into what should I do based on what is known about physics of the damn thing I am trying to model. As you see, in phenix.refine you can combine any B-factor refinement strategy with any (group, individual iso, aniso, tls), and apply it to any selected part of your structure. So, I assume at this point of the software automation, it is up to a smart researcher to decide which refinement strategy to use. You cannot blame the software for giving you the freedom to do what you may want to do. I don't, and I am sorry if the impression was that I do... I see, I said implementation in CNS and phenix which in some way makes it sound like
Re: [ccp4bb] What is an acceptable spread in ADP values?
On Thursday 04 February 2010 11:13:01 Ed Pozharski wrote: Cherry-picking points to comment on, so lots of previous discussion snipped... with properly chosen restraints individual B-factor refinement is applicable at 3.1A resolution and, as it appears from results shown by Jose Antonio, may be better than two-adp-groups-per-residue refinement. I don't see why two-B per residue wouldn't capture this distribution throughout the structure (it definitely wouldn't throughout the residue). Because it generates discontinuity. Exactly. That is why I do not consider the two-B-per-residue model to be physically meaningful, and do not recommend using it. Think of it this way. If the number of observations is so low that you can only afford to spend 2 refinement parameters per residue on describing atomic displacements, what is the best way to spend those parameters? Assigning two fixed B values per residue is, I suggest, about the worst possible way. A better alternative has been described by Dale Tronrud: J. Appl. Cryst. (1996). 29, 100-104. This approach establishes an empirical model for the increase of B along the atoms of a sidechain, then scales this model for application to a particular residue. You can implement this as two parameters per residue, one base B and one scale factor for the empirical increase along the sidechain, without introducing any discontinuities. I am not sure if any program other than TNT offers this option. Another alternative is to create a segmented TLS model. If you split the chain into groups as small as 10 residues, then the 20 parameters of each TLS description can be regarded as 2 parameters per residue. In practice it is not necessary to make the segments that small, so you don't need to spend even that many parameters. Note that I am talking about a pure TLS model here, with no refinement of individual Biso terms. In my recent experience using structures being refined in the lab, these pure TLS models do as well as restrained Biso refinement starting at roughly 2.8A resolution. Unfortunately, if you decide to go for a segmented TLS model there is a chicken-and-egg problem. How to split the chain into segments for subsequent refinement? I created the TLSMD tools to guide this choice, but TLSMD itself needs to start with a set of refined B factors of some sort. So for the purpose of bootstrapping the TLS model generation and refinement, I think it is acceptable to use even crude models like 1-B-per-residue for initial refinement whose only real purpose is to prime the TLSMD analysis. Ethan -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
[ccp4bb] radiation damage
I am pleased to announce that this year's ACA meeting (Chicago, IL, July 24-29, 2010) will include a return of the highly popular session on radiation damage. We all know that damage can be a problem, but the interesting developments over the last few years are that there are finally some accurate ways to predict what you can expect from your sample and that new experimental strategies and even new machines are being developed to push the limits even farther. Janet Smith and I are organizing, and we have already managed to obtain Elspeth Garman, Ed Stern and Bob Fischetti as speakers, but all remaining lectures must be selected from submitted abstracts. So, I strongly encourage all those who do radiation damage research as well as those who are tired of struggling with data that just won't solve to submit an abstract and register for the meeting! The deadline for abstract submission is March 31, 2010, and the advanced registration deadline is May 31, 2010. A preliminary meeting program with all session topics is available on the ACA website: http://www.amercrystalassn.org/content/pages/2010-program I think it will be a good meeting this year, and I hope to see you all in Chicago, -James Holton MAD Scientist, ALS 8.3.1 -Janet Smith Director, GM/CA CAT
[ccp4bb] Slow COOT with Fedora 12
Hello, Does anyone know why COOT is suddenly as slow as molasses on my Fedora 12 desktop? I had and old version of Coot working after my initial Fedora 12 install (from FC7 after a disk crash). However, now all versions of COOT have the same problem, very slow response and refresh rates. It does not seem to matter whether the directory is local or NFS, even before a PDB file is loaded it slows to a crawl. With a PDB file loaded the interface becomes catatonic. Centering takes several seconds. Any idea what the problem could be? COOT was amazingly fast on the same hardware with FC7, so it must be Fedora12 specific. The glxgears speed seems slow to me. # COOT 0.6.1 coot-Linux-i386-fedora-10-gtk2-python/ coot-Linux-i386-fedora-12-gtk2/ coot-Linux-i386-fedora-4-gtk2/ COOT 0.4.1 coot-Linux-i386-fedora-5 # Hardware TYAN S2865A Tomcat K8E Dual Core AMD Opteron 2.4GHz 2 GB RAM ATI Radeon RV530 (Radeon X1600pro) kernel-PAE-2.6.31.12-174.2.3.fc12.i686 xorg-x11-server-Xorg-1.7.4-1.fc12.i686 # glxgears 8071 frames in 5.0 seconds = 1614.093 FPS 8105 frames in 5.0 seconds = 1620.857 FPS Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
Re: [ccp4bb] Slow COOT with Fedora 12
Hi Mark, Is it possible that you used to have coot set up to use the slow computer settings and now you don't. Try adding the slow computer configuration settings to your .coot file. Information can be found at: http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_8.html#SEC2 02 Good luck, Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Thu, 4 Feb 2010, Mark A. White wrote: Hello, Does anyone know why COOT is suddenly as slow as molasses on my Fedora 12 desktop? I had and old version of Coot working after my initial Fedora 12 install (from FC7 after a disk crash). However, now all versions of COOT have the same problem, very slow response and refresh rates. It does not seem to matter whether the directory is local or NFS, even before a PDB file is loaded it slows to a crawl. With a PDB file loaded the interface becomes catatonic. Centering takes several seconds. Any idea what the problem could be? COOT was amazingly fast on the same hardware with FC7, so it must be Fedora12 specific. The glxgears speed seems slow to me. # COOT 0.6.1 coot-Linux-i386-fedora-10-gtk2-python/ coot-Linux-i386-fedora-12-gtk2/ coot-Linux-i386-fedora-4-gtk2/ COOT 0.4.1 coot-Linux-i386-fedora-5 # Hardware TYAN S2865A Tomcat K8E Dual Core AMD Opteron 2.4GHz 2 GB RAM ATI Radeon RV530 (Radeon X1600pro) kernel-PAE-2.6.31.12-174.2.3.fc12.i686 xorg-x11-server-Xorg-1.7.4-1.fc12.i686 # glxgears 8071 frames in 5.0 seconds = 1614.093 FPS 8105 frames in 5.0 seconds = 1620.857 FPS Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
[ccp4bb] ccp4-6.1.3 phaser sigmaa weighted maps problem
Hi , I just switched to ccp4-6.1.3 and ran the phaser which is bundled with the ccp4-6.1.3 release. After molecular replacement I get a pretty good solution (TFZ 59.2) and output pdb and mtz files. I am then looking at the maps from the phaser output mtz i.e the FWT , PHWT map and the FWT PHIC map . Both maps look very crappy and look like noise. I tried the fft inside of coot and separately as a FFT inside ccp4 and these maps look bad. So the FWT PHWT calc seem to be off. However , if I take the phaser solution output model and do the sigmaa myself. The map looks normal and sensible. It seems like phaser inside of ccp4-6.1.3 is not generating the output mtz correctly . Anyone else seeing this or is there something wrong with my setup. Hari
Re: [ccp4bb] ccp4-6.1.3 phaser sigmaa weighted maps problem
Hi, Similar problem occured even in CCP4-6.1.0 in our case. So, we used to take the phaser output model and do rigid body refinement with REFMAC and see the density (in coot), which normally much better than output from PHASER mtz. I am not sure whether it is for case to case or it is general problem? -Karthik Hi , I just switched to ccp4-6.1.3 and ran the phaser which is bundled with the ccp4-6.1.3 release. After molecular replacement I get a pretty good solution (TFZ 59.2) and output pdb and mtz files. I am then looking at the maps from the phaser output mtz i.e the FWT , PHWT map and the FWT PHIC map . Both maps look very crappy and look like noise. I tried the fft inside of coot and separately as a FFT inside ccp4 and these maps look bad. So the FWT PHWT calc seem to be off. However , if I take the phaser solution output model and do the sigmaa myself. The map looks normal and sensible. It seems like phaser inside of ccp4-6.1.3 is not generating the output mtz correctly . Anyone else seeing this or is there something wrong with my setup. Hari
[ccp4bb] how to improve resolution
Hi, All, We are trying to crystallize a protein and found some initial hit in the following conditions, pH 4.8, 0.2 M AS or some other salts ( NaCl,LiCl, MgCl2 ), 32% PEG4000 or PEG3350 ). However the quality of the crystal is not so great,some of them look like needle cluster(very long in length), some of them look like multi-crystals or hollow inside. We tried to optimize the pH and PEG and tested one that diffracts at 2.9A. For the next, how to improve resolution?Any suggestions? Even mutate the protein to get a high resolution is ok, generally what kind of mutation would make proteins crystallize better? Thanks.
Re: [ccp4bb] Strange problem running cpp4i over nx - job reported as failed even though it succeeds-log file has nx errors
Ethan Merritt wrote: On Thursday 04 February 2010 05:14:24 hari jayaram wrote: [...] The program run with command: /mega/ccp4-6.1.3/ccp4-6.1.3/bin/sortmtz HKLOUT /mega/hj-8-2-1/hjbr5-1/hjbr5-1_sorted_mosflm.mtz has failed with error message ERROR: ld.so: object '/usr/NX/lib/libesddsp.so.0' from LD_PRELOAD cannot be preloaded: ignored. My guess is that your machine configuration includes a file that initializes LD_PRELOAD for NX on login. But it should not do this. The LD_PRELOAD setting applies to all programs, so it should not be set blindly to include program-specific libraries. Unfortunately, some ccp4 configuration files also change PYTHONPATH. And exactly the same could be said: The PYTHONPATH setting applies to all programs, so it should not be set blindly... My personal workaround is to start a new shell, then only in this one source the ccp4 configuration files. But this is just a workaround, I hope it can be solved in future releases of ccp4 (ccp4 could creates a CCP4_PYTHONPATH and use this one instead of using the system-wide one). Regards, Francois.
[ccp4bb] HKL-MTZ conversion
Dear All, can anyone of you using Bruker PROTEUM X8? How can I convert HKL to MTZ in CCP4i? I want to do data analysis (TRUNCATE) for the dataset. Many thanks! stephen -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
Re: [ccp4bb] HKL-MTZ conversion
Use combat -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dr. STEPHEN SIN-YIN, CHUI Sent: Friday, February 05, 2010 8:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] HKL-MTZ conversion Dear All, can anyone of you using Bruker PROTEUM X8? How can I convert HKL to MTZ in CCP4i? I want to do data analysis (TRUNCATE) for the dataset. Many thanks! stephen -- Dr. Stephen Sin-Yin Chui Research Assistant Professor, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China. Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory) htmlpfont face = verdana size = 0.8 color = navyThis 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 authorized 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./font/p/html
Re: [ccp4bb] how to improve resolution
Hi Rui, In addition to what Fred has advised, you could also try varying other parameters like temperature and protein concentration. 32 % is a very high concentration of precipitant. Maybe you could try using a bigger PEG (like PEG 8000), at a lower concentration. It worked for me once. Also, if ever you are at ESRF, you could try the crystal dehydrating device. Ganesh ** The boast of heraldry, the pomp of power, And all that beauty, all that wealth e'er gave, Awaits alike the inevitable hour. The paths of glory lead but to the grave. -Thomas Gray, Elegy Written in a Country Churchyard ** On Thu, 4 Feb 2010 23:39:14 -0500, rui wrote: Hi, All, We are trying to crystallize a protein and found some initial hit in the following conditions, pH 4.8, 0.2 M AS or some other salts ( NaCl,LiCl, MgCl2 ), 32% PEG4000 or PEG3350 ). However the quality of the crystal is not so great,some of them look like needle cluster(very long in length), some of them look like multi-crystals or hollow inside. We tried to optimize the pH and PEG and tested one that diffracts at 2.9A. For the next, how to improve resolution?Any suggestions? Even mutate the protein to get a high resolution is ok, generally what kind of mutation would make proteins crystallize better? Thanks. --
