Re: [ccp4bb] DM - NCS averaging after phaser molecular replacement run-confused about coefficients
Not real advice, but be careful if Phaser and DM use the same column labels by default - best to assign them to something distinctive. I have had cases where programs got confused between input and output. And to be safe I would run REFMAC with the output model then use the FO PHIC FOM after a bit of refinement.. Eleanor hari jayaram wrote: Hi everyone, I have a phaser molecular replacement solution for my membrane protein which crystallized in spacegroup P3. The diffraction data is good to about 3.3 A. The model I used had 39% homology to the given protein. A solvent content analysis suggests that there probably are three dimers in the ASU ( to give about 67% solvent) Phaser sucessfuly found two dimers in the ASU with good density and a third dimer with very weak almost non-existent density. I am now trying to do some NCS-averaging using DM to see If I can improve the desnity for dimer 3 and have a question about the different co-efficients I should be using for the averaging DM run. Question1: The phaser output mtz file has a PHWT and a PHIC . For carrying out DM with flattening, averaging and histogram matching which phases do I use PHIC or PHWT along with observed Fo. Also for the weight do I use the FOM. Question2: The output mtz from DM run either way above , now has a PHIDM and a PHWT along with a FWT and FC. Which coefficients should I be using to get a map after DM for building. FWT and PHWT or Fo and PHIDM or FWT and PHIDM. Thank you for your help Hari
[ccp4bb] MrBump CCP4i task
Hi all, I'm having problems to install the ccp4i task for MrBump 0.4.2. The error message I get is the following UnpackTaskArchive: uncompress failed to create ./install_MrBUMP-ccp4i/MrBUMP-ccp4i.tar ExamineTaskArchive: failed to unpack temporary copy of /home/linux/xtal/ccp4-6.0.2-all-packages/ccp4-6.0.2/ccp4i/MrBUMP-ccp4i.t ar.gz I've checked I can unpack that archive by tar -xvzf, and I think I've no permission issues. I'm running CCP4 6.0.2 with CCP4 interface 1.4.4.2 on a Red Hat 4.0 64bit machine. Any help would be appreciated, Thanks Roberto --- Roberto T. Bossi tel.: +39 0331 58 1914 fax.: +39 0331 58 1360 E-Mail: [EMAIL PROTECTED] Structural Chemistry Department of Chemistry NERVIANO MEDICAL SCIENCES Viale Pasteur 10 20014 Nerviano (MI) - Italy Web: www.nervianoms.com
[ccp4bb] New improved flexible licence for CCP4 libraries
Dear All, We are happy to announce a change in CCP4 library distribution. The current CCP4 libraries can now be downloaded under v3 of LGPL. This should now give all developers the security they need to use the current and all future CCP4 libraries. We have always intended the CCP4 libraries to be freely available for development. The new version of LGPL allowed us to satisfy the legal concerns of STFC about UK law regarding liability issues. We are particularly grateful to the gpp4 initiative which has highlighted the problems the previous licence was causing. See http://www.ccp4.ac.uk/ccp4license.php for further details. Best Jim Naismith Chair of CCP4 The University of St Andrews is a charity registered in Scotland : No SC013532
[ccp4bb] which concentrated salt has lowest vapour pressure?
Dear all, a protein which we work on is available in low quantity. The only crystallization screen we set up is completely clear, no precipitate, nothing. Now we would like to modify the reservoirs of this screen, by adding LiCl or Ammoniumsulfate or ... , with the goal of reducing the vapour pressure, to at least get the protein concentration in the drop into the range where something happens. Does anyone have advice as to which salt we should add (to the reservoir only)? AmSO4 is only soluble to 4M, LiCl goes to 10M. But vapour pressure reduction is not the same as molarity. thanks for any insight, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
Re: [ccp4bb] which concentrated salt has lowest vapour pressure?
We normally use AmS or glycerol. Poul On 07/04/2008, at 15.46, Kay Diederichs wrote: Dear all, a protein which we work on is available in low quantity. The only crystallization screen we set up is completely clear, no precipitate, nothing. Now we would like to modify the reservoirs of this screen, by adding LiCl or Ammoniumsulfate or ... , with the goal of reducing the vapour pressure, to at least get the protein concentration in the drop into the range where something happens. Does anyone have advice as to which salt we should add (to the reservoir only)? AmSO4 is only soluble to 4M, LiCl goes to 10M. But vapour pressure reduction is not the same as molarity. thanks for any insight, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
Re: [ccp4bb] which concentrated salt has lowest vapour pressure?
I'm not entirely sure this paper will answer your question, as I can't access the full article at home, but I seem to remember it may contain what you seek. It's certainly worth giving it another airing... http://scripts.iucr.org/cgi-bin/paper?S0907444905002726 Acta Cryst. (2005). D61, 490-493[ doi:10.1107/S0907444905002726 ] Expanding screening space through the use of alternative reservoirs in vapor-diffusion experiments J. Newman HTH Dave On 07/04/2008, Kay Diederichs [EMAIL PROTECTED] wrote: Dear all, a protein which we work on is available in low quantity. The only crystallization screen we set up is completely clear, no precipitate, nothing. Now we would like to modify the reservoirs of this screen, by adding LiCl or Ammoniumsulfate or ... , with the goal of reducing the vapour pressure, to at least get the protein concentration in the drop into the range where something happens. Does anyone have advice as to which salt we should add (to the reservoir only)? AmSO4 is only soluble to 4M, LiCl goes to 10M. But vapour pressure reduction is not the same as molarity. thanks for any insight, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz -- David C. Briggs PhD Father Crystallographer http://www.dbriggs.talktalk.net AIM ID: dbassophile
[ccp4bb] Crystallization: focus on memebrane proteins 2008
Crystallization: Focus on Membrane Proteins June 18-22, 2008 http://www.nsls.bnl.gov/newsroom/events/workshops/2008/crys/ Purpose Scope of Workshop: The purpose of this course is to provide participants with hands-on experience of a variety of crystal growth methods. The course will address both conventional and non-conventional methods in membrane proteins. Introductory lectures will precede the practical sessions. Time for discussions and informal meeting with speakers and tutors is scheduled. Participants will be divided into groups of four to five members according to their main interests and follow practical sessions during the course.A special session on cryogenic protection and crystal quality assessment of crystals will be conducted at the X6A beam line on the last day. Intended Audience Graduate students, post-doctoral fellows and research scientists interested in learning about different approaches to crystallization. Selection Criteria There is no selection criteria. The inclusion of a small resume and a statement of interest with the registration form are strongly recommended, as groups will be organized according to their common level. Travel Grants A grant from The International Union of Crystallography will support the attendance of a limited number of attendee's. Preference will be given to Young Scientists [graduate students, post-graduate students or post-doctoral fellows with a maximum age of 30 (exceptionally 35)] from developing countries. For additional inofrmation refer to the course webpages: http://www.nsls.bnl.gov/newsroom/events/workshops/2008/crys/ or contact the organizers. In addition to submitting an Application Form for this workshop, all attendees must obtain a BNL guest appointment. Please register in BNL's Guest Information System (https://fsd84.bis.bnl.gov/guest/guest.asp). Approval, which can take 30 days or more, must be granted prior to attending this workshop. Travel Grants A grant from The International Union of Crystallography will support the attendance of a limited number of attendee's. Preference will be given to Young Scientists [graduate students, post-graduate students or post-doctoral fellows with a maximum age of 30 (exceptionally 35)] from developing countries.
Re: [ccp4bb] OMIT map from Sfcheck
my model has 1600 atoms. the memory allocation for the linux (worked) and OS X (failed) binaries is the same: Sol_ Sol_ - Sol_ --- SFCHECK --- /Vers 7.2.02; 01.10.2006/ - Sol_ Memory: 30 Mb N_atom_max: 5 - Sol_ - Sol_ compiling from source or downloading the mac intel binary worked with no errors. Thanks, Mike On Fri, Apr 4, 2008 at 1:58 AM, Jovine Luca [EMAIL PROTECTED] wrote: On 4 Apr 2008, at 01:36, Michael Giffin wrote: i get the same error on OS X 10.5.2 and 10.4.11: sfcheck -f refmac2.mtz -m refmac2.pdb -out y -nomit 2 -map the error: Open failed: Unit: 11, File: sfcheck_scr.dat (logical: sfcheck_scr.dat) BFONT COLOR=#FF!--SUMMARY_BEGIN-- Last system error message: Bad file descriptor CCP4: Open failed: File: sfcheck_scr.dat CCP4: Open failed: File: sfcheck_scr.dat the binary file sfcheck_scr.dat exists. Hi Mike, I encountered the same exact issue under OS X not long ago, and it turned out to be caused by memory/atom limitations of Fink's sfcheck (I assume that's what you are using?): Sol_ --- SFCHECK --- /Vers 7.2.02; 01.10.2006/ - Sol_ Memory: 30 Mb N_atom_max: 5 - = !!! so that using the sfcheck binary included with BALBES: Sol_ --- SFCHECK --- /Vers 7.02.4; 02.05.2007/ - Sol_ Memory: 60 Mb N_atom_max: 10 - solved the problem. How many atoms are you playing with? HTH, Luca Luca Jovine, Ph.D. Karolinska Institutet Department of Biosciences and Nutrition Hälsovägen 7, S-141 57 Huddinge, Sweden Voice: +46.(0)8.6083-301 FAX: +46.(0)8.6089-290 E-mail: [EMAIL PROTECTED] W3: http://ki.se
[ccp4bb] Crystallization and cryo with Li at high concentration!
Hi all, I have some crystals from a condition with a high concentration of LiCl (3.5M is a need). The crystals look pretty, however I had no luck because they diffract very poorly (~8Å). Dehydration pushes resolution to ~4 Å, however, it damages the crystal lattice and makes disorder especially in one direction. One thing I learned is that LiCl releases a huge dilution heat at high concentration, to which my crystal seems to be very sensitive. Does anyone have some successful experience in crystallization and cryo with LiCl at such a high concentration like 3.0 M? Thanks a lot. Lijun Liu, PhD Institute of Molecular Biology HHMI Department of Physics University of Oregon Eugene, OR 97403 541-346-4080
