Re: [ccp4bb] arp/warp ligand
Dear Sangeetha, what you noticed is a bug that appears under particular circumstances. Sorry for your inconvenience. From your logfile excerpt I think that this bug has been observed before and been fixed. The next release will include the fixed version, however useless this might sound to you now. So if you are in urgent need to get the software running now, please contact me in a private communication and send me details about your case and your computing environment and we will see what we can do. Greetings from Hamburg, Gerrit.
Re: [ccp4bb] Error message while refining protein-DNA complex structure in Refmac5
Dear Garib Thank you very much as you suggested, I removed SCALE card in the pdb file, then it is running smothly. Rajakumara --- Garib Murshudov ga...@ysbl.york.ac.uk wrote: It seems that something may be wrong with your input file. Specifically with the SCALE card in the pdb file. Could you please remove SCALE lines from the pdb and try again. If it does not help then could you please send me your pdb file and I will try to sort out. Garib On 16 Mar 2009, at 22:43, E rajakumar wrote: Dear All I am refining proitein-DNA complex structure in Refamac5. When I used coordinate file containing 2 bases less, then the refinement is running smoth and perfect. But when I built 2 exta bases to the existing DNA in the coot then refinement is failed with the following error message. /usr/local/ccp4-6.1.0/bin/refmac5 XYZIN/usr6/rajkumar/APS/hem/mar9/H2/molrep/BCDNA-built2-NCS- refm2.pdb XYZOUT /tmp/rajkumar/hemCG_19_2_pdb_1.tmp HKLIN /usr6/rajkumar/APS/hem/mar9/H2/molrep/P6122.mtz HKLOUT /tmp/rajkumar/hemCG_19_3_mtz_1.tmp LIBOUT /usr6/rajkumar/APS/hem/mar9/H2/molrep/hemCG_19_lib.cif has failed with error message At line 2486 of file /usr/local/xtal/ccp4-6.1.0/src/refmac5_/make_PDB.f Fortran runtime error: Bad value during floating point read It seems there is error in LIB file generation. Coordinate format and atom labelling is accoring to refmac convention. Please can anybody suggest me how do I trooubleshoot. Thanking you Rajakumara E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) Get your preferred Email name! Now you can @ymail.com and @rocketmail.com. http://mail.promotions.yahoo.com/newdomains/aa/ E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile) Get your new Email address! Grab the Email name you#39;ve always wanted before someone else does! http://mail.promotions.yahoo.com/newdomains/aa/
[ccp4bb] refmac5 v5.5.0066 bug - CRYST angles swapped
Hi we regularly update our intel mac refmac5 ( and ccp4) installs from W.G . Scotts fink packages We just add an unusual error with refmac5 v5.5.0066 doing a routine rigid body refinement. The program v5.5.0066 seemed to be swapping the beta and gamma angles in the mtz produced after the refinement. We immediately downloaded the v5.5.0089 binaries from garibs refmac5 page and replaced them in-place. Now the rigid body refinement works well and all the CRYST and mtz CELL labels are correct. Is anyone using refmac5 v5.5.0066 seeing this . Thanks Hari Jayaram Brandeis University
[ccp4bb] Postdoctoral position available
Applications are invited for a postdoctoral position to work on the structure determination of membrane transport proteins critical in cardiovascular function. The transporters we study have been linked to human disorders such as cardiomyopathy, ischemia-reperfusion injury, and various cancers. Our aim is to understand the molecular regulation of the transporters with the goal of rational design of novel inhibitors and activators. We seek an enthusiastic candidate experienced in macromolecular x-ray or electron crystallography. Experience with membrane protein biochemistry would be an asset. In addition, the successful candidate should be well-versed in one or more of the following areas: molecular biology, protein purification, crystallization, and membrane protein and lipid biochemistry. This is an opportunity to join a lab experienced in the expression and crystallization of membrane proteins [See Biophysical Journal (2006) 90:4213-23, JBC (2007) 282:9748-57, and JBC (2008) 283:4145-54]. Our department provides interaction with numerous structural biologists. In addition, the University of Alberta Membrane Protein Research Group provides a dedicated forum for membrane protein research that includes 14 research laboratories (http://www.mprg.med.ualberta.ca/index.php ). The University of Alberta, located in Edmonton, Alberta (Canada), is home to a large and interactive community of biomedical scientists http://www.med.ualberta.ca/; support and facilities for structural biology are excellent. A state-of-the-art facility is available for electron microscopy at the National Institute for Nanotechnology, University of Alberta (http://nint-innt.nrc-cnrc.gc.ca/research/micro/index_e.html), and a newly commissioned synchrotron facility is located a short drive away. Edmonton, having a population of approximately 1 million, offers a cosmopolitan environment with world class performing arts, sports, culinary and recreational opportunities. In addition, the citys proximity to the Rocky Mountains including the towns of Jasper and Banff is an additional bonus. Salary is commensurate with training and experience at the CIHR standard rates. A medical and dental benefit package is included with salary. Funding is also available through several competitive funding agencies, including CIHR (http://www.cihr.ca/ ) and Alberta Heritage Foundation for Medical Research (http://www.ahfmr.ab.ca/ ). The University of Alberta hires on the basis of merit. We are committed to the principle of equity in employment. We welcome diversity and encourage applications from all qualified women and men, including persons with disabilities, members of visible minorities, and Aboriginal persons. The records arising from this competition will be managed in accordance with provisions of the Alberta Freedom of Information and Protection of Privacy Act (FOIPP). Please direct CV's or inquiries to the following email address: hyo...@ualberta.ca. Howard S. Young Associate Professor Department of Biochemistry University of Alberta Medical Science Bldg, room 327 Edmonton, AB, Canada T6G 2H7 National Institute for Nanotechnology, National Research Council of Canada Membrane Protein Research Group (http://www.mprg.med.ualberta.ca/group-members.php)
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
Hi Sun, For 2.5A data you can try phenix or arp/warp to autobuild the the model using the phase form MR ,then you can get the most of model you want if you are lucky enough or you need more manual bulding or another cycle MR again . Good luck! liu Sun Tang wrote: Dear All, Recently I solved a structure at 2.5 A with PHASER, with two molecules in assymetric unit. There are no short contacts in the solution. However, the Rfree stays at about 50% after the refinement of rigid boby and restrained refinement in CNS. The sequences homology is about 30%. What is the usual way to deal with this kind of problems? Should I just refine the backbone of the structure and then build the side chains? Your suggestions are greatly appreciated!!! Best wishes, Sun
[ccp4bb] Beam time available @X6A NSLS
Beam time available @ X6A http://protein.nsls.bnl.gov The NIGMS beam line X6A at the National Synchrotron Light Source has recently replaced its end-station. The beam line now operates a ADSC Q270 CCD detector and a Crystallogic diffractometer equipped with an air-bearing single rotation axis. For screening large numbers of sample an ALS like automounted sample changer capable of screen 16 samples in 40 minutes is available upon request. Beam time can be scheduled as fast as making reservations for a trip. Just locate the available beam time on the schedule and use the drop down menu to select the date that fits best into your schedule. Of course you need to have a project first, but this is easy too.. just submit a small abstract (http://protein.nsls.bnl.gov) and your project will be reviewed within a few days. If you like to know more send an email: x6an...@bnl.gov or call: +1 (631) 344 8375 Vivian Stojanoff National Synchrotron light Source Brookhaven National Laboratory Bldg 725D Upton, NY 11973 USA Email: stoja...@bnl.gov;vivian.stojan...@gmail.com phone: +1 631 344 8375 fax: +1 631 344 3238
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
Dear Sun, if I remember correctly phaser already carries out a rigid body refinement of its solution. To avoid and remove as much model bias as possible, I suggest you look at the solution from phaser and build _as_ _much_ _as_ _possible_ BEFORE you do any further refinement, i.e., try to match the sequence, correct side chains, etc. Only once you cannot do any bettermanually you should run a refinement program and after that again build as much as possible, etc. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 17 Mar 2009, Sun Tang wrote: Dear All, Recently I solved a structure at 2.5 A with PHASER, with two molecules in assymetric unit. There are no short contacts in the solution. However, the Rfree stays at about 50% after the refinement of rigid boby and restrained refinement in CNS. The sequences homology is about 30%. What is the usual way to deal with this kind of problems? Should I just refine the backbone of the structure and then build the side chains? Your suggestions are greatly appreciated!!! Best wishes, Sun
[ccp4bb] Job
A Senior Scientist position at the initial level of Research Associate is available immediately in the laboratory of Dr. Dmitry Vassylyev (University of Alabama at Birmingham). The main focus of research in the lab is structural and functional analysis of biological macromolecules with emphasis on bacterial RNA polymerases and associated transcription factors (for recent publications see Nature 2009, 457:332-5; Nature 2008, 455:988-91; Nature 2007, 448:163-8; Nature 2007, 448:157-62; Cell 2005, 122:351-63; Nature 2004, 430:700-4; Cell 2004, 118:297-309; Cell 2004, 117:299-310; Cell 2004, 116:381-91; Nature 2002, 420:43-50; Nature 2002, 417:712-19). A successful candidate would have Ph.D. in biochemistry, molecular biology, chemistry or physics and a considerable proved expertise in all techniques required for efficient protein expression and purification. Experience in structural and/or functional studies of transcription is desirable, but is not required. A salary will be in a range of $50,000-100,000 depending on a demonstrated record of research experience. Based on the research achievements of a first year position might be converted to a higher rank at the Research Assistant Professor or Research Associate Professor level. To apply send a CV, letter of intent, and names and contact information of 3 referees to klyu...@uab.edu. Additional information might be found on the Web page: http://138.26.140.2/vassylyev/
[ccp4bb] map coefficients for padded reflections Fobs=0
Dear All, during processing some mtz files I noted that some programs complete the reflection list by padding missing reflections. a) for Refmac (which did not pad reflections automatically) I read that 1) for 2mFo-DFc: Fwt = DFc in case Fo=0 2) for mfo-fc : Fwt=0 for Fo=0 b) how does PHENIX/refine handle the fobs = 0 reflections in either case? c) Prime and switch maps also have padded reflections, but here I am at a loss, because the maps seem to acquire very high positive density - i.e. the distribution seems atypical when read into say Xtalview. Might be a result of the density modification procedure? Can I get the observed reflections only from PS? Could the program authors kindly shed some light or references on the treatment of absent reflections in their respective programs? In most cases, the padded reflections have not much effect, as expected from their weights. Thx, br Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. -
[ccp4bb] map coefficients for padded reflections Fobs=absent
I mean *absent* reflections here with fobs=0 Dear All, during processing some mtz files I noted that some programs complete the reflection list by padding missing reflections. a) for Refmac (which did not pad reflections automatically) I read that 1) for 2mFo-DFc: Fwt = DFc in case Fo=absent 2) for mfo-fc : Fwt=0 for Fo=absent b) how does PHENIX/refine handle the fobs = absent reflections in either case? c) Prime and switch maps also have padded reflections, but here I am at a loss, because the maps seem to acquire very high positive density - i.e. the distribution seems atypical when read into say Xtalview. Might be a result of the density modification procedure? Can I get the observed reflections only from PS? Could the program authors kindly shed some light or references on the treatment of absent reflections in their respective programs? In most cases, the padded reflections have not much effect, as expected from their weights. Thx, br Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. -
Re: [ccp4bb] map coefficients for padded reflections Fobs=absent
On 18 Mar 2009, at 01:47, Bernhard Rupp wrote: I mean *absent* reflections here with fobs=0 Dear All, during processing some mtz files I noted that some programs complete the reflection list by padding missing reflections. a) for Refmac (which did not pad reflections automatically) I read that 1) for 2mFo-DFc: Fwt = DFc in case Fo=absent 2) for mfo-fc : Fwt=0 for Fo=absent It is true. Although there are other options (i.e. ignore them). Many tests showed that recovering missing reflections this way (i.e. replacing them with their approximately expected values) give better maps that not using them at all. b) how does PHENIX/refine handle the fobs = absent reflections in either case? c) Prime and switch maps also have padded reflections, but here I am at a loss, because the maps seem to acquire very high positive density - i.e. the distribution seems atypical when read into say Xtalview. Might be a result of the density modification procedure? Can I get the observed reflections only from PS? Could the program authors kindly shed some light or references on the treatment of absent reflections in their respective programs? In most cases, the padded reflections have not much effect, as expected from their weights. Thx, br Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. -
[ccp4bb] Conference announcement: Molecular Modelling 2009
Dear Colleagues, Registration for MM2009, Molecular Modelling from Dynamical, Biomolecular and Materials Nanotechnology Perspectives is now open. MM2009 will be held at the Gold Coast, Australia from 26-29 July 2009. The meeting will focus on the latest developments in molecular modelling in both the life sciences and materials sciences, particularly in the areas of Methodology Development; Drug Design; Materials Nanotechnology; Dynamics Chemical Reactivity; Self Assembly Biomolecular Simulations; and Sustainable Energy Environment. For further information on the meeting, please go to http://web.aibn.uq.edu.au/mm2009 . Please register on-line at http://web.aibn.uq.edu.au/mm2009/Registration.htm The deadline for early bird registration is 30th April, 2009. Abstracts are invited for both Oral and Poster presentations. All papers must be presented by a registered delegate. The deadline for submission of abstracts for consideration as an oral presentation is 30th April, 2009. Please see http://web.aibn.uq.edu.au/mm2009/AbstractnPoster.htm for details on abstract submission. We are looking forward to your participation. On behalf of the organising committee, Debra Bernhardt (Searles) Conference Secretary -- Dr Andreas Hofmann FHEA Associate Professor, Program Leader -- Structural Chemistry Eskitis Institute for Cell Molecular Therapies Griffith University Don Young Road, Brisbane Innovation Park Nathan, Brisbane, Qld 4111, Australia Telephone/Facsimile: +61-7-3735-4425 Web: http://www.structuralchemistry.org/ -- European Annexin Homepage: http://www.annexins.org/ -- Molecular Modelling 2009 Gold Coast, 26 - 29 July 2009 http://web.aibn.uq.edu.au/mm2009/
Re: [ccp4bb] map coefficients for padded reflections Fobs=0
Hi Bernhard, b) how does PHENIX/refine handle the fobs = 0 reflections in either case? phenix.refine outputs two series of maps: - one pair of (2mFo-DFc, mFo-DFc) maps is computed using original untouched Fobs; - and the other pair of (2mFo-DFc, mFo-DFc) maps is computed using manipulated Fobs, where missing Fobs are filled in with DFc (only for map calculation!!!). To avoid any confusion, this is clearly indicated in output MTZ file with map coefficients. As I said, by default missing Fobs are filled with DFc, but there are other options available to play with, such as Fobs, simply Fc, random numbers, and... I forgot the whole list but I re-call I implemented a bunch of possibilities. I did a number of tests (and even documented it!) and actually spent quite a bit of time playing with this... My observation was that filling with DFc or Fobs, or with even random numbers (generated around Fobs) did NOT produce any visible difference between each other (indicating the overwhelming importance of phases) - all of them were almost equally good. Sure, there were the cases where filled maps were giving much more interpretable maps NOT only because of bias, but just because of eliminating data incompleteness effects by putting at least something into missing Fobs slots. I've seen bias as well. Overall feeling is: it is the best to look at BOTH maps: filled and not filled, to help overcoming a difficult cases and still staying on a safe side. You can play with this in phenix.refine if you like. Overall, this whole thing requires more tests, and care before any generalizations is made. Cheers, Pavel.
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
I've found CNS's simulated annealing composite omit maps to be very useful in situations like this to avoid phase bias. RESOLVE's prime and switch offers similar functionality, but I've had less experience with it. ho UC Berkeley
Re: [ccp4bb] How to refine a solution obtained by molecular replacement
Dear All, Thank you very much for all your suggestions. They are very helpful in my further refinements. I am adding some more information about the problem: 1) The Z-score is 11.2 and LLG is 125. 2) The model has 390 aa while my structure has about 440 aa. Please let me know of any further suggestions. I will try all your suggestions and let you know the updated information about the refinement. Best regards, Sun From: Ho-Leung Ng hole...@berkeley.edu To: CCP4 bulletin board CCP4BB@jiscmail.ac.uk; suntang2...@yahoo.com Sent: Wednesday, March 18, 2009 12:10:29 AM Subject: Re: How to refine a solution obtained by molecular replacement I've found CNS's simulated annealing composite omit maps to be very useful in situations like this to avoid phase bias. RESOLVE's prime and switch offers similar functionality, but I've had less experience with it. ho UC Berkeley
