- phenixbb - phenix-online.org

an error in the operation of SF-Tool
by Dialing Pretty 18 Jan '12

18 Jan '12

Dear All, By the RCSB SF-Tool I have tried to convert my PDB file and the corresponding mtz file into mmCIF for the purpose of RCSB depositation, by the Automatic (default) mode. I got the following message: "Converting structure factor to mmCIF format.... Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file" Obviously there is an error message, although the conversion is succesful. As for I intend to deposit the structure including the mmCIF file into RCSB, I am afraid I have lost some message in the MTZ file and mmCIF file. Will you please tell me how can I add the labels, which have been lost I think, to the mtz file, so that the labels message will also be included into the mmCIF file if it was necessary? Cheers, Dialing

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tool for dispersive difference fourier ?
by Francis E Reyes 17 Jan '12

17 Jan '12

I'd like to make a dispersive difference fourier using phases from a model. Is there a tool to do so? phenix.maps doesn't seem to have the 'map_type' to do this.. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Rosetta rebuilding...
by Francis E Reyes 16 Jan '12

16 Jan '12

Phenixers, I'm curious about using rosetta to rebuild an existing model (phenix.mr_rosetta it seems) [0] What is being rebuilt in rosetta? The whole model? Or is the model divided into chunks and each chunk sent to rosetta? [1] Can a specific region be chosen to be rebuilt? (In the case where most of the model is correct) [2] How are the rosetta models scored ? Specifically, "(d) refine Rosetta models, average density from top 20%, continue rebuilding each Rosetta model using averaged density". What's the scoring function (mapCC, R-Free, LLG??) How's the top 20% obtained? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Only two weeks left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 13 Jan '12

13 Jan '12

Many seats are still available for RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Simulated annealing omit maps
by SEKHAR1＠pitt.edu 12 Jan '12

12 Jan '12

Hello friends, I have a couple of questions regarding simulated annealing composite map calculations. (1) Is there a way of specifying the percentage of residue co-ordinates to be omitted each time as we move through the asymmetric unit? I have found, when using CNS earlier, that depending on the structure, the map quality often varies if you change this from the usual 5% to 4% or even 3%, sometimes getting clearer. (2) Does the 'number of boxes' you can specify in the GUI only affect the fine structure/grid spacing of the map? The map probably does not get better all the time as we keep on increasing the number of boxes; when do we reach the point of diminishing returns and what would be the best way to estimate it? Thank you very much and wish you all a Very Happy 2012. K. Chandrasekhar

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phenix.find_ncs
by Ursula Schulze-Gahmen 11 Jan '12

11 Jan '12

I am working with a complex of 3 different proteins, and there are 3 complexes in the asymmetric unit. During phenix.refine I used automatic NCS and it worked fine. I now wanted to determine the NCS parameters with phenix.find_ncs. The output file gives me 3 NCS groups, 2 groups with 3 chains, and 1 group with 2 chains.I cannot figure out why one chain is not included. I tried to run it with only pdb input, or pdb anf map coefficients, same result. Any suggestions hat else to try? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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brainpool research associate position
by intekhab alam 11 Jan '12

11 Jan '12

Dear members Have a look on the advertisement for the position of research associate in structural biology. Interested candidates please reply to khkim(a)korea.ac.kr. Informal enquiries can also be made. Structural Bioinformatics Lab, Department of Biotechnology & Bioinformatics, Korea University, Seoul KoreaBrainpool Research Associate – Full time, fixed term appointment for up to two years The Structural Bioinformatics Lab is seeking a Brainpool Research Associate to carry out structural analysis (x-ray crystallography) and biophysical studies of complexes related to virus-host interaction. The group is led by Professor Kyung Hyun Kim and has over the years produced good results (PNAS, NAR, JGV). The research programme is funded by a grant from the Korean Federation of Science and technology Societies (www.brainpool.or.kr) to which both the applicant and our team apply together. Further details on the research group can be found at http://sbl.korea.ac.kr/. Applicants should have a PhD in Structural Biology, Biophysics or a related area, with at least 5 years of research experience after Ph.D., or high profile publications in the highest impact journals. Salary range will be from $45,000-$55,000 per annum plus plane ticket, moving expense and medical insurance. Initial salary for possibly the two months will be dependent on the skills and experience of the successful applicant. Closing date for completed applications: 5 February 2012. To apply for this position please send emails to khkim(a)korea.ac.kr with your resume. Korea U is an equal opportunities employer and encourages applications from all candidates irrespective of gender, race, disability, sexual orientation, age, religion and belief or another protected characteristic. -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Re: [phenixbb] phenix.find_ncs
by Thomas C. Terwilliger 11 Jan '12

11 Jan '12

Hi Ursula, In that case...sounds like something I need to fix! Would it be possible to send me (off-list, terwilliger(a)lanl.gov) the entire PDB file and I'll have a look? In the meantime, I guess if you run each group separately you have the information that you are looking for... All the best, Tom T >> I just did waht you suggested. I ran phenix.find_ncs on the problem group >> only. This time it found all 3 chains in the group. >> >> Ursula >> >> On Wed, Jan 11, 2012 at 10:16 AM, Thomas C. Terwilliger < >> terwilliger(a)lanl.gov> wrote: >> >>> Hi Ursula, >>> >>> I am not sure why find_ncs did not get the 3rd chain for the third >>> group. >>> I think that when you run phenix.refine it is (for the moment) actually >>> just calling find_ncs to get the NCS groups, so the groups found there >>> should (if everything is working the way I think it should) be identical >>> to the ones you would find with phenix.find_ncs. >>> >>> Here is something to try: Split your model into just protein #3 (you can >>> use phenix.pdbtools and keep="chain C or chain F or chain I" to do >>> this), >>> and also just protein #1 and #2. Then run find_ncs separately on these. >>> Can find_ncs get the ncs for your 3 copies of protein #3 all by >>> themselves? >>> >>> If not...then it indicates that perhaps one of the chains is actually >>> different (maybe very different conformation, maybe mostly missing, >>> maybe >>> different sequence...?) >>> >>> All the best, >>> Tom T >>> >>> >>> >> I am working with a complex of 3 different proteins, and there are 3 >>> >> complexes in the asymmetric unit. During phenix.refine I used >>> automatic >>> >> NCS >>> >> and it worked fine. I now wanted to determine the NCS parameters with >>> >> phenix.find_ncs. The output file gives me 3 NCS groups, 2 groups with >>> 3 >>> >> chains, and 1 group with 2 chains.I cannot figure out why one chain >>> is >>> not >>> >> included. I tried to run it with only pdb input, or pdb anf map >>> >> coefficients, same result. Any suggestions hat else to try? >>> >> >>> >> Thanks >>> >> >>> >> Ursula >>> >> >>> >> -- >>> >> Ursula Schulze-Gahmen, Ph.D. >>> >> Assistant Researcher >>> >> UC Berkeley, QB3 >>> >> 356 Stanley Hall #3220 >>> >> Berkeley, CA 94720-3220 >>> >> _______________________________________________ >>> >> phenixbb mailing list >>> >> phenixbb(a)phenix-online.org >>> >> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> >> >> >> >> -- >> Ursula Schulze-Gahmen, Ph.D. >> Assistant Researcher >> UC Berkeley, QB3 >> 356 Stanley Hall #3220 >> Berkeley, CA 94720-3220 >>

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Phenix for CUDA?
by Schubert, Carsten [JRDUS] 10 Jan '12

10 Jan '12

Hi, are there any development plans for phenix in the works to take advantage of NVIDIA's CUDA platform? Cheers, Carsten

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Question about unrestrained refinement
by Louis Lazar 10 Jan '12

10 Jan '12

Hello all, I had a question about unrestrained refinement. I have several data sets (right near 1 A resolution) that are nearly fully refined, but to finish I would like to run one round of unrestrained refinement. At this point, I want to focus on unrestrained refinement of just the protein, and not any waters. How would the syntax for refining just the chains of the protein (and not water) look in the command line? I also want to include anisotropic refinement of B-factors in this last refinement run. Should it look something like: strategy=individual_sites+occupanices+individual_adp \ adp.individual.anisotropic="not water and not element H" wc=0 wu=0 Then what should I add after this to include just my protein chains and omit waters from the unrestrained refinement? Also, if I wanted to not refine the waters at all in this round of refinement, what should I add to the command line to make that happen? Thank you in advance as always. Regards, Louis

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