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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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zn anomalous
by Pengfei Fang 10 Jan '12

10 Jan '12

Dear All, I collected a dataset at 0.9774 angstrom. the structure is already by MR. Can you please teach me how to tell a specific site has Zn-atom anomalous signal or not using phenix? thank you! Pengfei

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phenix.refine request: output den restraints to a file...
by Francis E Reyes 10 Jan '12

10 Jan '12

Hi phenixbb (Jeff probably), I wanted to try a few different protocols with the den refinement. It occurred to me that phenix.refine won't take den restraints as an external file, instead it seems to be generating them on the fly. Can I have an option to output (and also read in) den restraints? I'd like to generate them once and use the same restraints to test a different refinement params. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Output for den optimization runs
by Francis E Reyes 09 Jan '12

09 Jan '12

Is there a refine.log for each den (gamma, weight) optimization? I can't seem to find one anywhere and I'm curious to see how it's doing. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Chirality of Ribityl chain of FMN inverted
by Yuri 09 Jan '12

09 Jan '12

Hello Developers, When I built Ligand restraints using eLBOW, my resulting .pdb had an inverted chiral center in the ribityl chain of the flavin mononucleotide particularly C4'. In the database the ligand had an S configuration (correct), but after minimization and restraint generation the output had R configuration at that particular center. I wonder if there is a way to enforce the configuration for each center, although I suspect it could be a little bug, because I noticed my restraints have that center annotated as S eventhough it is R in the actual .pdb Cheers, -- Yuri Pompeu

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molecular replacement of protein/DNA complex
by Wei Shi 07 Jan '12

07 Jan '12

Hi all, I have been trying to solve a protein-DNA complex structure using molecular replacement. I suspect two copies of protein bind one piece of the DNA, and the angle between the two copies of protein is somewhere between 130 to 180 degrees. I could get molecular replacement solution using a search model of protein/DNA complex I made with deletion in part of the protein and with the angle between the two proteins about 145 degrees. Only 1 copy of this two-protein/one-DNA complex is expected in the ASU. Below is the statistics for the solution. RFZ=2.9 TFZ=6.9 PAK=0 LLG=111 TFZ==14.6 LLG=111 And when I open the pdb file and generate symmetry mates, no clashes and I could see contacts between the end of DNA, but space instead of contacts between layers of the protein/DNA complex. I suspect that the angle between the two proteins I use in the search model is not quite right. No solution if I search with DNA and protein separately. I am trying to find a way to move the protein a little bit around the original solution and see whether that can help me make the solution better. I just read that “ROTate AROUnd option of the brute rotation serch” and “NMAPdb” might do this? Does anyone have any suggestions about what I could try? Thank you so much! Best, Wei

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Only three weeks left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 06 Jan '12

06 Jan '12

We are offering 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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CCI-Apps - Cygwin incompatibility after upgrade
by Schubert, Carsten [JRDUS] 05 Jan '12

05 Jan '12

Hi, After upgrading my cci_apps install on Windows from 1.7-718 to 1.7.3-928 the interoperability with cygwin is gone. Calling phenix.refine just gives a 'Command not found' error. Turns out that the little .exe files for each subprogram were replaced by .bat files. That is fine if one just wants to use the DOS CLI, but cygwin is not able to call programs via .bat files as far as I know. Is there a workaround for this problem besides working in the DOS CLI (yuk)? Thanks Carsten

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