- phenixbb - phenix-online.org

adding exchangeable H to a perdeuterated structure with ready set?
by Maxime Cuypers 19 Jan '12

19 Jan '12

hello, how can i add exchangeable H to a perdeuterated structure with readyset? (other than manualy editing the file please) i see readyset does the opposite. thanks in advance Maxime

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an error in the operation of SF-Tool
by Dialing Pretty 19 Jan '12

19 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 14 Jan '12

14 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 12 Jan '12

12 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 12 Jan '12

12 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 12 Jan '12

12 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 10 Jan '12

10 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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phenix.metal_coordination
by Young-Jin Cho 04 Jan '12

04 Jan '12

Hi everyone and wish your happy new year. I have a question regarding phenix.metal_coordination. when I typed my pdb file that has two alternative conformations of different species including metal such as a metal(B) and a water(A). It seems like, in this case, phenix.metal_coordination doesn't read the metal. Otherwise, is there other way I can let make .edits file for this pdb file? Thanks always in advance, Young-Jin

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whether my following data are acceptable
by Dialing Pretty 02 Jan '12

02 Jan '12

Dear All, Following is the data range of my x-ray statistics by resolution bin: FOM between 0.84 to 0.86 Phase error between 17.90 to 24.14 scale factor from 0.88 to 1.07 SigmaA from 0.85 to 0.95 #work from 2688 to 2922 #test from 133 to 157 Do these data are within the acceptable range? Cheers, Dialing

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reference model restraints
by Ursula Schulze-Gahmen 24 Dec '11

24 Dec '11

I am refining a 3.1 A structure and are trying to use model restraints for this. There are 3 molecules in the asymmetric unit of my structure. I input the high resolution structure of one molecule of the reference structure to create restraints during the refinement. From looking at the log file, it seems to me that the reference structure is aligned to only one of my molecules, but not the other 2. How can I make sure the restraints are valid for all 3 molecules. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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eLBOW generates Mogul geometries
by Nigel Moriarty 23 Dec '11

23 Dec '11

Folks For a few weeks now eLBOW has been able to generate Mogul geometries. If you have CCDC's mogul installed and accessible at the command-line, eLBOW can request Mogul provide an experimentally accurate geometry. Simply use the --mogul option at the command-line and eLBOW will query Mogul for the geometry to use to generate a restraints file and a PDB file. Stay tuned for more details in the Computational Crystallography Newsletter. Happy Holidays, Merry Christmas and Happy New Year Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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partial model in autobuild?
by Yarrow Madrona 21 Dec '11

21 Dec '11

Hello, I would like to use autobuild to start from a partial model. I have done Phaser EP with phases from MR. I can see the fourth molecule but it is not well defined and I am not exactly sure where to place it. Is it possible to run autobuild from the partial model to fill in the fourth model? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] Reflection file woes phenix/ccp4/PDB
by Machius, Mischa Christian 20 Dec '11

20 Dec '11

Robbie, Yes, the thought that the anomalous R free flags could have something to do with it occurred to me as well, so I checked. As far as I can see, the test reflections are evenly distributed between the + and - sets; they were not selected from the + or - set only. For the vast majority of the test reflections, both Bijvoet mates were measured and both were flagged properly. For some, however, only one Bijvoet mate was measured and flagged. It probably wouldn't do any harm to consolidate the test flags, discarding the few with only one measured Bijvoet mate, but I really don't see why it should be necessary to do so. For now, I have converted the reflection file into the CNS format and sent to the PDB, hoping that they will be able to deal with that one properly. Bit surprised though that no one has run into that problem before. Thanks for your suggestion. MM On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten wrote: > Hi Mischa, > > Your mtz file seems to contain 'anomalous' free R-flags (that is what I gather from Pavel's post). This is kind of weird. Do you really want I+ in the work set and I- in the test set? That would bias your R-free. If the two flags match (which I really hope), then you can leave one column out before you (re)deposit your data. This will hopefully solves the problem. > > Cheers, > Robbie Joosten > > Netherlands Cancer Institute > > On 12/15/2011 05:40 PM, Machius, Mischa Christian wrote: >> Y'all, >> >> While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing. >> >> The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928. >> >> Indeed, using this file in CCP4 fails with the message: >> "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q" >> >> The file contains anomalous data. I have no problems with files that do not contain anomalous data. >> >> Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility. >> >> When I use iotbx.reflection_file_reader, I cannot detect any anomalies. >> >> I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them. >> >> Anybody ran into this issue before? Any ideas for how to resolve it? >> >> Many thanks in advance! >> >> MM >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

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Failure in installing Phenix-1.7.3
by arka chakraborty 20 Dec '11

20 Dec '11

Hi all I am facing a problem while installing phenix 1.7.3 on Redhat Enterprise 5 OS. I have tried with fedora 3 binary as instructed in the download page and also with others but nothing works. I have tried installing from the root. Every time the error log is states that GLIB 2.4 is unavailable which is required by user/local/.. Please help! Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

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