January 2012 - phenixbb - phenix-online.org

Real_space_refinement at low resolution question
by fulvio saccoccia 20 Jan '12

20 Jan '12

Dear phenix users, I was wondering if it could be correct to exclude the real_space_refinement step working with a 3.3 A resolution map: I noted that in every real_space_refinemet step phenix told me that it was not useful. How can I exclude the routine from the command line? I am using 1.7.3-928 version. Fulvio Saccoccia, PhD student Dept. of Biochemical Sciences Sapienza University of Rome

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problem converting PDB file to mmcif for deposition
by Salameh, Mohd A., Ph.D. 20 Jan '12

20 Jan '12

Hi Everybody, I encountered a problem recently in converting my PDB file to mmcif using the pdb_extract tool in rcsb. It simply writes out an empty file!! I wonder if any of you have faced such a problem before and know the solution!! I carefully examined the PDB file header and I couldn't really find a reason why this PDB failed to be converted. I only use PHENIX for molecular replacement and refinement. I used the default TLS refinement so I assume the whole structure will be refined as a group. I hope somebody is familiar with this can help me out. Thank you very much, Mohd

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real space correlation
by Jerome Nwachukwu 19 Jan '12

19 Jan '12

Hi: I am trying to run phenix.real_space_correlation from the command line and received the following error message. Is there a specific syntax i should use? Thank you, -Jerome Syntax error: expected "=", found "Date" (file "3_refine_001.pdb", line 1) Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/command_line/real_space_correlation.py", line 9, in <module> command_name = "phenix.real_space_correlation") File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/real_space_correlation.py", line 332, in cmd_run track_unused_definitions = True) File "/usr/local/phenix-1.7.1-743/cctbx_project/libtbx/phil/__init__.py", line 1718, in fetch assert source.name == self.name AttributeError: 'NoneType' object has no attribute 'name'

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noisy sa-omit maps in solvent region.
by Francis E Reyes 19 Jan '12

19 Jan '12

Hi phenixers I'm calculating a composite sa-omit map for my entire molecule at 4 A. While my molecule more or less has density (very good for backbone, not so much for sidechains), the solvent region seems to be particularly noisy. Is this the normal experience for composite sa-omit maps at this resolution? I'm particularly interested in what autobuild does when it 'stitches' the individual maps together, is it a direct stitch of the 2fo-fc's after refinement or is there some kind of real space density modification involved? Or a combination of both? Any suggestions appreciated, F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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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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