- phenixbb - phenix-online.org

where is the fo-fc omit map?
by Yu, Hongjun 06 Mar '12

06 Mar '12

hello, It is so good that phenix can caculate sa-omit map so easily. But I am new to this. When I finish caculating, I can only get acess to 2fo-fc map whe I use coot to open the file: resolve_composite_map.mtz . How can I open the fo-fc omit map? I notice this from phenix.autobuild manual page "Note 1: be sure to use the weights in both resolve_composite_map.mtz and omit_region.mtz". I don't understand this because the omit_regin.mtz seem to be the omit box I specify. Is this correlated with my problem? Any advice is appreciated. Thank you in advance! Sincerely, Hongjun

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phenix.get_cc_mtz_pdb but allow for atom selections.
by Francis E Reyes 06 Mar '12

06 Mar '12

It'd be wonderful to pass in an atom selection (say backbone, or ligand or what have you) into phenix.get_cc_mtz_pdb . Is this functionality available in some other phenix util? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Batch conversion
by Theresa H 06 Mar '12

06 Mar '12

Hi all How can I use ADXV to batch conversion of diffraction image to tiff format? Would like to put about 20 of them in Powerpoint slides. Thank you. Theresa

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fwd: Reminder: CCP4 summer school at APS, in USA
by Nathaniel Echols 02 Mar '12

02 Mar '12

FYI, Paul Adams and Tom Terwilliger will both be presenting at this workshop. ---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Cc: Date: Fri, 2 Mar 2012 14:22:53 -0600 Subject: Reminder: CCP4 summer school at APS, in USA Dear Colleagues, This is a reminder that the deadline for applications for the 5th annual CCP4 Summer School “From data collection to structure refinement and beyond” is April 17, 2012. The school will take place from June 19 through June 26, 2012 at the Advanced Photon Source (APS) near Chicago. There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2012/index.php The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: Sanishvili, Ruslan Sent: Monday, December 19, 2011 11:39 AM To: 'phenixbb(a)phenix-online.org' Subject: Annual CCP4 summer school in USA, at APS, June 19-26 Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 19 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 17. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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xtriage output
by wtempel 02 Mar '12

02 Mar '12

Hello, this question is about the summary of xtriage output. I submitted merged scalepack intensity in space group P3. From scaling, the apparent point group is P622. H-tests for all three applicable twin laws indicate twin ratios around 45%. Does this merely indicate underestimated symmetry? STDOUT ends with this nugget: <stdout> The results of the L-test indicate that the intensity statistics Show more centric character than is expected for acentric data. </stdout> My questions: 1. What if anything should I infer about twinning from this last sentence? 2. What other data defects could this sentence indicate? Many thanks, Wolfram Tempel

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DEN refinement under phenix
by Melania Strycharska 02 Mar '12

02 Mar '12

Hi All, I was wondering whether anybody has successfully run the DEN refinement under phenix yet. I am having some problems with my scripts stalling without any error messages. What sort of reference models do people use? The following issues I am not quite clear on: - if I don't have a reference model should I call on my current pdb where the script calls for a reference model? - is it ok to use a single domain as a reference model or is it not enough to get the whole protein refined? - is it possible to use more than one reference model; in a case where I had structures of each domain solved separately? - can a reference model be a different protein or does it have to have the same sequence? Thanks a lot!

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Rfree refuse to come down
by #HEW KAI LI KELLY# 02 Mar '12

02 Mar '12

HI, I have a few questions about a dataset that I am working on currently. So I ran Xtraige and it tells me that other than pseudoNCS, there is no other problems like twinning etc. And then I used autoMR and Phaser from Phenix to run molecular replacement with a the structure of the same protein (but that is with DNA bound). The TFZ is more than 9 after from both the runs. Autobuild managed to build the 4 molecules in my ASU (Rfactor/Rfree = 28/32 for a resolution of 2.4A). But because there are some clashes and outliers in the Ramachandran Plot etc, I started to manually refine them in coot. In addition, there is a loop that is unable to fit into the density, so I chopped about 10 residues off each molecule in the ASU. However, as I started to refine the model from AutoBuild, my Rfree begins to climb. So currently, I am at Rfactor/Rfree=27/36. I don't know if there is anything wrong with I had done. So many thanks in advance for your advices on this!! Warmest Regards, Kelly Hew Nanyang Technogical University School of Biological Sciences Division of Structural Biology & Biochemistry Address : #07-01, IMCB, 61 Biopolis Drive, Proteos, Singapore 138673 Telephone (O): +65 65869673 Telephone (HP): +65 98713553

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Fwd: Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 02 Mar '12

02 Mar '12

Sue: I am not sure they are being included... I have the option checked, but the R values and difference maps tell me otherwise Pavel: A bug? That would be consistent with the behavior I observe. Even when I enable refinement with hydrogens individual or riding, i see essentially no difference in maps or Rfree values. -- Yuri Pompeu

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Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 02 Mar '12

02 Mar '12

Dear users, I am refining a 400 aa protein with data out to 1.16 A (real data). I am almost finished with refinement. I have good geometry, complete model and ligands Rw 0.11 Rf 0.13. Difference maps seem to be asking for more. See attached screen shot.Both maps 2Fo-Fc (non-filled) and Fo-Fc are contoured at 3 sigma. How should I handle this? I have used hydrogens all along (riding). Thanks for your time -- Yuri Pompeu

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phenix.reciprocal_space_arrays question
by Michael Thompson 01 Mar '12

01 Mar '12

Hi All, I have a very simple question about phenix.reciprocal_space_arrays. I apologize if this is obvious, but I could not find any info in the documentation or the bb archives. I just want to make sure that I am actually doing what I think I am doing. If I provide phenix.reciprocal_space_arrays with an .mtz file containing Fobs and a .pdb file for which I would like to calculate Fmodel and PHImodel, will the resulting Fmodel (and Fcalc, Fmask, Fbulk, etc.) be scaled to the Fobs from the input .mtz? Thanks for the help! Mike T. -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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