- phenixbb - phenix-online.org

Re: [phenixbb] making coarse maps
by Terwilliger, Thomas Charles 30 Jan '15

30 Jan '15

Hi Scott, You can use the reflection file converter in the GUI to write out map coefficients with any resolution cutoff that you like. That may be the easiest. Alternatively you can take your refined model and use phenix.maps to calculate a map at any resolution that you like without further refinement. You might also consider just adjusting the sharpening on your map which will have something of the same effect as cutting the resolution. All the best, Tom T ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Scott Horowitz [horowsah(a)umich.edu] Sent: Friday, January 30, 2015 6:09 AM To: PHENIX user mailing list Subject: [phenixbb] making course maps Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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making course maps
by Scott Horowitz 30 Jan '15

30 Jan '15

Hi all, Although I realize this sounds counterproductive, I'd really like to be able to make a map with grid spacing that is around 3 A, even though I have a ~2 A structure, and I don't want to have to cut data before refinement. However, it seems like the max number I can give to the grid resolution factor is 0.5. Is there a way to break this limit without it crashing? Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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calculating map from pdb
by Scott Horowitz 29 Jan '15

29 Jan '15

Hi all, I was wondering how to quickly back-compute an electron density map from a PDB using phenix from the command line. I'm assuming it's not hard, but I can't find documentation that would lead me to it. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226

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question about mmtbx.prepare_pdb_deposition
by Gerwald Jogl 28 Jan '15

28 Jan '15

Hi, How does the sequence file for this tool have to be formatted when there are more than one proteins/sequences in the asu? Does the program match this automatically? Thanks, Gerwald

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Old Phenix jobs
by Mark A Saper 27 Jan '15

27 Jan '15

I was looking at some old Phenix GUI jobs run in Sept 2010 with Phenix version 1.6.4. Can these jobs be opened with the current (dev-1932) GUI ? When I try to restore a refinement job opens, a window opens with the parameters used for the job, but no tab with the results. When I try to restore other jobs, I receive an error when trying to open them: “UnicodeDecodeError : ‘utf8’ codec can’t decode byte 0x81 in position 35: invalid start byte”. Another thing I noticed about some of these jobs was that there are *.libtbx_info files in the phenix/tmp subdirectorty that are >100 Mbytes, even one that is 1.2 Gbytes! Can these files be deleted. I only see such large files for one particular structure. Any info about this would be helpful. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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R/ R free (overall) and R/Rfree (for highest resolution shell)
by George Devaniranjan 26 Jan '15

26 Jan '15

Hi, I calculated/validated several PDB structures in Phenix.Validation (GUI) The R/R-free (overall) is 0.1271/0.1348 Further down I looked at the R/R-free for the highest resolution shell. Its 0.2538/0.2446 I am curious why the R-free for the *highest resolution shell* seems to be LOWER than R (work). Am I reading the information wrong? PDB: 3QL9 Thank you, George

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Re: [phenixbb] phenixbb Digest, Vol 110, Issue 12
by Kay Diederichs 25 Jan '15

25 Jan '15

Patrick, see my posting at https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;f6735c0c.1501 . The "Advanced Search" interface of the RCSB also lets you search for resolution range and many other criteria. "Text search" won't help you much if you are searching specific numeric values, I guess. best, Kay Am 25.01.15 um 09:21 schrieb phenixbb-request(a)phenix-online.org: > Date: Sat, 24 Jan 2015 09:41:36 -0800 > From: Patrick <patrick.cossins(a)inbox.com> > To: PHENIX list <phenixbb(a)phenix-online.org>, ccp4bb(a)jiscmail.ac.uk > Subject: [phenixbb] extracting PHENIX structures > Message-ID: <5D1147D5283.0000050Apatrick.cossins(a)inbox.com> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > not directly related but I wanted to know how to extract from the PDB all the PHENIX/CCP4 refined structures currently deposited. > > Do I use the "text" search in quarry to get the result or do I use the software? > > I tried it for both but seems to give different results (no's). > > I tried for another refinement package (shelx) and same, different no's > > Using software, and looking for contains 320 > > using text search 130 > > Is there another way to get structure of a certain resolution ? > > Patrick

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extracting PHENIX structures
by Patrick 24 Jan '15

24 Jan '15

Hi, not directly related but I wanted to know how to extract from the PDB all the PHENIX/CCP4 refined structures currently deposited. Do I use the "text" search in quarry to get the result or do I use the software? I tried it for both but seems to give different results (no's). I tried for another refinement package (shelx) and same, different no's Using software, and looking for contains 320 using text search 130 Is there another way to get structure of a certain resolution ? Patrick ____________________________________________________________ Can't remember your password? Do you need a strong and secure password? Use Password manager! It stores your passwords & protects your account. Check it out at http://mysecurelogon.com/password-manager

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Crystallography Workshop in South America - CCP4 / Institut Pasteur de Montevideo 2015
by Alejandro Buschiazzo 24 Jan '15

24 Jan '15

Dear colleagues, We wish to remind you about the upcoming Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). Dates: April 6 - 16, 2015 Invited speakers and tutors: Alejandro Buschiazzo, Montevideo, Uruguay Kay Diederichs, Konstanz, Germany Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Victor Lamzin, Hamburg, Germany Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Rob Nicholls, Cambridge, UK Randy Read, Cambridge, UK William Shepard, Paris, France Pavol Skubak, Leiden, the Netherlands Clemens Vonrhein, Cambridge, UK This edition will count with an optional introductory day. A Scientific Satellite Symposium will take place during the course. Sponsored by the Insttitut Pasteur and the Institut Pasteur International Network, this symposium will gather top research scientists from the Pasteur Network, who will discuss about Structural Biology in the study of infectious diseases: Pedro Alzari and Michael Nilges (Inst Pasteur, Paris), Beatriz Guimaraes (Fiocruz, Parana) and Joo Hwan No (Inst Pasteur, Korea), together with several scientists from Inst Pasteur Montevideo. Please find the program of the Workshop and Satellite Symposium, the application form and further contact information, at www.pasteur.edu.uy/mx2015 <http://www.pasteur.edu.uy/mx2015> The site will be updated regularly, stay tuned. We acknowledge the support from the Reseau International des Instituts Pasteur (RIIP); the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Applicants: 24 students will be selected, aiming at advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site <http://www.pasteur.edu.uy/mx2015> for details on application procedures. The application deadline is February 16, 2015. The results will be announced by March 6. Please address further inquiries to: mx2015(a)pasteur.edu.uy <mailto:[email protected]> Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom We look forward to welcoming you soon in Montevideo! -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Problem during refinement
by Almudena Ponce Salvatierra 24 Jan '15

24 Jan '15

Dear all, I have partially rebuilt my model after autosol and now I would like to submit it for refinement to Phenix refine. However when I do so, even though the R factors go down when I have a look at the result, it just looks awful! All the model is placed out of the electron density map, plus the electron density map doesn't look anymore like a 3 A one, but just like sausages. Why is this happening? The truth is I have no idea... What I do is to provide Phenix refine with overall_best_refine_data.mtz (coming from autosol) as phases, x Ray data and x Ray r free data. Additionally, the starting model and the sequence. Any suggestions are more than welcome. Thanks a lot in advance. Best wishes, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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