- 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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resolve phases/fom
by "Weiergräber, Oliver H." 24 Jan '15

24 Jan '15

Hello, while compiling phasing stats for a manuscript, I came around the following question: Having run autosol (on a SAD dataset) from the command line, where to find the latest density-modified phases (with associated FOMs) _before_ the onset of model building? The PHIM and FOMM columns in the denmod_i.mtz files are obvious candidates - just want to be sure since this particular FOM does not seem to be echoed in the log files, as far as I can see. Best regards Oliver ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Reflection file editor. copying Free set from one to other mtz.
by Tarek DawoD 23 Jan '15

23 Jan '15

Unfortunately i did not find a detailed explanation for how to use reflection file editor (GUI) i just want to know if i am right and i have a questions about how it works as well 1- if i have 2 myfile-data.mtz files (for the same structure but 2 different ligands, one of them 1.9 A and the other 1.6 A) and i want to copy free set from one to the other. so i have in the (ALL Input Arrays) 2 intensity and 2 R-free flag. so what i did is to add in the (output array) one of the intensity which belongs to one and one R flag which belong to other. i was not sure how to use the other output options??? what should i check or uncheck in this particular case??? 2- How this works? suppose i have h k l (6 7 21) has flag 1 in the data.mtz file (the one i used to copy the free set to other mtz), if i will copy this to other mtz (which has no R flag of course), the program will look for (6 7 21) h k l in the other mtz to give it also flag 1. Am i right.??? 3- if i am right in number 2, Suppose the other mtz has no (6 7 21) h k l what will happen? if it is just ignoring it or assign flag 1 for other h k l which did not exist in the first data.mtz.this means it is impossible to get 100% free set similar between say the 2 mtz files in this case. thank you in advance thank you Dr Pavel and Dr Georg for your reply to my previous query TK DawoD

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Solving installation problems on network volumes in Yosemite
by Chris Richardson 23 Jan '15

23 Jan '15

I thought I’d post this in case anyone has a similar problem in the future. It’s taken me a couple of days of frustration to find the solution; maybe I can save someone else some pain. This problem only occurs when trying to install Phenix on an NFS-mounted volume in OS X 10.x, Yosemite. If this doesn’t apply to you (and I might be the only person doing this), you can happily ignore what follows. The problem: In an effort to save us from malware, OS X now adds a ‘quarantine’ attribute to downloaded files. This includes tar and compressed tar files. For most users the quarantine flag only really comes into play if the downloaded file is an application or installer package. When Yosemite untars an archive with the quarantine attribute, it adds the quarantine attribute to every file it extracts from the archive. This doesn’t present a problem if you’re extracting the archive to a local disk, or an AFP-mounted network volume. If you’re extracting the archive to an NFS-mounted network volume, it can’t store the quarantine flag as a resource fork on the file itself. Instead, it creates a ._<filename> file for each extracted file. The Phenix installer doesn’t like having an install tree full of unexpected ._ files. In some cases, such as where generate_henke_cpp.py tries to generate tables from all the files in a directory, it tries to read ._ files as normal files and dies. The solution: The solution is trivial once you know what the problem is. Remove the quarantine attribute from the tar file before extracting its contents. For example: xattr -d com.apple.quarantine phenix-installer-1.9-1692-mac-intel-osx-x86_64.tar.gz Of course, if the Phenix installer could be modified so that it doesn’t die when it finds unexpected ._ files, that would be lovely. Chris -- Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Rfree % calculation
by Tarek DawoD 22 Jan '15

22 Jan '15

Dear ALL when you start you refinment in phenix with ***.sca file, fraction of reflection in test set will be created. under options (bottom) in phenix refine, you could see that fraction of reflection in test set is 0.1 which means 10 %by looking to the PDB header for completely different structures (below) you will find different percentage but always FREE R VALUE TEST SET COUNT is around 3800. so it always take the same 3800 count regardless the number of reflections. when you look in generated mtz file after the refinment, you see under R-free-flags(+) and R-free-flags(-) either 0 or 1. what does 0 or 1 mean? thank you in advance for explaination. TKDawoD ----------------------------------------------------------------------------------------------------REMARK 3 NUMBER OF REFLECTIONS : 47312 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 24389 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1673REMARK 3 R VALUE (WORKING SET) : 0.1636REMARK 3 FREE R VALUE : 0.2084REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.21 REMARK 3 FREE R VALUE TEST SET COUNT : 3882------------------------------------------------------------------------------------------------------REMARK 3 NUMBER OF REFLECTIONS : 107005 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 56251 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1457REMARK 3 R VALUE (WORKING SET) : 0.15.34REMARK 3 FREE R VALUE : 0.1997REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.51 REMARK 3 FREE R VALUE TEST SET COUNT : 3809-----------------------------------------------------------------------------------------------------NUMBER OF REFLECTIONS : 48150 REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 25296 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT.REMARK 3 R VALUE (WORKING + TEST SET) : 0.1507REMARK 3 R VALUE (WORKING SET) : 0.1470REMARK 3 FREE R VALUE : 0.1918REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.98 REMARK 3 FREE R VALUE TEST SET COUNT : 3841

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Problems installing Rosetta
by 신인철 20 Jan '15

20 Jan '15

Hi, I am trying to install rosetta on Fedora 21. I downloaded rosetta_bin_linux_2015.02.57538_bundle.tgz and copied the unpacked whole directory under /usr/local/ and rename "rosetta_bin_linux_2015.02.57538" as "rosetta" simply. And I edited .cshrc file like: setenv PHENIX_ROSETTA_PATH "/usr/local/rosetta" setenv ROSETTA3_DB "usr/local/rosetta/main/database" But encountered the following messages: [root@localhost ~]# rosetta.build_phenix_interface nproc=8 False scons: Reading SConscript files ... Running versioning script ... Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/rosetta/main/source/SConstruct", line 172: main() File "/usr/local/rosetta/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/rosetta/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) What am I going to do? Please, help!! ------------------------------------------------- Inchul Shin School of Agricultural Biotechnology Seoul National University Seoul, KOREA 151-921 Tel: +82-2-880-4633 Fax: +82-2-873-4950 Mobile: +82-10-6215-2896 Email: ichul96(a)snu.ac.kr<mailto:[email protected]>

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Font woes in Debian with latest nightly builds
by Miguel Ortiz Lombardía 20 Jan '15

20 Jan '15

Hi, I recently updated from dev-1805 to dev-1924 (in both cases I used CentOS5 installers for a Debian testing -jessie- machine; dev-1922 gave the same problem) During installation I observed these messages: <...> updating fonts/local.conf file running mkfontdir Couldn't determine weight for Vera.pfa Couldn't determine weight for VeraMono.pfa rebuilding font cache Fontconfig error: Cannot load default config file /usr/local/phenix-dev-1922/base/bin/fc-cache: "/usr/local/phenix-dev-1922/base/share/fonts": skipping, no such directory /usr/local/phenix-dev-1922/base/bin/fc-cache: succeeded <...> I found a previous post to this list with a similar report (january 29, 2013) but there it was said that these messages could be ignored... However, when I run phenix I see these in the terminal: $ phenix Linux /usr/local/phenix-dev-1922/build/bin/phenix: 109: [: Linux: unexpected operator Fontconfig error: Cannot load default config file Phenix data directory: /home/ortiz-lombardia/Phenix (python2.7:11563): Pango-WARNING **: No builtin or dynamically loaded modules were found. Pango will not work correctly. This probably means there was an error in the creation of: '/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/base/etc/pango/pango.modules' You should create this file by running pango-querymodules. (python2.7:11563): Pango-WARNING **: pango_shape called with bad font, expect ugly output (python2.7:11563): Pango-WARNING **: pango_font_get_glyph_extents called with null font argument, expect ugly output (python2.7:11563): Pango-WARNING **: pango_font_get_metrics called with null font argument, expect ugly output (python2.7:11563): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (python2.7:11563): GdkPixbuf-WARNING **: Cannot open pixbuf loader module file '/home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos5/base/etc/gtk-2.0/gdk-pixbuf.loaders': No such file or directory (python2.7:11563): Gtk-WARNING **: Error loading theme icon for stock: Couldn't recognize the image file format for file '/usr/share/icons/gnome/48x48/status/gtk-dialog-error.png' (python2.7:11563): Pango-WARNING **: _pango_cairo_font_install called with bad font, expect ugly output ^C Indeed, it is ugly output... No readable text just little empty boxes. I can send a snapshot if required. If I run: dpkg -l \*pango\* un gir1.0-pango-1 <none> <none> (no description available) ii gir1.2-coglpan 1.18.2-3 amd64 GObject introspection data for th ii gir1.2-pango-1 1.36.8-3 amd64 Layout and rendering of internati ii libcogl-pango2 1.18.2-3 amd64 Object oriented GL/GLES Abstracti ii libpango-1.0-0 1.36.8-3 amd64 Layout and rendering of internati ii libpango-perl 1.226-2 amd64 Perl module to layout and render ii libpango1.0-0: 1.36.8-3 amd64 Layout and rendering of internati ii libpango1.0-de 1.36.8-3 amd64 Development files for the Pango un libpango1.0-do <none> <none> (no description available) ii libpangocairo- 1.36.8-3 amd64 Layout and rendering of internati ii libpangoft2-1. 1.36.8-3 amd64 Layout and rendering of internati ii libpangomm-1.4 2.34.0-1.1 amd64 C++ Wrapper for pango (shared lib ii libpangox-1.0- 0.0.2-5 amd64 pango library X backend ii libpangox-1.0- 0.0.2-5 amd64 pango library X backend - develop ii libpangoxft-1. 1.36.8-3 amd64 Layout and rendering of internati un pango-graphite <none> <none> (no description available) un pango1.0-multi <none> <none> (no description available) Also, dpkg -l \*fontconfig\* produces: ii fontconfig 2.11.0-6.3 amd64 generic font configuration librar ii fontconfig-con 2.11.0-6.3 all generic font configuration librar un libfontconfig <none> <none> (no description available) un libfontconfig- <none> <none> (no description available) ii libfontconfig1 2.11.0-6.3 amd64 generic font configuration librar ii libfontconfig1 2.11.0-6.3 i386 generic font configuration librar ii libfontconfig1 2.11.0-6.3 amd64 generic font configuration librar I would appreciate any clues to solve this issue. Cheers, Miguel

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Bug in phenix.carbo_load in latest nightlies
by Roger Dodd 20 Jan '15

20 Jan '15

Hi all, I've been using the carbo_load tool to add in GlcNAc residues to Asn side chains and have noticed that in recent nightlies there is a bug that throws up the following error message (this occurs even if carbo_load is just run in "mode 1"): Traceback (most recent call last): File "/Applications/phenix-dev-1924/build/../modules/elbow/elbow/command_line/carbo_load.py", line 705, in <module> run(args) File "/Applications/phenix-dev-1924/build/../modules/elbow/elbow/command_line/carbo_load.py", line 417, in run from elbow.saccharide import carbohydrate_classes File "/Applications/phenix-dev-1924/modules/elbow/elbow/saccharide/carbohydrate_classes.py", line 28, in <module> from phenix.ligands.DensityBlobsClassConnectivity import DensityBlobsClassConnectivity ImportError: No module named DensityBlobsClassConnectivity I get this with dev-1894 and dev-1924 but not the last stable 1.9-1692. Cheers, Roger -- Roger B. Dodd, PhD Cambridge Institute for Medical Research University of Cambridge School of Clinical Medicine Wellcome Trust/MRC Building Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY

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Molecular replacement with fixed solution
by Muhammed bashir Khan 19 Jan '15

19 Jan '15

Hi There; I want to solve the structure with molecular replacement using phaser in phenix GUI. When I get solution from the one, how I can use as it as already solution using phenix in the next run. I use the "ensamble is fixed partial solution" but seems its not working. Any suggestion will be highly appreciated. Thanks Regards -- Muhammad Bashir Khan ************************************************** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522

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sudden increase of clashscore
by Smith Lee 18 Jan '15

18 Jan '15

Dear All, In a Phenix refinement, with refinement settings as default in the graphics interface, at 2' rsrl stage the clashscore suddenly increases to more than 50, and then gradually decreases to lower than 20. Will you please tell me why this can occur? And what its effect on the refinement? Smith

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Re: [phenixbb] questions related to Phenix refinement
by Kay Diederichs 18 Jan '15

18 Jan '15

Dear Pavel, Am 18.01.15 um 07:23 schrieb phenixbb-request(a)phenix-online.org: > Date: Sat, 17 Jan 2015 20:36:30 -0800 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: Smith Lee <smith_lee123(a)yahoo.com>, "phenixbb(a)phenix-online.org" > <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] questions related to Phenix refinement > Message-ID: <54BB384E.30602(a)lbl.gov> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > Hello Smith, > >> > In the X-ray statistics by resolution bin of the Phenix.refine result, >> > there is a column "%complete". For my refinement data, I find the >> > better the resolution (from lower resolution to the higher >> > resolution), the lower the completeness (for example for 40-6 A, >> > %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, >> > %complete is 6%). >> > >> > Will you please tell me what does this "%complete" mean? why it >> > decreases in the better diffraction bin? > Completeness is how many reflections you have compared to theoretically > possible. So the higher completeness the better. Ideally (and it's not > that uncommon these days) you should have 100% complete data set in > d_min-inf resolution. Anything below say 80 in any resolution bin is > bad, and numbers you quote 6-60% mean something is wrong withe the dataset. > Given your standing in the community, the last sentence will lead many unexperienced people to believe that they should cut their data at the resolution where the completeness falls below "say 80"%. But that would be wrong. There is no reason to consider a completeness as "too low in a high-resolution shell" as long as the data in that shell are good. Particularly in refinement any reflection helps to improve the model, and to reduce overfitting. Of course, more complete is better! Nowadays there should be no reason _not_ to get >95% (>99% in high-symmetry spacegroups) completeness in the low resolution shells, unless people stick to the "collect minimum rotation range" paradigm, and get the starting angle (or the point group!) wrong. best, Kay

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FW: question regarding Table1
by SD Y 17 Jan '15

17 Jan '15

From: ccp4_sc(a)hotmail.com To: phenixbb-request(a)phenix-online.org Subject: question regarding Table1 Date: Fri, 16 Jan 2015 20:30:47 -0600 Hi Everyone, I used phenix refined pdb, mtz and original mtz in the latest version of phenix to generate Table 1 and I felt the following was not right. I am not sure of the reason. R-merge 1.193e-17 (1.036e-17) R-meas 1.688e-17 CC1/2 1 (1) CC* 1 (1) Let me know . I appreciate your comments. Regards,SDY

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questions related to Phenix refinement
by Smith Lee 17 Jan '15

17 Jan '15

Dear All, In the X-ray statistics by resolution bin of the Phenix.refine result, there is a column "%complete". For my refinement data, I find the better the resolution (from lower resolution to the higher resolution), the lower the completeness (for example for 40-6 A, %complete is 98, for 3.1-3.0 A, %complete is 60%, for 2.2-2.1 A, %complete is 6%). Will you please tell me what does this "%complete" mean? why it decreases in the better diffraction bin? For the Ramachandran restrain in the Phenix.refine, there was a recommendation that for good resolution (I forget how much exactly, maybe 2.5 A), do not use Ramachandran restrain. But for a crystal data with resolution better than 1.5 A, in the X-ray statistics by resolution bin of the Phenix.refine result, there are more rows with resolution poorer than the defined 2.5 A (for example 40-6 A,6-3 A), although the crystal has a resolution better than 1.5 A (for example 1.4 A), can I use Ramachandran restrain in the Phenix.refine in this situation? If I use Ramachandran restrain in the Phenix.refine, I find the R-work and R-free level goes up, can we say the strategy of Ramachandran restrain in my refinement was not appropriate? I am looking forward to getting your reply. Smith

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Xray / neutron joint refinement
by Anna Makal 16 Jan '15

16 Jan '15

Hi, I have just done a joint x-ray / neutron refinement in Phenix using 5PTI structure and data from PDB. The input contains H atoms, with positions as refined against neutron dataset. In the resulting model, all H atoms ended up in 'idealized X-ray' positions (C-H distance of 0.96A), just as they would if I performed refinement against xray data only with riding model for H hydrogen atoms. Is it possible to run joint X-ray neutron refinement in such a manner that final H atoms positions are based on neutron data? Regards, Anna Makal

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Phenix - Research Scientist Position
by Paul Adams 15 Jan '15

15 Jan '15

Lawrence Berkeley Laboratory Career-track Research Scientist Job ID: 80447 Division: Physical Biosciences Date Opened: 1/14/2015 https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=80447 Summary: A research scientist position is available to work on developing new methods for macromolecular structure determination and refinement with the PHENIX software system. To learn more about Phenix visit: http://www.phenix-online.org Duties: This position will develop and maintain a powerful graphical user interface for the PHENIX system, and develop code within the Computational Crystallography Toolbox (cctbx). This position will include the development of new methods for crystallographic structure determination and completion in the context of the PHENIX program. This position also has a significant responsibility for the maintenance of PHENIX automated compilation tools, web-based interfaces for software downloads and coordinating releases of Phenix to the user community. The incumbent will work under the general direction of the Principal Investigator (PI; Paul Adams) for this project. Duties will also include testing, documentation writing, and extensive interaction with users and other developers. Qualifications: Demonstrated expertise with computational methods for protein crystallography. First-author publications in the area of macromolecular crystallography. Familiarity with software development: C++ and the Python scripting language. Advanced knowledge of Python-based or similar graphical user interface development tools. Solid interpersonal skills and the ability to work in a team environment are critical. A Ph.D. in computational crystallography, biophysics, chemistry, computer science, or related field is strongly preferred. Note that this is a multi-year position that is renewed annually on the basis on performance and continued funding. Berkeley Lab addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status. Learn more at http://www.lbl.gov. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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Reducing R/R-free
by George D 14 Jan '15

14 Jan '15

Hi Phenix users, I was looking at the phenix-refine manual and it mentions running optimize_mask=true optimize_xyz_weight=true optimize_adp_weight=true I was wondering what else I could try to bring the Rw/Rf down by 1-2% if possible, just wondering if there are any other strategies I could try. Thank you, George

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phenix.pdb_as_cif
by jp d 14 Jan '15

14 Jan '15

hi,of course, i should have included the versionphenix.version_1.9-1692 the pdb has done more digging and included this comment "Aside from the asym_id, there is another way we use for the mapping, _atom_site_anisotrop.id should map(for ANSIO) to _atom_site.id(for ATOM). This is one-by-one match for each atom. If you look at the file, you see that in the ATOM section, you have ATOM 99999 N3 . U . 367 ? -23.56200 29.36600 106.68800 1.000 135.52000 N ? UC ? 11964 1 ATOM 100000 C4 . U . 367 ? -23.35700 30.62600 106.16100 1.000 133.22000 C ? UC ? 11964 1 But in the ANISO section, you have 99999 N3 . U . 367 ? 2.04230 1.43260 1.67410 -0.19220 -0.28280 -0.16500 A0000 C4 . U . 367 ? 2.00150 1.41600 1.64420 -0.1 8730 -0.28010 -0.16450 i.e. the atom No. after 99999 is inconsistent between the two sections. The ANISO should use 100000. " thanksjpd

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Importing project to Phenix
by Emilia C. Arturo (Emily) 14 Jan '15

14 Jan '15

Hello, I'd like to take a phenix project (on which I've been working successfully on the Mac where I initially created the project) from one Mac to another Mac. When I tried to use the 'Import project' tool on the new computer, I got a notification that "[...] the directory must contain the PHENIX project tracking data (a sub-directory named 'phenix' or '.phenix', and associated files)." Unfortunately, I didn't see a sub-directory named 'phenix' or '.phenix' in the folder where all my project files had been created and stored, and wasn't sure what to do about it, so I proceeded with the Import anyway, to see what would happen. On the new computer, the project was imported seemingly successfully (e.g. the project history is all there), but when I tried to Run a refinement I'd configured for this project, I got an error about the missing '.phenix' file. The error is: "Cannot open file for write: [...] No such file or directory: [...]/.phenix/project_data/refine_22.eff' Can someone help me figure out how to properly move a project from one computer to another? Thank you, Emily.

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pdb_as_cif
by jp d 14 Jan '15

14 Jan '15

hi,I am making a large deposit to the pdb. To convert it to cif i usedphenix.pdb_as_cif model.pdb it looks like the ANISOU lines lose chain information.the PDB responded with this comment "The model coordinates file you output from Phenix is not complete. In the cif format file you deposited, if you look at the cif item _atom_site_anisotrop.pdbx_auth_asym_id, i.e. the column 5 of the Aniso section, you see value for every atom is dot ("."). The _atom_site_anisotrop.pdbx_auth_asym_id is just like the chain ID in the legacy PDB format, it should be consistent with the values of cif item _atom_site.auth_asym_id in the xyz section, otherwise there is no way to map between xyz Cartesian values and aniso values that are now separated in two sections." Do you reccomend another way to convert it to cif ? Thanksjpd

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map coefficients file
by Dialing Pretty 14 Jan '15

14 Jan '15

Dear All, Will you please tell me the subfixer of the map coefficients file, or which file is the map coefficients file? Dialing

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Applications for RapiData 2015 are now open
by Thomas Eriksson 13 Jan '15

13 Jan '15

The 2015 RapiData Course on Data Collection and Structure Solution will take place at the Stanford Synchrotron Radiation Lightsource (SSRL) from May 3-8 2015. The aim of the course is to educate and train scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on sample preparation, data collection and reduction, phasing and complementary methods. For a more complete description of the course goals and format see http://www-ssrl.slac.stanford.edu/conferences/rapidata-2015/about.html The deadline for applications is February 23rd 2015. To apply follow this link: http://www-ssrl.slac.stanford.edu/conferences/rapidata-2015/apply.php Several scholarships are available from the International Union of Crystallography to cover partial travel and subsistence for Latin-American students, postdocs and junior faculty. Additional funds may be also be awarded to other participants (no restrictions) on a per need basis. Interested participants should apply for the course, and contact the organizers, enclosing a letter of recommendation from their supervisor. The Organizing Committee of RapiData2015 shall observe the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist which would prevent the participation of bona fide scientists. Ana Gonzalez and Clyde Smith -- ------------------------------------------- Ana Gonzalez <ana(a)slac.stanford.edu> Staff Scientist Stanford Synchrotron Radiation Lightsource 2575 Sand Hill Road, MS 99 Menlo Park CA 94025 Phone: (650) 926 8682 Fax: (650) 926 3292 -------------------------------------------

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Rosetta MR mmcif file subprocess failed
by Christian Roth 12 Jan '15

12 Jan '15

Hi phenix developers, I started a Rosetta MR run with a model pdb and the target sequence file. It seems that the initial MR run went fine and the Rebuilding Job for the best MR solution started. A sequence alignment is shown in the log file and than the job stops suddenly with the message Sorry: mmcif file must contain at least one data block. I can't even find a mmcif file in one of the folders. Any idea what might went wrong. Thanks in advance for your help. Christian

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6th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 12 Jan '15

12 Jan '15

Firth announcement 6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 10, 2015. Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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Rw/Rf -phenix - wwPDB Validation Server
by Haytham Wahba 11 Jan '15

11 Jan '15

1- after getting structure refined with phenix.refine to 0.145 , 0.164 Rw/Rf. and then you feel happy with that. then after using validation server from PDB you get 0.158 , 0.181 Rw/Rf. why this big jump for R free. why phenix.refine giving us low R free where in reality is not? 2- if i want to show kick map for metal binding site for publication, which map and how could i generate it. thank you for your help. HWUdeM

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A question related to phenix refine
by Dialing Pretty 11 Jan '15

11 Jan '15

Dear All, In a Phenix refinement process, the RMS angles fluctuates between 1.50 and 1.60, i..e., it does not decrease gradually. Can I accept the refinement result or not, and why? I am looking forward to getting a reply from you. Dialing.

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how can I merge denzo output files
by lbetts0508 . 10 Jan '15

10 Jan '15

I hope I am a dummy and I missed the obvious, but if I have a list of ".x" files from DENZO integration and want to merge and scale them as an mtz file in phenix or xds (I don't have access to scalepack) is there a pre-written program for that? Laurie Betts

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a question related to Phenix and Coot
by Dialing Pretty 10 Jan '15

10 Jan '15

Dear All, When I use WinCoot 0.8.1 to open a PDB file got by Phenix.refine, it comes, Fix Nomenclature Errors. Correct them? Asp [spec: 1 "A" 128 ""]PHE[spec: 1 "A" 134""]PHE [spec: 1 "A" 371""] But when I check the 3 residues, I cannot find any error. Will you let me know the issue? Dialing

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A question related to Phaser-MR (simple interface)
by Dialing Pretty 08 Jan '15

08 Jan '15

Dear All, When I run Phaser-MR, I met a fatal error "The composition you have entered has a protein/nucleic acidcontent of 132.513%, which is impossible. DECREASE your composition". Can you remind me in which black I fill the composition? And how to decrease it? Dialing

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advice on 'Fit rotatable H or D' refinement stage in phenix.refine
by Anna Makal 07 Jan '15

07 Jan '15

Hi, I would like to ask for advice concerning 'Fit rotatable H or D' refinement stage in phenix.refine. I am attempting to run unconstrained refinement on a certain high-resolution protein dataset: just XYZ and ADPs refinement for every single atom in the structure, with hydrogen atoms treated with individual approach. It turns out that when I set more then 3 macrocycles, the 'Fit rotatable H or D' refinement stage is activated in every macrocycle prior to 'XYZ individual' refinement stage. I am using version 1.9, release 1692 for windows. When I last worked with PHENIX, it was distribution 1342, and I am positive I have not come across such refinement stage. It seems that TARDY is involved at that stage. As I specifically do not want to introduce any kind of torsion angle dynamics in my current refinement, I would like to ask, what command/option shall I use to deactivate this stage of H-atom fitting in my refinement? With regards, Anna Makal

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Coot failed to launch in Phenix after CCP4 update
by Shun Liu 06 Jan '15

06 Jan '15

Dear all, After I updated ccp4 to a new version (ccp4-6.5), I found that coot failed to launch in phenix. /Applications/PHENIX-1.9-1692/Contents/phenix-1.9-1692/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/start_coot.sh: line 37: /Applications/ccp4-6.4.0/coot.app/Contents/MacOS/coot: No such file or directory Apparently it requires ccp4-6.4.0, which has been deleted. I tried to modify find_coot_command.py in phenix, but it didn’t work. Can anybody give me some suggestions so that I can figure this problem out? Thanks! Best, Shun

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Coot launch failure
by Shun Liu 06 Jan '15

06 Jan '15

Dear all, After I updated ccp4 to a new version (6.5), I found that coot failed to launch in phenix. Can anybody give me some suggestions to figure this problem out? Thanks! Best, Shun

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a question related to Phaser-MR
by Wind Sui 05 Jan '15

05 Jan '15

Dear All, In the Phenix Phaser-MR (simple interface, will you please tell me what should I input for the "sequence identities"? I am looking forward to getting your reply. Wind

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FEM maps
by Colin Levy 04 Jan '15

04 Jan '15

Dear All, when using FEM maps I notice that some solvent structure has clean (ish) 2Fo-Fc but not FEM density. Is this indicative of the water without FEM density being simply noise or is it more complicated than that? Many thanks, Colin Manchester Protein Structure Facility Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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phenix.refine reference?
by Ulrich Baumann 04 Jan '15

04 Jan '15

Dear colleagues, a very happy New Year 2015 to all of you! Is there a specific reference for phenix.refine, please? Or is it ok if we cite Adams et al., Acta Cryst D66, 213-221 (2010) or the 2011 paper on Phenix? What about Xtriage? Thanks you very much for your kind help! Best wishes, Ulrich

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a command on Phenix refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, I use the graphic phenix.refine to do a refinement, and Phenix informed me I need to have a command "refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None". Will you please tell me by graphic phenic.refine, how can I input this command? Wind

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a question related to phenix.refine
by Wind Sui 04 Jan '15

04 Jan '15

Dear All, After I finished a refinement by Phenix.refine and I closed the Phenix software, is any method I can get the exact phenix.refine window as the moment the Phenix.refine just finished the refinement? I mean by all the documents saved automatically by the Phenix.refine after it finished a refinement, how can I get the Phenix refine window once more, for the check of Log output, Run status, Results, MolProbity, Real-space correlation, Atomic properties, and sequence check? Wind

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Fw: Reading a shelx file
by Rex Palmer 25 Dec '14

25 Dec '14

Can I read a Shelx file with Phenix and output the new pdb in Phenix format? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com

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Announcement: Membrane Protein Structures 2015 Meeting (MPS 2015)
by Nagarajan Venugopalan 22 Dec '14

22 Dec '14

Posted on behalf of the organizing committee: Registration is now open for Membrane Protein Structures 2015 Meeting (MPS 2015) Location: Argonne National Laboratory, Lemont, IL, USA Dates: April 10 - 12, 2015 Accompanying workshops: Membrane Protein Technologies Location: Argonne National Laboratory, Lemont, IL, USA Date: April 9, 2015 Meeting WEBsite: http://aps.anl.gov/mps2015. _Important dates_: _Registration deadline_: February 15, 2015 (https://www.regonline.com/mps2015) _Accommodation deadline_: March 10, 2015 (http://www.aps.anl.gov/Users/Communications/User_News/2014/MPS_hotel_info.p…) Thanks Naga -- ************************************************************************ Nagarajan Venugopalan, Ph.D. GM/CA@APS, Sector 23, X-ray Science Division Bldg 436, D005 Argonne National Laboratory 9700 S Cass Ave, Argonne IL 60439 Tel: 630-252-0669 Fax: 630-252-0667 email: vnagas(a)anl.gov ************************************************************************

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29th European Crystallographic Meeting
by Igor Sabljić 22 Dec '14

22 Dec '14

Dear Phenixbb users, I am delighted to tell you the registration for the 29th European Crystallographic Meeting is open. Just to remind you ECM29 (August 23-28, 2015) is taking place in beautiful city of Rovinj in Croatia. You can find more information on our web site, and please visit, like and share our Facebook page! I hope I will see you all there! Web: http://ecm29.ecanews.org/ Facebook: https://www.facebook.com/29thEuropeanCrystallographicMeeting?ref=hl Sincerely, Igor [1] IGOR SABLJIĆ _Social networks editor_ Ruđer Bošković Institute Division of Physical Chemistry Bijenička cesta 54, 10000 Zagreb, CROATIA http://ecm29.ecanews.org [1] Facebook [2] home [3] Links: ------ [1] http://ecm29.ecanews.org [2] http://www.facebook.com/29thEuropeanCrystallographicMeeting [3] http://www.irb.hr/eng/Research/Divisions-and-Centers/Division-of-Physical-C…

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Phenix Rosetta install
by Felipe Trajtenberg 22 Dec '14

22 Dec '14

Dear all, I am trying to build the hybrid installation between Rosetta and Phenix using the rosetta.build_phenix_interface command Phenix version: phenix-1.9-1692 Rosetta version: rosetta_2014.35.57232 I have no problem in compiling rosetta alone but when I try to build the hybrid system I get the following error: False scons: Reading SConscript files ... Running versioning script ... Done. (0.0 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 172: main() File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/home/Xtal/Phenix/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd) thanks in advance Felipe

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Cross-validation when test set is miniscule
by Derek Logan 19 Dec '14

19 Dec '14

Hi everyone, Right now we have one of those very difficult Rfree situations where it's impossible to generate a single meaningful Rfree set. Since we're in a bit of a hurry with this structure it would be good if someone could point me in the right direction. We have crystals with 1542 non-H atoms in the asymmetric unit that diffract to only 3.6 Å in P65, which gives us a whopping 2300 reflections in total. 5% of this is only about 100 reflections. Luckily the protein is only a single point mutation of a wild type that has been solved to much better resolution, so we know what it should look like and I simply want to investigate the effect of different levels of conservatism in the refinement, e.g. NCS in xyz and B, group B-factors, reference model, Ramachandran restraints etc. However since the quality criterion for this is Rfree I'm not able to do this. I believe the correct approach is k-fold statistical cross-validation, but can someone remind me of the correct way to do this? I've done a bit of Googling without finding anything very helpful. Thanks Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science www.maxlab.lu.se/crystal Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com

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