June 2011 - phenixbb - phenix-online.org

rosetta fragment files
by Leonid Sazanov 16 Jun '11

16 Jun '11

Hi, I am trying to use mr_rosetta with phenix-1.7.1-743 and rosetta 3.2.1. All rosetta tests passed OK. I have several large protein chains in the starting model (already placed). So I had to get several pairs of fragment files from robetta server and list all of them in the script. Then mr_rosetta fails at the REBUILD_1 stage with the message: could not open file (fragment file), although file is definitely there. Is the reason that one can have only two input fragment files (3/9)? Can several fragment files be combined into two 3/9 ones? Thanks -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY

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IUCr satellitte
by Gloria Borgstahl 16 Jun '11

16 Jun '11

I am forwarding this information to you on behalf of Marc. Best regards, Gloria The Commission on aperiodic Crystals is organizing a * two days satellite meeting just after the IUCr Congress in Madrid: 'Aperiodic Crystals for Beginners', in Alcala de Henares, 31 August-1st September 2011. ** This school will present in a simple way the methods used for the structural analysis of Aperiodic Crystals*, namely incommensurately modulated phases, incommensurate composites crystals and quasicrystals. It is intended for beginners in the field and will alternate step by step lectures and tutorials. You will find more information in the attached leaflet or on the web site * **http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html*<http://sig3.ecanews.org/aperbeg2011/aperbeg2011.html> Best regards Marc de Boissieu -- -- Marc de Boissieu Sciences de l'Ingéniérie, des Matériaux et des Procédés (SIMaP) Grenoble INP, CNRS, UJF 1130 rue de la piscine BP 75 38402 Saint Martin d'Hères Cedex (France) Tel 33 (0)4 76 82 67 03 Fax 33 (0)4 76 82 66 44 e-Mail: *Marc.de-Boissieu(a)simap.inpg.fr* <Marc.de-Boissieu(a)simap.inpg.fr>

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refinement of twinning dataset
by Ms Chiung-Wen Chang 14 Jun '11

14 Jun '11

hi everyone i have some issues with the refinement of my twinning dataset the dataset has 2.1 A resolution the twin fraction is around 0.43 i did not detwin and ran the refinement directly (with twinning refinement) The attached is the polygon so far the R: 0.1905 Rfree: 0.21 RMSD angles: 0.91 bonds: 0.006 clashscore: 28.176 average B: 45.8 are the clashscore and Average B in the reasonable range ? because the pattern of the polygon is looked wired what can I do more to get them better ? thanks for your help : ) Mary

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[Fwd: Re: elbow.join_cif_files error]
by Maia Cherney 14 Jun '11

14 Jun '11

Hi, I run command line elbow.join_cif_files ligand1.cif ligand2.cif ligand3.cif. As I understand, ligand1.cif and ligand2.cif are cif files present in the directory, the ligand3.cif should be made after joining the first two cifs. I get this error Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 245, in <module> run(filenames, target) File "/usr/local/phenix-1.7.1-743/elbow/elbow/command_line/join_cif_files.py", line 145, in run include_commented_restraints=1, #include_commented_restraints, File "/usr/local/phenix-1.7.1-743/elbow/elbow/formats/monomer_library_cif_parser.py", line 185, in parse_cif raise RuntimeError('long tmp') RuntimeError: long tmp Maia

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Using rosetta for domain search with partial model solution
by Daniel Mattle 14 Jun '11

14 Jun '11

Dear Phenix Developers, Is there a possibility within rosetta searching only for a domain (using hhr files) while one has already a partial pdb model lacking a particular domain? I was unable to find this feature? Do you have implemented that? If this is not implemented yet, would it be possible to add this feature? Best, Daniel

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sca file & anomalous difference map: understanding the story from the scratch,
by Haytham Wahba 13 Jun '11

13 Jun '11

i am new user first Q?? with HKL2000 (with scale anomalous option: ON) the output.sca file is like that (for example): 1 -985 38.064 89.066 51.543 90.000 100.446 90.000 p21 0 0 2 3433.6 77.1 0 0 3 735.6 14.0 0 0 11 1564.7 25.4 0 0 12 5643.2 88.3 0 0 13 541.5 9.7 0 0 14 1701.0 27.4 0 1 1 2060.5 47.0 0 1 2 4115.3 75.3 4257.1 97.5 0 1 3 8782.0 280.6 7728.9 173.9 0 1 5 1760.8 28.4 1778.5 33.5 0 1 6 6650.2 122.2 6843.2 126.0 0 1 7 1935.8 36.6 1794.2 29.1 is that one is merged or unmerged????? if i compare with the output.sca with scale anomalous option (off): 0 0 2 3444.4 77.3 0 0 3 734.9 14.0 0 0 4 1705.0 27.5 0 0 5 2693.8 49.4 0 0 6 8383.1 153.9 ------------------------------------------------------- second Q? using output.sca (with scale anomalous option on) for molecular Replacment generate MR.mtz which shows F,SIGF in data labels under phenix.refine the generated (refine_data.mtz) shows: I-obs(+),SIGI-obs(+),I-obs(-),SIGI-obs(-) what is going on in first and second run? ----------------------------------------------------------------- third Q? i want to generate anomalous difference map using phenix.map but when i use output.sca (with scale anomalous option: ON) as reflections file the data label show ((i-obs,sigma)) how to convert this SCA file (if it is merged) to unmerged sca file to creat anomalous difference map for protein contains Br, Sn and Sulpher?? i want to see peaks for these 3 elements to confirm their presence. N.B: the wavelenght was 1.00900 N.B: resolution 1.78 A N.B: i use GUI phenix i am sorry for that long e-mail. thank you in advance haytham wahba biochemi UdeM Canada

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again: XDS files
by Kay Diederichs 11 Jun '11

11 Jun '11

Hi everybody, it has been possible for many years to produce MTZ files from XDS data; I do that all the time, going through xdsconv (filetype CCP4, or CCP4_F, or CCP4_I depending on what type of data one wants - see the docs). This works very well. Others use the xds/pointless/scala/truncate route or the older xds/combat route or ... - as long as it works that's fine. Thus my message was not meant to discourage people from doing that. Rather I see a new possibility to go _directly_ into Phenix, which clearly may be desirable in some cases (less programs involved means less work and maybe fewer bugs), and I wanted to describe the options. If Autosol can use unmerged data (which was new to me), then going from XDS through pointless to a unmerged MTZ file should be the easiest and best way (http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Pointless). best, Kay

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installation problem on Ubuntu
by Daqi Tu 11 Jun '11

11 Jun '11

Hi, I was trying to install the 32 bit Phenix-dev-782 or the official release 1.7.1-743 onto a virtual ubuntu 10.04 32-bit machine. Both of them failed with this error: /bin/tar: ./build/intel-linux-2.6/base/bin/wx-config: Cannot create symlink to `/net/longnose/scratch2/phenix/phenix-dev-782/build/intel-linux-2.6/base/lib/wx/config/gtk2-ansi-release-2.8': Operation not supported /bin/tar: Exiting with failure status due to previous errors /mnt/hgfs/windubuntu/phenix-installer-dev-782/bin/install-from-binary: 352: /usr/local/phenix-dev-782/build/intel-linux-2.6/base/bin/python: not found Any comments? Thanks. Daqi Tu

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low-resolution refinement
by Jennifer Weinreich 11 Jun '11

11 Jun '11

Hello, I am refining a low-resolution structure of a protein complex (4.4 Å). The structure was solved by molecular replacement using structures of individual subunits as search models. Here are some of the questions that I have (and also points raised by our reviewers.) Your thoughts and suggestions on how to proceed with this will be very much appreciated. 1) The B factors are very high (300-400). The Wilson B calculated by phenix.xtriage is ~200. Is this something I should be concerned about? 2) What is the expected (or 'acceptable') gap between R and Rfree at this resolution. (Current R = 27%, Rfree = 33%) Does this sound reasonable? 3) It has been suggested to me that I should try adding riding hydrogens during the last round of refinement (to help with geometry). Is this something I should do? And if so, should I remove them when I deposit the file to the PDB. (Hydrogens at 4.5A are probably going to raise a lot of eyebrows... 4) What is the 'acceptable' coordinate and phase errors for structures at this resolution. (They are now 1.4Å and 36˚) 5) I have been using secondary structure restraints during the refinement, which seems to work reasonably well. I also tried refinement using reference model (the structure of the individual components). But refining with reference models seems to result in high RMSD bonds/angles. Is there something I'm missing? Short of growing better crystals, are there other strategies I should be trying with the existing data? Thank you! Jenn

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XDS files in Phenix
by Kay Diederichs 10 Jun '11

10 Jun '11

Dear Ralf, dear all, Recently there was some discussion about reading of XDS output files here on PhenixBB, and I'd like to try and shed some light on this. First, I'm glad to hear this is possible in principle! However, the caveat is, that three types of "native" output files are written by programs from the "XDS program package": a) the main program ("xds", or "xds_par") writes only one type of file, called XDS_ASCII.HKL. This has _unmerged_ observations, and this is therefore currently _unsuitable_ for reading by Phenix programs (since the Phenix routine expects merged, unique reflections). If this is nevertheless tried, I see the danger that Phenix might "eat" all observations of a unique reflections except one, possibly without telling about this problem (? - I didn't try!!) - this is definitely not what you want! b) the program "xscale" can write an output file with unmerged observations. This is the default, and corresponds to MERGE=FALSE in XSCALE.INP . As for a), this is also not what you want! c) the program "xscale" can write an output file with merged observations. This is not the default, but can be obtained by using MERGE=TRUE in XSCALE.INP . This is what you want to read with Phenix programs. Thus only possibility c) will give you a "native XDS" file that is ready to be read by Phenix programs. In addition to this possibility, one can use of course use "xdsconv" to go from XDS_ASCII.HKL (or any file written by "xscale") to a (non-native XDS) filetype that Phenix programs can read. The most general should be to write a MTZ file, but CNS/X-PLOR type files can also be produced. If someone would implement merging of observations in the Phenix routines (it should be straightforward: negative sigmas indicate that observations should not be used; otherwise the standard formulas could be used; symmetry-related reflections of course have to be handled correctly but they are already sorted by unique reflection), then possibilities a) and b) would also work. But until this is implemented, c) should be used. Hope this helps, Kay P.S. The filetypes and everything else around XDS is accurately documented at http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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