- phenixbb - phenix-online.org

scattering factors
by Goragot Wisedchaisri 20 Jun '11

20 Jun '11

Hi, I am new to Phenix but I have used Solve/Resolve in the past. I am currently using Phenix 1.6.2 and I have electron diffraction data to ~2A from a 300kV electron microscope that I would like to use Autobuild and phenix.refine to iteratively rebuild and refine my partial structure. I have a file containing electron scattering factors for 300kV EM that has been used successfully for refinement with CNS before for electron diffraction data. How can I tell Phenix to use electron scattering factors during refinement? I think currently Phenix has 4 choices for X-ray and neutron scattering factors but not for electron scattering. Is there a good way to implement electron scattering factors into phenix library? Any suggestions are welcome. George Wisedchaisri

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phenix.validate ? Or RSCC from command line?
by Francis E Reyes 20 Jun '11

20 Jun '11

Phenixers Is there a great phenix cmd line utility that computes a real space correlation for each residue given model and data? I'll take a .py if necessary. Thanks! --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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Errors in latest build dev-790
by Yuri 19 Jun '11

19 Jun '11

Dear phenixers, I ran into some errors after my last upgrade. First, I noticed that all of the data plots are gone in the GUI, instead I get a message that says :plotting disabled due to missing library. Second I was running phenix.refine and got the following message, they may be related I am not positive: AttributeError : 'RefinementStatsPlot' object has no attribute 'null_fmt' Traceback (most recent call last): File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Runtime.py", line 172, in OnUpdate self.propagate_event(event, "OnUpdate") File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Runtime.py", line 228, in propagate_event fn(event) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 536, in OnUpdate self.stats_plot.update_stats(callback.data) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 796, in update_stats stats.bs_ave) File "/home/local/UFAD/yuri.pompeu/Desktop/PHENIX_installation/phenix-installer-dev-790/phenix-dev-790/phenix/wxGUI2/Programs/Refine/Output.py", line 809, in set_plots ax1().xaxis.set_major_formatter(self.null_fmt) AttributeError: 'RefinementStatsPlot' object has no attribute 'null_fmt' Platform info: __FILE__ = /net/anaconda/scratch1/phenix/phenix-dev-790/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = Jun 17 2011 __TIME__ = 04:12:36 __x86_64__ __linux __GNUC__ = 3 __GNUC_MINOR__ = 4 __GNUC_PATCHLEVEL__ = 2 boost::python::cxxabi_cxa_demangle_is_broken(): false __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 61 __SSE2__ = 1 BOOST_LIB_VERSION = 1_47 PY_VERSION = 2.7.2 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 gnu libc version: 2.5 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG os.name: posix sys.platform: linux2 sys.byteorder: little platform.platform(): Linux-2.6.18-238.12.1.el5-x86_64-with-redhat-5.6-Tikanga platform.architecture(): ('64bit', 'ELF') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 2 Memory total: 3,692,077,056 Memory free: 16,236,544 import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å -- Yuri Pompeu

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phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

I just realized it is under Comprehensive Validation! -- Yuri Pompeu

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phenix.model_vs_data
by Yuri 17 Jun '11

17 Jun '11

> I would refine in parallel with and without the twin law and check > the > resulting maps and R-factors. > I had a case where the twin fraction was 0.06, which I expected to be > negotiable. When I included the twin law in refinement, my R-factors > dropped dramatically. >This is what phenix.model_vs_data does: it runs Xtriage internally and >tries all suggested twin laws, scores the results by R-factor and > prints >out the verdict: >phenix.model_vs_data model.pdb data.mtz >phenix.model_vs_data: >http://phenix-online.org/documentation/model_vs_data.htm >Pavel. Is this accomplished in polygon in the GUI? -- Yuri Pompeu

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General Questions about Joint x-ray/neutron refinement
by Louis Lazar 17 Jun '11

17 Jun '11

Developers/all: I have been running some Joint X/N jobs, and I have some questions that perhaps you can help me with. First, doing joint refinement gave a total of 53 waters (thanks to ordered_solvent=true), yet the electron density seems to show that there are several more waters that are actually present (however it should be noted that there is no nuclear density associated with those waters, and in some cases no nuclear density associated with the 53 that were chosen by ordered_solvent=true). Should I add in manually to the electron density what I believe are these extra waters, or simply ignore them? Second, when I try to real space refine any of the residues, I get an error message telling me about exploding atoms. What is the cause of this message, and is it possible to real space refine any of these residues and specifically the hydrogen atoms associated with them. Third, during the joint refinement run, I chose to refine occupancies of all atoms. This breaks down into several questions: A) Should I be refining occupancies at 2.0 A resolution (of the neutron structure; 1.05A for the X-ray)? B) How does Phenix go about refining occupancies of hydrogen/deuterium sites? C) If the resulting occupancies result in values of, for example, 60% deuterium and 40% hydrogen, am I to presume that deuterium presence is significant if the nuclear density looks "good". At what point of deuterium occupation (while examining the nuclear density), would I say that there is likely no deuterium present (or that it is insignificant)? Hopefully all of these questions make sense, and if I need to clarify anything, please let me know. Thanks so much in advance for the help, I appreciate it as always. Regards, Louis

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tls group and anisotropic
by ChenTiantian 16 Jun '11

16 Jun '11

Dear Phenixers, I refined my structure with TLS, I did not mean to refine it with anisotropic strategy, but I got ANISOU record. As the manual metioned, when doing TLS refinement, It always happens like this. What does this ANISOU record mean ? Does that mean TLS is a grouped anisotropic refinement? Tiantian -- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai, 201203, P.R. China

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no density on the anchored proteins
by zhangh1＠umbc.edu 16 Jun '11

16 Jun '11

Hi, I am using phenix.refine to calculate the map of the 50S RNA (1FFK). It is weird that there is no density on the anchored proteins even for the Fc map. Following is the code I am using: phenix.refine ${f}.pdb ${f}.mtz main.number_of_macro_cycles=0 xray_data.high_resolution=${res} xray_data.r_free_flags.generate=True export_final_f_model=mtz Thanks for any advice! Hailiang

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Re: [phenixbb] rosetta fragment files -- adjusting residue numbers to combine them
by Thomas C. Terwilliger 16 Jun '11

16 Jun '11

Hi Leonid and others wanting to use phenix.mr_rosetta with large chains, After looking at the Rosetta code and conferring with Frank DiMaio from the Baker laboratory... You can paste several fragment files together to represent your entire chain, but you need to edit all but the first one to set the position in the sequence file that each set of fragments goes with. Here is a little script that will take a fragments file that you have created that started with residue 651 and edit it in a way that you can just add to the end of your fragments file for residues 1-650. Run it with: phenix.python adjust_robetta_resid.py \ fragments_in fragments_adjusted 651 -------------------------------- # adjust_robetta_resid.py # use: phenix.python adjust_robetta_resid.py fragments_in fragments_adjusted 651 # to adjust the first residue of fragments_in to be 651 import sys args=sys.argv[1:] if len(args) != 3: print "USE: phenix.python adjust_robetta_resid.py fragments_in fragments_adjusted <start_resno>" sys.exit() file_in=args[0] file_out=args[1] start_resno=int(args[2]) print "Copying %s to %s offsetting start residue number to %d" %( file_in,file_out,start_resno) f=open(file_out,'w') new_resno=0 for line in open(file_in).readlines(): if line.find('position:') > -1 and line.find('neighbors:')>-1: spl=line.split() current_resno=int(spl[1]) new_resno=current_resno+start_resno print "Residue %d changed to %d" %(current_resno,new_resno) spl[1]=" %d " %(new_resno) new_line=" ".join(spl) else: new_line=line print >>f, new_line.rstrip() f.close() -------------------------------- I will add this to phenix as "phenix.adjust_robetta_resid" as well. However...there still is a problem if you have multiple chains...as mr_rosetta has only one set of fragments files the same fragments files are being applied to all your chains. I will add a way to specify which fragments files go with which chains. All the best, Tom T >> [phenixbb-bounces(a)phenix-online.org] On Behalf Of Leonid Sazanov [sazanov(a)mrc-mbu.cam.ac.uk] >> Sent: 16 June 2011 13:11 >> To: phenixbb(a)phenix-online.org >> Subject: [phenixbb] rosetta fragment files >> >> 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 >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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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 10 Jun '11

10 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 10 Jun '11

10 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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Possible Twinned data
by Yuri 10 Jun '11

10 Jun '11

Dear Peter, I sent you my log file off list. I realize now that p43 21 2 doesnt allow for twil law. I reprocessed my data in P222 and P4, dont know if it was the right move, but xtriage now gives me the possible PM and M twin laws, respectively. (Would be happy to send you those log as well). If anyone has input on this issue please join in. I am not greatly experienced on twinned crystals. cheers, -- Yuri Pompeu

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Fragment library for mr_rosetta
by riya doreen 09 Jun '11

09 Jun '11

Hi Everyone, I am trying to generate a fragment library for my sequence of interest to use with mr_rosetta. The Robetta server has a sequence limit of 650 amino acids. For longer sequence, will it make sense to divide the sequence into 650 amino acid fragments and generate multiple fragment files ? Thanks Thanks

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Possible Twinned data
by Yuri 09 Jun '11

09 Jun '11

Hello phenixers, I am a little bit at loss since this is the first time I have encountered this situation. I just collected preliminary data on a ligand soaked crystal. It goes to about 1.85 A. The centrics and acentrics reflections tests look a little deviant from ideal untwinned. I was looking at my xtriage log file and it seemed to me like I have some twinned fraction. Phenix says not. I realize too my completeness is not good. Any educated insight would be helpful as I have never dealt with twinning (if this actually the case). Log file section: Wilson ratio and moments Acentric reflections <I^2>/<I>^2 :1.650 (untwinned: 2.000; perfect twin 1.500) <F>^2/<F^2> :0.839 (untwinned: 0.785; perfect twin 0.885) <|E^2 - 1|> :0.649 (untwinned: 0.736; perfect twin 0.541) Centric reflections <I^2>/<I>^2 :2.099 (untwinned: 3.000; perfect twin 2.000) <F>^2/<F^2> :0.749 (untwinned: 0.637; perfect twin 0.785) <|E^2 - 1|> :0.703 (untwinned: 0.968; perfect twin 0.736) NZ test (0<=z<1) to detect twinning and possible translational NCS ----------------------------------------------- | Z | Nac_obs | Nac_theo | Nc_obs | Nc_theo | ----------------------------------------------- | 0.0 | 0.000 | 0.000 | 0.000 | 0.000 | | 0.1 | 0.052 | 0.095 | 0.171 | 0.248 | | 0.2 | 0.126 | 0.181 | 0.285 | 0.345 | | 0.3 | 0.197 | 0.259 | 0.371 | 0.419 | | 0.4 | 0.271 | 0.330 | 0.440 | 0.474 | | 0.5 | 0.334 | 0.394 | 0.499 | 0.520 | | 0.6 | 0.394 | 0.451 | 0.553 | 0.561 | | 0.7 | 0.447 | 0.503 | 0.600 | 0.597 | | 0.8 | 0.497 | 0.551 | 0.629 | 0.629 | | 0.9 | 0.541 | 0.593 | 0.660 | 0.657 | | 1.0 | 0.581 | 0.632 | 0.697 | 0.683 | ----------------------------------------------- | Maximum deviation acentric : 0.062 | | Maximum deviation centric : 0.078 | | | | <NZ(obs)-NZ(twinned)>_acentric : -0.050 | | <NZ(obs)-NZ(twinned)>_centric : -0.021 | ----------------------------------------------- L test for acentric data using difference vectors (dh,dk,dl) of the form: (2hp,2kp,2lp) where hp, kp, and lp are random signed integers such that 2 <= |dh| + |dk| + |dl| <= 8 Mean |L| :0.441 (untwinned: 0.500; perfect twin: 0.375) Mean L^2 :0.270 (untwinned: 0.333; perfect twin: 0.200) The distribution of |L| values indicates a twin fraction of 0.00. Note that this estimate is not as reliable as obtained via a Britton plot or H-test if twin laws are available. Cheers, -- Yuri Pompeu

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March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 08 Jun '11

08 Jun '11

Dear Users, Please note: Due to an extended shutdown, proposals will not be solicited in May for the July-August 2011 beamtime. The next cycle will be September-October 2011. The deadline to submit proposals will be July 15th. Regards Banu

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Fwd: Neutrons in Biology 2011 - REGISTRATION NOW OPEN
by Nathaniel Echols 08 Jun '11

08 Jun '11

---------- Forwarded message ---------- From: Teixeira Susana <teixeira(a)ill.fr> To: phenixbb(a)phenix-online.org Date: Wed, 08 Jun 2011 17:10:52 +0200 Subject: Neutrons in Biology 2011 - REGISTRATION NOW OPEN Dear Colleagues, We are pleased to introduce an intensive 3-day hands-on *Neutrons in Biology 2011 School* (Oct. 21-23, 2011) at the European Photon and Neutron Science Campus (Grenoble, France) - a satellite school to the *Neutrons in Biology and Biotechnology meeting *(Oct. 19-20, 2011). During the course of this school participants will be tutored in the joint use of X-ray and neutron scattering techniques applicable to structural biology – Macromolecular Crystallography (PHENIX), Small Angle Scattering and Reflectometry - with emphasis on their complementary nature. The students will be given "hands-on" training in the use of state-of-the-art data analysis and modelling software. By the close of the course the participants should be able to access the suitability of neutron scattering techniques for their scientific projects using large scale facilities. Pre-registration deadline is August 15, 2011 – a limited number of applications will be accepted! Please visit the website for more information: http://www.ill.eu/nib2011 Best regards, The organisers -- ------------------------------ *Susana TEIXEIRA*, Institut Laue Langevin, LSS Group [image: View Susana Teixeira's profile on LinkedIn]<http://fr.linkedin.com/in/scmteixeira> <http://fr.linkedin.com/in/scmteixeira>

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Re: [phenixbb] mr_rosetta - homology search with hhr file - Cannot contact EBI DbFetch
by iulek＠interponta.com.br 08 Jun '11

08 Jun '11

That must make things easier for me, say, to prepare a single script to use, eg, the 10 best alignments from the hhr file. If I understand well, the "simple alignment file" proposed below must suite both sculptor and mr_rosetta. Many thanks. I will go to download the latest nightly build. J. > Hi Jorge, > > In your version of phenix yes, you need a special format for the alignment > files. I just changed it to allow a simple alignment file: > >> target > sequence-of-target >> template > sequence-of-template > > which is also used by sculptor. This is available in a current nightly > build. You can then just paste the alignment from hhpred into such a > file. > > I hope that helps! > -Tom T > > >>>> Thanks, Tom. >>> Yes, phenix.mr_model_preparation fails just like phenix.mr_rosetta: >>> >>> " >>> Traceback (most recent call last): >>> File >>> "/usr/local/phenix-1.7.1-743/phaser/phaser/command_line/mr_model_preparation.py", >>> line 9, in<mod ule> >>> mr_model_preparation.run( args = sys.argv[1:], out = sys.stdout ) >>> File >>> "/usr/local/phenix-1.7.1-743/phaser/phaser/mr_model_preparation.py", >>> line 255, in run >>> proxy = proxy.DbfetchHTTP( database = "pdb", format = "pdb" ) >>> File "/usr/local/phenix-1.7.1-743/phaser/phaser/proxy.py", line 108, in >>> __init__ >>> raise RuntimeError, "Cannot contact %s" % str( self ) >>> RuntimeError: Cannot contact EBI DbFetch service >>> " >>> >>> I think I will have to go to phenix sculptor. This seems to require >>> the alignment in ".aln (CLUSTAL format), .pir (PIR-format) and .ali >>> (relaxed PIR-like format)" maybe I could prefer to keep the hhr >>> alignment but I will have to check if there is an easy way to translate >>> one format into the other. Apart from this, phenix.mr_rosetta, seems to >>> require the alignment "MODELLER-style". >>> Therefore, to keep the alignment as output by hhr (is this wise? >>> Does this use multialignment and maight this be better that pairwise >>> alignment?) I have to translate it to either aln/pir/ali (for phenix >>> sculptor) and then to MODELLER-style for phenix.mr-rosetta. >>> A suggestion to make this more straight forward? >>> >>> J. >>> >>>> Hi Jorje, >>>> >>>> Yes, you can prepare your model separately from mr_rosetta. You can do >>>> this (for example) with: >>>> >>>> phenix.mr_model_preparation 3800765_mod_ed.hhr >>>> >>>> If that fails with the same download problem, you can create an >>>> alignment >>>> file and use phenix.sculptor to edit your model. >>>> >>>> Then as you suggest, you can use your edited model directly as a >>>> "search_model" and skip the .hhr files entirely. >>>> >>>> Let me know if that doesn't do it! >>>> All the best, >>>> Tom T >>>> >>>>>> Dear all, >>>>>> >>>>>> >>>>>> I would like to use mr_rosetta with homolgy search. I followed >>>>>> the >>>>>> instructions at >>>>>> http://www.phenix-online.org/documentation/mr_rosetta.htm , generated >>>>>> the hhr and the fragment files, but at submitting the job I receive >>>>>> the >>>>>> message: >>>>>> >>>>>> ******************* ERROR ENDING *************** >>>>>> Cannot contact EBI DbFetch service >>>>>> >>>>>> ******************* ERROR ENDING *************** >>>>>> >>>>>> after both loading the file 3800765_mod_ed.hhr and generating the log >>>>>> file mr_model_preparation.log. >>>>>> >>>>>> Concerning this problem, I saw >>>>>> http://www.phenix-online.org/documentation/faqs.htm#anch8 . But I am >>>>>> not >>>>>> behind a proxy and even disabling completely the firewall, the message >>>>>> still appears. >>>>>> Maybe this is more linux related, I use openSuSE 11.4. >>>>>> One workaround would be that I write a script to wget the pdb >>>>>> files >>>>>> (listed in .hhr) and select the due chains, putting these in a certain >>>>>> location and indicating in my script where they are. But I am a kind >>>>>> of >>>>>> confused, might >>>>>> >>>>>> search_models= >>>>>> >>>>>> do this. I am not sure I could use a hhr file together with it. >>>>>> Anyway, >>>>>> this might be a desirable solution for me yet I use to run my stuff in >>>>>> a >>>>>> laptop which goes around by. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Jorge >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>> >

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