- phenixbb - phenix-online.org

high resolution bin statistics
by Sebastiano Pasqualato 31 Aug '09

31 Aug '09

Hi there, i just wanted to know how is determined the number of bins for which the statistics of refinement are given in the header of the pdb refined with phenix.refine, and if there's a way to have more than the number of bins that is default output. For example, what if I'd like to have statistics for the 2.6-2.5 bin, here: REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.4159 - 3.9625 0.99 2545 131 0.1921 0.2232 REMARK 3 2 3.9625 - 3.1460 1.00 2447 116 0.1650 0.2289 REMARK 3 3 3.1460 - 2.7486 1.00 2433 121 0.1917 0.2682 REMARK 3 4 2.7486 - 2.4974 1.00 2405 130 0.2244 0.2890 thanks a lot in advance, ciao s -- Sebastiano Pasqualato, PhD IFOM-IEO Campus Dipartimento di Oncologia Sperimentale Istituto Europeo di Oncologia via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5094

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question about kick map
by crystallogrphy 28 Aug '09

28 Aug '09

Hi, I am trying to use kick map to remove model bias with the following script phenix.refine MR.1_refine_data.mtz MR.1_refine_001_refine_001.pdb output.prefix=refine-090828a simulated_annealing=True simulated_annealing.start_temperature=8000 strategy=individual_sites refine.params However, the program says: Sorry: Unknown file format: refine.params I do not understand why the format of refine.params cannot be read, which has the following contents. Does anyone know why? refinement { electron_density_maps { map { mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT likelihood_weighted = True obs_factor = 2 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } map { mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT likelihood_weighted = True obs_factor = 1 calc_factor = 1 kicked= True fill_missing_f_obs_with_weighted_f_model=True } }

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reflection file utility and use of modified phases in refinement
by Engin Ozkan 28 Aug '09

28 Aug '09

Hi everybody, I had some trouble with the reflection file utility today. I've been trying to import Rfree-flag column from one of the mtz's to my combined mtz, and it never does. The R-free flag is always left out of the output even when I have it selected. Have you guys seen this (I'm using 147)? Another question I have is about the output of phenix.autobuild. Phenix.autobuild tells me to use modified phase probabilities (HLAM, etc.) in refinement. I am assuming this is density-modified phases. But I've always thought that this would be bad practice (possibly because of unrealistically high FOMs and possible flattening of loops, etc, but maybe resolve does a better job than, say DM). Any ideas on that one? Thanks, Engin -- Engin Özkan Post-doctoral Scholar Dept of Molecular and Cellular Physiology Howard Hughes Medical Institute Stanford University School of Medicine ph: (650)-498-7111

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Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Hi Phenix community, I'm tracing a 3.3A averaged electron density map of a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? Thanks in advance for the feedback, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution
by Gino Cingolani 28 Aug '09

28 Aug '09

Sean, thanks to you and to whoever else responded to my email. Yes, I'd like to get your script. Thanks in advance! Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) ---- Original message ---- >Date: Fri, 28 Aug 2009 08:35:08 +0100 >From: Wai-Ching Hon <hon(a)mrc-lmb.cam.ac.uk> >Subject: Re: [phenixbb] Tracing and refining b-strands at 3.3A resolution >To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > >Dear Sean, > >That sounds wonderful. Can I have your scripts too? > >many thanks > >waiching. > >Sean Johnson wrote: >> Gino, >> >> My lab recently refined a 3.4 A structure and dealt with similar >> problems. We found that using secondary structure restraints was the >> only effective way to maintain reasonable geometry during refinement. It >> is kind of a daunting task to input all of the definitions by hand, so >> we wrote a couple python scripts that are integrated with PyMol to write >> the appropriate restraint definition files. All you have to do is click >> on the atoms that you want restrained. You are welcome to the scripts if >> you like. Feel free to contact me if you are interested. >> >> Sean Johnson >> >> >> Gino Cingolani wrote: >> >>> Hi Phenix community, >>> >>> I'm tracing a 3.3A averaged electron density map of >>> a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement? >>> >>> Thanks in advance for the feedback, >>> >>> Gino >>> >>> >>> >>> >>> ****************************************************************************** >>> Gino Cingolani, Ph.D. >>> Associate Professor >>> Thomas Jefferson University >>> Dept. of Biochemistry & Molecular Biology >>> 233 South 10th Street - Room 826 >>> Philadelphia PA 19107 >>> Office (215) 503 4573 >>> Lab (215) 503 4595 >>> Fax (215) 923 2117 >>> E-mail: gino.cingolani(a)jefferson.edu >>> ****************************************************************************** >>> "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" >>> ("You were not born to live like brutes, but to follow virtue and knowledge") >>> Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>> >>> >> >> >________________ >hon.vcf (1k bytes) >________________ >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb

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P43212 spacegroup change to C2221?
by Leigh Allen 28 Aug '09

28 Aug '09

Hello Phenix users. I recently solved the structure of my enzyme using SAD to a resolution of 1.9A. The R values were 0.19/0.25 and the space group was P43212 with a unit cell ~80, 80, 220. I then starting collecting datasets cocrystallized with ATP analogs and noticed that a lot of my datasets have a different unit cell when scaled in P43212. It comes out to be ~60, 60, 220 and I can NOT get a solution in Phaser with this data. If I scale it in C2221, then the unit cell is the same (80, 80, 220), but upon refinement, the R factors don't go much below 0.26/0.32. Has anyone ever seen something like this happen? I'm unsure if I should feel like the solution is C2221 since there are space groups of higher symmetry with similar residuals that seem plausible in indexing just the smaller unit cell. Should I keep trying to get a solution out of the data that leads to different unit cell parameters, but has higher symmetry? Xtriage seems to find twinning, but I think it's from NCS since my ASU contains a homodimer. I could also be wrong about this... Thanks in advance for any advice! ******* Leigh Allen Ph.D Candidate McCafferty Lab Duke University Department of Chemistry

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Questions about molecular replacement.
by Yuan Cheng 27 Aug '09

27 Aug '09

Hi, I am working on solving a protein structure using phenix.automr. There is likely four monomers in a ASU based on phenix.xtriage.I am using a search model with 30% identity with my protein. After finding three monomers in a ASU, the LLG is 1740 and R factor is 56%. After finding the fourth monomer, the LLG increased to 2080,but the R factor also increased to 58%. I have several question here: 1) how much should LLG and R factor be if the model from molecular replacement is correct? I guess the answer might not be a exact number. But I am still wondering what should be the correct range. 2) Whether R factor and LLG should always be positively correlated? I used phenix.refine to refine the model with 3 monomers and the model with 4 monomers in a ASU. The Rwork and Rfree are similar for these two models,47% and 53% respectively. I think that one more monomer should either improve or ruin the model.I don't quite understand why one extra monomer doesn't matter too much here. In addition, do you think it is worthy to keep doing model building and refinement in consideration such high R factors. All you suggestions and opinions will be greatly appreciated! Yuan

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Finding correct Se sites with autosol
by YS. Chung 27 Aug '09

27 Aug '09

Dear all, I have a 3 angstrom structure which I am trying to solve with MAD or SAD. The structure was previously solved with molecular replacement but refinement could not continue due to poor phasing at the N-terminal domain of the protein. I have run solve and autosol which are able to find the Se sites. However, Se sites are not anywhere near the methionines when I superimpose the ha.pdb and the pdb file that I obtain from a new run of molecular replacement. The exptl_fobs_phases_freeR_flags.mtz and the overall_best.pdb do not show any connected densities. I have also tried autobuild with the solutions from AutoSol, but the model that it builds in is incorrect. Any suggestions would be appreciated. Thank you, Yu Seon Chung

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Re: [phenixbb] another difficult space group
by Maia Cherney 26 Aug '09

26 Aug '09

Hi Randy, thank you for your help. Today we collected at the CLS two newer crystals of this form. I will process them and see, if they give me better results. For the dataset that I have done mor. rep, here is information from the headers of solutions P6222: LLG 2194 in p32: LLG 6840 C222: LLG=5252 C2: LLG 7942 P62: LLG 4058 Z-scores are very high, too, between 40 and 60. Refinement of any of these solutions gives Rfree around 50-55%, actually, it goes up at every cycle of refinement. Randy, what is the best file to send to you: which space group for the sca or mtz file , which solution? Maia Randy J. Read wrote: > Hi Maia, > > If it's a molecular replacement issue, we might be able to help. I'd > be happy to look at your data. > > All the best, > > Randy > > On Aug 25 2009, Maia Cherney wrote: > >> Thank you Peter for your reply. >> >> I will try the p1 expansion. Thank you for the suggestion. And really >> data look very good, the Rmerge is very low, chi squares are around >> one, looked like a perfect data set to me; >> >> one molecule in AU (in p6222). The model is exactly the same protein >> solved in two other space groups. >> >> And it's not one crystal, all these bipyramids are like this. I can >> send you my p1.sca if you are curious to look at it. >> >> Maia >> >> >> Peter Zwart wrote: >>> Hi Maia, >>> >>> Two points: >>> >>> 1) : >>> >>> Given that fact that you can process the data in p622, you can expand >>> the data to p1: >>> >>> phenix.reflection_file_converter mydata.sca --sca=p1.sca --expand_to_p1 >>> >>> Eventhough this is not the same as having 'real' p1 data, you know >>> that the data merges well in p622, so no harm is done (or at least not >>> a lot). >>> >>> Do you have pseudo translational symmetry by any chance? I wasn't able >>> to find any relation between the two provided unit cells. It is very >>> curious that their volume are equal though. >>> >>> >>> >>> 2): >>> >>> The fact that you cannot solve it might also be due to the fact that >>> your MR model is incorrect for some obscure reason. >>> >>> >>> HTH >>> >>> Peter >>> >>> >>> >>> >>> >>> >>> >>> >>> 2009/8/25 Maia Cherney <chern(a)ualberta.ca>: >>> >>>> Hi everybody, >>>> >>>> I have two types of hexagonal crystals: rods and bipyramids with >>>> dimensions 150x150x83 (rods) and 142x142x93 (bipyramids). Both >>>> types of >>>> crystals give the same spacegroup P6222. However, the rods gave a good >>>> solution and refined to low R factors, whereas the bipyramids give a >>>> solution with high LLG and Z-score, but don't refine at all (R factors >>>> around 50%). The xtriage does not indicate any twinning. Lower >>>> symmetry >>>> spacegroups (trigonal and monoclinic) have the same problem: give >>>> solutions with high scores that would not refine. The resolution is >>>> 2.3A. Unfortunately, the dataset processed in p1 has only 60% >>>> completeness (as it was collected according to p3 strategy). Should I >>>> try to solve in p1 with this low completeness? What can be a problem? >>>> >>>> Maia >>>> >>>> >>>> >>>> Peter Zwart wrote: >>>> >>>>> Good point. >>>>> >>>>> For now the best thing to do is to read the RvsR paper cited in >>>>> the text. I'll add a section to the manual as well. >>>>> >>>>> Ideally of course, xtriage should make its own judgement. Some >>>>> code is >>>>> there, but I took it out as it is not well-tested (and didn't do the >>>>> job) >>>>> >>>>> P >>>>> >>>>> >>>>> 2009/8/25 Pavel Afonine <PAfonine(a)lbl.gov>: >>>>> >>>>> >>>>>> Hi Peter, >>>>>> >>>>>> do you have any guidance to how interpret this table summarized >>>>>> somewhere in the documentation? Otherwise it looks a bit cryptic >>>>>> to me (I tried it while ago, may be it is improved now). >>>>>> Alternatively, it would be nice if Xtriage prints out its own >>>>>> verdict based on that table. >>>>>> >>>>>> Thanks! >>>>>> Pavel. >>>>>> >>>>>> >>>>>> On 8/25/09 10:47 AM, Peter Zwart wrote: >>>>>> >>>>>> >>>>>>> Subsequently, run >>>>>>> >>>>>>> phenix.xtriage p1data.mtz reference.structure.file=MR.1.pdb >>>>>>> >>>>>>> and start interpreting the RvsR tables. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> phenixbb(a)phenix-online.org >>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> >>> >>> >>> >>> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Thanks for everyone's help! I got the refinement working in version 1.4-125 and am all set. -Sam On Tue, Aug 25, 2009 at 4:19 PM, Ben Eisenbraun <bene(a)crystal.harvard.edu>wrote: > There's version 1.4-125 in the SBGrid software tree. Did you try it? Is > that version too old? > > You should ask Katya to update her user list. You're not in our database. > > -ben > > On Tue, Aug 25, 2009 at 04:13:44PM -0400, Sam Stampfer wrote: > > I couldn't get the source code to compile- the final message was: "error: > > configuration step incomplete, exiting". Any ideas? > > Thanks, > > -Sam > > > > [A copy of my problem is pasted here]: > > > > I'm running the latest complete version of phenix (version 1.4-147, on > Linux > > 2.6-x86 64). When I run my .csh file I get the following error (with the > 4 > > previous lines included): > > > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) > > [0x446bdd] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4396e4] > > > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python > > [0x4470a9] > > /lib64/libc.so.6 [0x30fca322a0] > > Segmentation fault (Python and libc call stacks above) > > This crash may be due to a problem in any imported > > Python module, including modules which are not part > > of the cctbx project. To disable the traps leading > > to this message, define these environment variables > > (e.g. assign the value 1): > > BOOST_ADAPTBX_FPE_DEFAULT > > BOOST_ADAPTBX_SIGNALS_DEFAULT > > This will NOT solve the problem, just mask it, but > > may allow you to proceed in case it is not critical. > > > > When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run > my > > .csh file, it runs for a slightly longer period of time before ending > with a > > different error: > > > > 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 > > /lib64/libbz2.so.1.0.4 > > 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 > > 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 > > 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 > > 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 > > 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so > > 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 > > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so > > 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 > > /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort > > > > However, the file ran fine and successfully output an improved .pdb file > > without any BOOST-related problems on my PI's Mac- she is running version > 95 > > of Phenix (which I was unable to obtain for linux- is it available > > somewhere?) > > > > Can you help me with this? > > > > Thanks! > > > > -Sam > > > > > > On Tue, Aug 25, 2009 at 3:28 PM, Ralf W. Grosse-Kunstleve > > <rwgk(a)cci.lbl.gov>wrote: > > > > > Could you try with a source installation? > > > > > > > > > > https://www.phenix-online.org/download/phenix/nightly/?version=1.4-147&show… > > > > > > I recommend you rm -rf the binary installation before ./install from > > > sources. > > > Add > > > --nproc=N > > > to the ./install command to use all N cpus in your machine for the > > > installation. > > > > > > Let me know if the problem persists. > > > > > > Ralf > > > _______________________________________________ > > > phenixbb mailing list > > > phenixbb(a)phenix-online.org > > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > -- > | Ben Eisenbraun | Tools Sysadmin | > | Structural Biology Grid | http://sbgrid.org | > | Harvard Medical School | http://hms.harvard.edu | > >

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Problem with BOOST_ADAPTBX_FPE_DEFAULT and BOOST_ADAPTBX_SIGNALS_DEFAULT
by Sam Stampfer 25 Aug '09

25 Aug '09

Hi, I'm running the latest complete version of phenix (version 1.4-147, on Linux 2.6-x86 64). When I run my .csh file I get the following error (with the 4 previous lines included): /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python(PyDict_SetItem+0x1fd) [0x446bdd] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4396e4] /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/bin/python [0x4470a9] /lib64/libc.so.6 [0x30fca322a0] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. When I type the command "setenv BOOST_ADAPTBX_FPE_DEFAULT 1" and then run my .csh file, it runs for a slightly longer period of time before ending with a different error: 311240e000-3112410000 rw-p 0000e000 fd:00 14237822 /lib64/libbz2.so.1.0.4 2ad973412000-2ad973414000 rw-p 2ad973412000 00:00 0 2ad973429000-2ad97346d000 rw-p 2ad973429000 00:00 0 2ad97346e000-2ad9734af000 rw-p 2ad97346e000 00:00 0 2ad9734e1000-2ad973563000 rw-p 2ad9734e1000 00:00 0 2ad973563000-2ad973567000 r-xp 00000000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973567000-2ad973666000 ---p 00004000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973666000-2ad973668000 rw-p 00003000 fd:00 5727920 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/time.so 2ad973668000-2ad97366d000 r-xp 00000000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lib/python2.6/lib-dynload/select.so 2ad97366d000-2ad97376c000 ---p 00005000 fd:00 5727941 /usr/local/phenix/phenix-1.4-147/build/intel-linux-2.6-x86_64/base/lAbort However, the file ran fine and successfully output an improved .pdb file without any BOOST-related problems on my PI's Mac- she is running version 95 of Phenix (which I was unable to obtain for linux- is it available somewhere?) Can you help me with this? Thanks! -Sam

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ruthenium parameters
by Terry Lang 24 Aug '09

24 Aug '09

Hey Everyone, I am working on an xray structure that contains a ruthenium. I have been able to use elbow to create a cif file that phenix can read and refine without throwing error messages. However, there is a large amount of positive electron density after the refinement. I am looking into modeling coordinate waters, but I first wanted to check that the ruthenium is being read correctly by phenix. How do I figure out if it is properly recognized (eg correct scattering factors, bond and angle restraints, etc)? Thanks, Terry -- P. Therese Lang Postdoctoral Scholar Alber Lab, UC Berkeley

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phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 23 Aug '09

23 Aug '09

Hi folks: About a year ago I refined a 1.6 Å RNA structure with phenix.refine 1.3b-rc6 and then got distracted. I picked it up today and essentially repeated the last round of refinement with 1.4-57 (and also 1.4-159). The maps are subtly different, but consistently slightly worse with 1.4. Here are two examples: http://sage.ucsc.edu/~wgscott/mystuff/old_vs_new.pdf In the second example, this would lead to deletion of one of the octahedrally coordinated waters on a known Mg++ ion. 2OEU is similar, except 2.0 Å resolution, and it has Mn2+ instead of Mg ++. A similar thing happens with the corresponding water in that structure. Has the weighting for the bulk solvent mask or something like that been increased? Thanks. Bill Scott

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difference in B factor for NCS groups
by James Whittle 21 Aug '09

21 Aug '09

Dear all, I'm working with a structure were one NCS copy has significantly high B-factors than the other. That one copy makes few crystal contacts to stabilize it. Is there a recommended way to adjust the refinement to reflect this ... using TLS? Decreasing b_factor_weight? Is there a way refine a group_b to be added to the b-factor of each atom in that chain? --James

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Error in running Autosol....
by S. Karthikeyan 19 Aug '09

19 Aug '09

Dear All, I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. I am trying to solve a structure of Se-Met through phenix.autosol_gui. Once the programs starts it goes to several stages including converting from mtz to sca, xtriage and so on. Finally it gives an error message as follows: ******************************************************************************** Failed to carry out AutoSol_scale_and_analyze_mad: None of the solve versions worked See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) ******************************************************************************** I found the LAST.LOG file is empty. I am trying to find out what could be problem? Any suggestions or help is much appreciated! Thanking you S.Karthikeyan

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Problem with LLP ligand
by James Naismith 19 Aug '09

19 Aug '09

Dear All, I am trying to refine a structure which has a Lys linked to PLP. In the PDB this is called LLP. When I take it through refine it crashes complaining about the ligand. "Sorry : Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 8 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Traceback: None " I know I have to use REEL to fix this in some way. I have used REEL to make ligands not bound to protein before. It is how to do this when the ligand is covalently bound that I am stuck with. Any help (particularly a cif restraints file!) gratefully received. best Jim ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxwidgets, wxPython, Boost, SCons, Clipper, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. ------------------------------------------------------------------------------- Processing inputs. This may take a minute or two. Working crystal symmetry after inspecting all inputs: Unit cell: (50.677, 137.283, 62.258, 90, 109.637, 90) Space group: P 1 21 1 (No. 4) Monomer Library directory: "/usr/local/phenix-1.4-115/chem_data/mon_lib" Total number of atoms: 13558 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6752 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 420, 6747 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 420} Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4} Chain breaks: 3 Conformer: "A" Number of residues, atoms: 420, 6747 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 420} Link IDs: {'PTRANS': 14, 'TRANS': 401, 'PCIS': 4} Chain breaks: 3 bond proxies already assigned to first conformer: 6820 Chain: "B" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6800 Unexpected atoms: {'LLP,HD3': 1, 'LLP,HG3': 1, 'LLP,HB3': 1, 'LLP,HE3': 1} Classifications: {'peptide': 423} Link IDs: {'PTRANS': 14, 'TRANS': 404, 'PCIS': 4} Chain breaks: 3 Chain: "M" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' SM': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Number of atoms with unknown nonbonded energy type symbols: 8 "ATOM 3149 HG3 LLP A 211 .*. H " "ATOM 3151 HE3 LLP A 211 .*. H " "ATOM 3153 HD3 LLP A 211 .*. H " "ATOM 3155 HB3 LLP A 211 .*. H " "ATOM 9896 HG3 LLP B 211 .*. H " "ATOM 9898 HE3 LLP B 211 .*. H " "ATOM 9900 HD3 LLP B 211 .*. H " "ATOM 9902 HB3 LLP B 211 .*. H " Time building chain proxies: 9.24, per 1000 atoms: 0.68 The University of St Andrews is a charity registered in Scotland : No SC013532

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RESOLVE with RNA/protein structure at low resolution
by Peter Grey 19 Aug '09

19 Aug '09

Hello all, I try to solve the structure of RNA and RNA/protein complex at low resolution (5A). Phases come from partial model MR solution. I would really welcome advice about density modification in such cases with RESOLVE.. Does the RESOLVE database of density distributions contain RNA/protein examples ? Can RESOLVE work at low resolution given that histograms profiles are at resolutions from 1.2 A to 4 A ? Many thanks for you help, Peter.

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AutoBuild help
by Timothy C. Umland 18 Aug '09

18 Aug '09

I am new to running the AutoMR and AutoBuild Wizards, and I am having a problem getting AutoBuild to run. I have run AutoMR and it appeared to run fine, yielding a solution. However, when it did the default hand-off of the MR solution to AutoBuild, AutoBuild crashed. I then tried to run AutoBuild by itself, using the MR solution as the input model. Again, AutoBuild crashed. The error was the same in both cases. I was running AutoMR and AutoBuild from the command line. I am running Phenix version 1.4-3 on an Intel Mac (OS X 10.5.8). The AutoBuild error was **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1' sort: invalid option -- 4 Try `sort --help' for more information. **************************************************************************** **** I tried the suggested "sort --help", but at least to me it wasn't helpful. I am guessing that I have some incompatibility with my local installation of "sort" and Phenix? Any help is appreciated. Thanks, Tim

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1-2 October: What is a Macromolecular Complex ? meeting at the NKI, Amsterdam
by Anastassis Perrakis 18 Aug '09

18 Aug '09

Dear all, This is a reminder and some news for the meeting: "What is a macromolecular Complex? Shades of Meaning Across Cellular, Systems, and Structural Biology" http://xtal.nki.nl/Oct2009 - Registration closes on Monday 7th September at 12:00 noon. No exceptions after the deadline. - There will be eight (8) fellowships for attending the meeting, 500 Euro (max) each (*) Best regards on behalf of the organizers, Tassos (*) Only available if your lab is NOT part of the EU programs that support the meeting (SPINE-2-Complexes, TEACH-SG, 3D-Repertoire) and you really wanted to attend but could not for financial reasons, but 500 Euro will make it possible for you to join us, please email a.perrakis.AT.nki.nl with a short motivation and research interests, 10-15 lines max (no attachments please, simple text). Preference will be given to people not yet registered, since we might well assume that people that already registered had the money already sorted. The amount is the MAXimum available per person for ALL expenses, and it will be reimbursed after the meeting, *** based on receipts ***!

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Re: [phenixbb] Error in running Autosol....
by Thomas C. Terwilliger 15 Aug '09

15 Aug '09

Hi Karthikeyan, I'm sorry for the trouble! I see that you are running the very latest phenix from last night. This version passed our automated tests and it appears fine in general. Somehow the solve scaling step is not working in your run. I haven't seen this happen before, but my guesses are: 1. I have been making small changes in the autosol printout and it is possible that there is a place where solve is printing something out and the format does not match the variable type, and I didn't catch it in our tests. If this is the case you should be able to find it by running from the command-line and adding the keyword debug=true and it should print out a clearer error message for you that you can send me. You can run from the command line in the same place you ran from the GUI by saying phenix.autosol autosol.eff debug=True because the GUI writes out autosol.eff when it runs, saving your inputs. Then you can override those values by putting debug=True on the command line. Other less-likely possibilities: 2. your input datafiles are of a type that was unexpected (normally .sca, .mtz are fine, but perhaps the columns in an mtz are unusual). 3. Your structure is very large or high-resolution. 4. Something is unusual in your setup so that not much memory is available. If none of these helps, you are welcome to send me the files and I'll check it out. All the best, Tom T >> Dear All, >> >> I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. >> >> I am trying to solve a structure of Se-Met through phenix.autosol_gui. >> Once the >> programs starts it goes to several stages including converting from mtz to >> sca, >> xtriage and so on. >> Finally it gives an error message as follows: >> >> ******************************************************************************** >> Failed to carry out AutoSol_scale_and_analyze_mad: >> >> None of the solve versions worked >> See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) >> ******************************************************************************** >> I found the LAST.LOG file is empty. >> >> I am trying to find out what could be problem? Any suggestions or help is >> much >> appreciated! >> >> Thanking you >> >> S.Karthikeyan >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] low resolution data/parameter ratio
by Pavel Afonine 14 Aug '09

14 Aug '09

Hi Gerwald, > Two more quick questions: > how would you identify the best strategy? I would look at Rfree and Rfree-Rwork, and maps of course. To help in deciding what are the "good / reasonable" values, use POLYGON (Acta Cryst. D65, 297-300 (2009)) (phenix.polygon), local real-space correlation (phenix.real_space_correlation). I think Nat bundled them all into his magic tool called phenix.validation with will do this and more (it is GUI based). > I would aim for the lowest number of parameters with reasonably low > Rfree? Yes, this sounds right in general. > Does phenix report the total number of parameters refined anywhere in > the log? It's trivial and not at the same time (at least the way I understand it, of course I might be very wrong). It's trivial to compute the number of refinable parameters given the strategy you choose, but how you will count the restraints which are kind of quasi-observables, and what about weight that if chosen too strong so it can turn the restraints into quasi-constraints? Pavel.

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low resolution data/parameter ratio
by gerwald jogl 14 Aug '09

14 Aug '09

Hi All, I am struggling with low resolution data (3.6 A) and I am concerned about overfitting. I have a ratio of about 3 reflections per atom. Possible refinement scenarios would be a) coordinates+tls, b) coordinates, group_adp, tls or c) coordinates, individual_adp, tls. The last scenario seems to be pushing the limits. I wonder if there are studies, thoughts or opinions out there on which refinement scenario to use. Thanks for any comment on this, Gerwald

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adding sutrates in phenix.refine
by Rune wederkinck Andersen 14 Aug '09

14 Aug '09

Hi everyone I'm running a refinement in phenix.refine. I'm now trying to ad two subtrates AMP and RP5. The phenix.refine seams to reconise AMP but not the RP5 molecules. It seams as if this molecules is well known for the program (phenix-1.4-3/ext_ref_files/chemical_components/r/data_RP5.cif). In my PDB file the two molecules are described like this: ... HETATM 19 C6 AMP A 301 35.852 19.986 36.427 1.00 22.32 A HETATM 20 N6 AMP A 301 35.448 19.736 37.693 1.00 24.44 A HETATM 21 N7 AMP A 301 36.400 17.540 35.616 1.00 23.01 A HETATM 22 C8 AMP A 301 36.853 17.097 34.416 1.00 21.98 A HETATM 23 N9 AMP A 301 37.034 18.126 33.560 1.00 19.84 A HETATM 1 P' RP5 A 302 30.291 24.910 31.815 0.25 10.66 A HETATM 2 C5' RP5 A 302 32.348 25.416 30.301 0.25 14.76 A HETATM 3 O5' RP5 A 302 31.481 24.448 30.868 0.25 12.67 A HETATM 4 C4' RP5 A 302 33.260 24.753 29.307 0.25 15.58 A HETATM 5 C3' RP5 A 302 33.017 25.227 27.872 0.25 15.17 A HETATM 6 O3' RP5 A 302 33.951 26.264 27.522 0.25 14.15 A HETATM 7 C2' RP5 A 302 33.282 23.935 27.083 0.25 16.11 A HETATM 8 O2' RP5 A 302 34.571 23.963 26.478 0.25 13.68 A HETATM 9 C1' RP5 A 302 33.351 22.848 28.160 0.25 16.92 A HETATM 10 O1' RP5 A 302 32.775 23.415 29.296 0.25 16.62 A HETATM 11 O1 RP5 A 302 32.631 21.639 27.867 0.25 20.12 A HETATM 12 O1X RP5 A 302 29.112 25.373 30.809 0.25 10.53 A HETATM 13 O2X RP5 A 302 29.912 23.844 32.781 0.25 10.59 A HETATM 14 O3X RP5 A 302 30.793 26.258 32.567 0.25 9.63 A ATOM 1 N MET B 1 63.305 2.511 45.667 1.00 64.80 B ATOM 2 CA MET B 1 62.528 3.463 46.463 1.00 68.29 B ATOM 3 C MET B 1 62.555 4.863 45.882 1.00 65.73 B ATOM 4 O MET B 1 63.607 5.325 45.446 1.00 64.47 B ... I have tried with phenix.elbow as well but didn't work... Please help... Rune _________________________________________________________________ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/

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Running Autobuild after Autosol
by Katya Heldwein 14 Aug '09

14 Aug '09

Hi, how do I specify running Autobuild after Autosol, in the command line mode? I see the "phenix.autobuild after_autosol" option in the manual, but how will Autobuild know which Autosol run to use? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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CC beamtime application deadline this saturday
by Banumathi Sankaran 14 Aug '09

14 Aug '09

Dear Users, The deadline for October/November/December 2009 Collaborative Crystallography proposals will be August 15, 2009. Thumbnail Description: Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "Structural Biology beamlines (includes protein SAXS)" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only ?) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2009 allocation period, proposals must be submitted by August 15, 2009. Please note that the ALS will be shut down in September, 2009. The deadline for CC proposals for the time period January/February 2010 will be November 15, 2009. Regards, Banumathi Sankaran

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Re: [phenixbb] phenix.refine special positions
by Ralf W. Grosse-Kunstleve 13 Aug '09

13 Aug '09

Hi Simon, To add to the previous answers, note that phenix.refine currently doesn't work well if you want to allow symmetry copies of your ligands to overlap. If you move to individual coordinate refinement you have to fix such ligands; i.e. it won't automatically repair bonds distorted by rigid-body refinement. Removing this limitation is on my to-do list. Ralf

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phenix.refine special positions
by Simon Kolstoe 13 Aug '09

13 Aug '09

Dear Pavel et al. Is there any way of defining a residue for rigid body refinement if a couple of the atoms are sitting on a symmetry axis? i.e. can I define the rigid body to be chain L but not the atoms that are giving the problems? I keep on getting the error: ================== Extract refinement strategy and selections ================= Some atoms selected for rigid body refinement are in special positions (listed below). Please remove these atoms from the rigid body selection and run refinement again. "ATOM 4 C4 A12 L 2 .*. C " Sorry: Atoms at special positions are within rigid groups. Thanks, Simon

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Shake
by esmael 13 Aug '09

13 Aug '09

Hi, Would be possible to only add "Shake" to the side-chain atoms during the refinement with Phenix? Thanks, Esmael

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phenix.xtriage says that entire res range contains anomalous signal but chart says differently?
by Francis E Reyes 13 Aug '09

13 Aug '09

Hi all I ran xtriage on my dataset to 4.5.here's the relevant section pertaining to anomalous signal Analyses of anomalous differences Table of measurability as a function of resolution The measurability is defined as the fraction of Bijvoet related intensity differences for which |delta_I|/sigma_delta_I > 3.0 min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 holds. The measurability provides an intuitive feeling of the quality of the data, as it is related to the number of reliable Bijvoet differences. When the data are processed properly and the standard deviations have been estimated accurately, values larger than 0.05 are encouraging. Note that this analyses relies on the correctness of the estimated standard deviations of the intensities. unused: - 90.6596 [ 0/1 ] bin 1: 90.6596 - 9.2614 [1371/1382] 0.0375 bin 2: 9.2614 - 7.3520 [1369/1376] 0.0033 bin 3: 7.3520 - 6.4230 [1380/1388] 0.0000 bin 4: 6.4230 - 5.8358 [1353/1359] 0.0016 bin 5: 5.8358 - 5.4176 [1367/1371] 0.0000 bin 6: 5.4176 - 5.0982 [1361/1369] 0.0000 bin 7: 5.0982 - 4.8429 [1378/1382] 0.0000 bin 8: 4.8429 - 4.6321 [1351/1359] 0.0000 bin 9: 4.6321 - 4.4538 [1383/1389] 0.0000 bin 10: 4.4538 - 4.3001 [1390/1393] 0.0000 unused: 4.3001 - [ 0/0 ] The full resolution range seems to contain a useful ammount of anomalous signal. Depending on your specific substructure, you could use all the data available for the location of the heavy atoms, or cut the resolution to speed up the search. If values larger than 0.05 are encouraging why is it telling me that the entire resolution contains a useful amount of anomalous signal? Did I process this incorrectly? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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General User Proposal Deadline for PX/SAXS at the ALS: August 15, 2009
by Peter Zwart 12 Aug '09

12 Aug '09

Dear All, August 15, 2009 is the deadline for the October - December 2009 Rapid Access Proposal cycle. (!!!!Please note that the ALS will be shut down in September, 2009.!!!!) Remote data collection is available on all beamlines at the Berkeley Center for Structural Biology (BCSB). The NX remote desktop technology provides the remote user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 24hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Beamlines 8.2.1 and 8.2.2: Both beamlines are now fully remote capable, which means that users are able control sample mounting, data collection and analysis from their home labs. This has dramatically increased the efficiency of data collection and significantly reduced the cost of protein crystallography experiments, since users no longer have to travel to the synchrotron. To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. As part of the beamline optics upgrades, a new toroidal focusing mirror was purchased and installed in beamline 8.2.1; new parabolic mirrors are currently being polished. When completed, the new optics will increase the brightness of beamline 8.2.1 by a factor of 4 to 5 and decrease the spot size to 30 microns, greatly facilitating structure solution on large macromolecular complexes. Beamlines 5.0.1, 5.0.2, 5.0.3: On Sector 5, improvements to the existing Berkeley Automounter sample handling system have dramatically improved both total capacity and reliability. Upgrades to the 5.0.1 and 5.0.3 monochromators have been completed. The operational energy of both beamlines has been increased, taking them above the Se K-edge and thus introducing a significant new Se SAD capability for experiments on Se derivatized proteins. The new monochromators also provide significantly better beam focus and performance under the increased power loads of ALS topoff operation. These improvements have been coupled with the introduction of enhanced positional feedback, diagnostic tools, and auto-alignment systems for the beamline components to improve the overall stability and quality of the beam delivered to users. Another mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology/Small Angle X-Ray Scattering (SAXS)." We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you'd like to apply for January-February 2010 beamtime at the Advanced Light Source, please submit a General User proposal by November 15, 2009. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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xtriage
by Francis E Reyes 12 Aug '09

12 Aug '09

Hi all I love the fact that xtriage can measure anomalous signal, but can it also do a quick check for isomorphous differences (with and without anomalous signal) similar to scalepack? Is there a phenix utility that can do this? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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duplicated label
by Jianghai Zhu 12 Aug '09

12 Aug '09

Hi, I am using phenix.refine-125 to do a MLHL refinement. I got an error at the end of the refinement while it was trying to exporting results. "Sorry: Duplicate mtz_label_amplitudes:FOFCWT". The output map_coeffs.mtz file is corrupted and the next def file is blank. The refined pdb file seems to be fine. Anyone knows how to fix this problem? Thanks. -- Jianghai

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where are the optimized wxc_scale and wxu_scale when optimize_wxc_scale and optimize_wxu_scale = True?
by Francis E Reyes 07 Aug '09

07 Aug '09

Hi all I went through the time to optimize_wxc and optimize_wxu to help pull out some density for ligands (i.e. all sequence assigned residues are built). However, it would be nice if the resulting .def was updated with the optimized wxc and wxu. Where are those values? I didn't think for wxc it was scale=XX in the following lines.. r_work= 0.2167 r_free= 0.2525 bonds= 0.003 angles= 0.70 scale= 7.00 r_work= 0.2097 r_free= 0.2502 bonds= 0.004 angles= 0.96 scale= 8.00 ... etc Refining with the scale= value that phenix ultimately chose didn't work form me (resulted in awful geometry and high r/rfree). Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Re: [phenixbb] Let's talk about maps...
by Dr. Mark Mayer 07 Aug '09

07 Aug '09

Hi Pavel, It would be really nice if the Electron density maps section in the online docs for phenix.refine http://www.phenix-online.org/documentation/refinement.htm#anch70 was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb. Mark --

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Re: [phenixbb] Autobuild error (FIXED)
by youssef ben ammar 07 Aug '09

07 Aug '09

Thanks for all replies, Autobuild error linked to the long path was solved based on the suggestion of Ben Eisenbraun (thanks Ben). I reinstalled tcsh, but only that did not solve the problem. So, I deleted csh from the path and kept only the newly installed tcsh after that everything is running perfectly. Youssef

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Re: [phenixbb] phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 06 Aug '09

06 Aug '09

Hi Paul et al: The yellow map is filled and the blue map is no-fill from the phenix- generated mtz file: http://sage.ucsc.edu/~wgscott/mystuff/filled_vs_unfilled.pdf So I think this is clearly what is going on. Thanks. Bill

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Segmentation Fault
by Waight, Andrew 06 Aug '09

06 Aug '09

Hello All, I've recently solved a membrane protein structure largely with the help of phenix refine. I also have been using the autobuild programs recently for ligand fitting and whatnot. The program during this time has been running flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR spontaneously started throwing this error. (boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Memtest 86 says my RAM is good. I have reinstalled phenix and am still getting the same error. I can't seem to find any other information on this error (segmentation faults are tricky I know) and am just wondering if anyone else has seen or solved this type of problem, thanks for your help. Andrew Waight Wang Lab Skirball Institute of Biomolecular Medicine NYU school of medicine </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

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Re: [phenixbb] Autobuild error
by youssef ben ammar 06 Aug '09

06 Aug '09

Thanks for your quick reply, I tried again to fix the problem as suggested by Thomas but this did not solve the problem. Actually I have two machines running phenix, one with the old version 1.3, and the other with 1.4-3 version. With the old version I have also coot, ccp4, and arp-warp, and all things are running without any problem in this machine. But in the other computer, I don't have arp-warp in it (ccp4 and coot exist also), and everything was running OK until I updated phenix to 1.4-3. But now even if I downgrade it to 1.3, autobuild does not work. If I compare echo $PATH results from both machines, I can notice that the path in the one with "defected" autobuild is too long. I will review again my path and try to fix it, or see if there are other recently-installed programs that interfere with phenix. Thanks Youssef.

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Autobuild error -
by Gino Cingolani 05 Aug '09

05 Aug '09

Dear Youssef and Tom, I had the same problem. I also emailed the Phenix classified and got a similar response from Tom. In reality, Tom suggestion didn't solve my problem. The funny thing is that in my case PHENIX.Autobuild worked fine for months before suddenly giving the 'Word too long' error. Weird!!! Believe it or not, the only thing I had to do to fix the problem was to uninstall the ARP/wARP package (sorry about that Tassos!). I realized that PHENIX.Autobuilt stopped working properly right when I installed ARP/wARP. I guess there may be a conflict between the two programs (could Phenix read some ARP/wARP library in the wrong directory?), or something like that. I'm not sure. I'm not claiming this is a general solution, but it worked in my case. I hope it will help you! Cheers, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Re: [phenixbb] Autobuild error
by Thomas C. Terwilliger 05 Aug '09

05 Aug '09

Hi Youssef, I'm sorry for the trouble! If you update to a recent "nightly build" such as 1.4-129 then this should go away. If it still doesn't, then have a look at your path: echo $PATH which is probably quite long....and identify a few things (perhaps ccp4 and coot for example) that you don't need while running phenix...and then add the keyword: remove_path_word_list="coot ccp4" All the best, Tom T remove_path_word_list = None .help = "List of words identifying paths to remove from PATH " "These can be used to shorten your PATH. For example..." "cns ccp4 coot would remove all paths containing these " "words except those also containing phenix. Capitalization" "is ignored." ">> Dear all, >> >> Recently I have problem with Autobuild. The process fails with the >> following >> message: >> Failed to carry out AutoBuild_build_cycle: >> child process stderr output: >> command: 'csh /home/phenix/p21/AutoBuild_run_1_/TEMP0/RUN_FILE_1' >> Word too long. >> Even if I set the path only to things related to phenix, the process fails >> with the same error. >> >> Any idea? >> >> Youssef >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Autobuild error
by youssef ben ammar 04 Aug '09

04 Aug '09

Dear all, Recently I have problem with Autobuild. The process fails with the following message: Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/phenix/p21/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Word too long. Even if I set the path only to things related to phenix, the process fails with the same error. Any idea? Youssef

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Using phenix.pdbtools to strip multiple conformations out of a PDB file?
by Stephen Graham 04 Aug '09

04 Aug '09

Dear all, Apologies if this is a dumb question, but I couldn't find the answer in the docs or by asking the googlebrain. Is there a simple way in phenix.pdbtools to strip "alternate conformations" of side chains, etc, from an input PDB file? By removing "alternate conformations" I mean I would like to keep the conformation with the highest occupancy (not necessarily denoted 'A' in the altLoc column) unless all conformations have an equal occupancy, in which case I'd arbitrarily keep conformation 'A'. I think it should be possible by a clever atom_selection command, but the correct syntax has thus-far eluded me! Thanks, Stephen -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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Is the twin refine conflict with order_solvent refine
by shi jiahai 04 Aug '09

04 Aug '09

Hi, Dear all, I am refine a twin dataset with phenix 1.4-3 and CCI (2008_02_08_1610) on a CenOS 5.2 workstation. When I run refine with twin law or order_solvent alone, the refinement is good. Everything goes smoothly. However if I enable refinement on both twin law and order_solvent, the error comes during the order_solvent refinement as below. Start model: number = 55 b_iso_min = 5.52 (limit = 1.00) b_iso_max = 60.32 (limit = 60.00) b_iso_mean = 24.19 anisotropy_min = 1.00 (limit = 0.10) occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.13 (limit = 1.80) dist_sol_mol_max = 4.38 (limit = 6.00) Traceback (most recent call last): File "/Application/CCI/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 80, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1162, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/Application/CCI/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 350, in refinement_machine log = log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 132, in __init__ map_cutoff = self.params.primary_map_cutoff).peaks_mapped() File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py", line 324, in find_peaks log = self.log) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/find_peaks.py", line 65, in __init__ symmetry_flags = maptbx.use_space_group_symmetry) File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2238, in electron_density_map w2 = w2).fft_map( File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py", line 2126, in map_coefficients "m_gradient" AssertionError Can anybody help me with this? Thanks a lot in advance! Best Regards, Shi Jiahai Department of Biological Sciences, National University of Singapore

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Assertion error while adding water
by Bishal Kumar Singh 03 Aug '09

03 Aug '09

Hi, Following error is showing while adding water. Every command-line is as default except "ordered_solvent = True". I will appreciate your suggestions. "0.7 1.17367178905 0.7 1.2044634853 0.7 1.18455476555 0.7 1.21102571346 0.7 1.20890773595 0.7 1.23028004675 0.7 1.2017635385 0.7 1.2151128962 0.7 1.20672093638 0.7 1.17881942233 0.7 1.21258440895 0.7 1.21100112067 0.7 1.22101928156 0.7 1.20955876073 0.7 1.17722437184 0.7 1.19891104532 0.7 1.18433797592 Traceback (most recent call last): File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 16, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/wrkhuge/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 394, in refinement_machine log = log) File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/solvent/ordered_solvent.py", line 159, in __init__ use_kick_map = self.params.use_kick_maps).peaks_mapped() File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/solvent/ordered_solvent.py", line 334, in find_peaks log = self.log) File "/wrkhuge/cci_apps/cci_apps_sources/mmtbx/find_peaks.py", line 93, in __init__ crystal_gridding_tags = fft_map.tags() File "/wrkhuge/cci_apps/cci_apps_sources/cctbx/maptbx/__init__.py", line 152, in tags return crystal_gridding_tags(self) File "/wrkhuge/cci_apps/cci_apps_sources/cctbx/maptbx/__init__.py", line 158, in __init__ assert gridding.symmetry_flags() is not None" regards, Bishal Singh

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Autosol error
by Francis E Reyes 31 Jul '09

31 Jul '09

All When issuing phenix.autosol native.data=scala_072809B_3_001.mtz deriv.data=scala_072909A_3_001.mtz deriv.atom_type=Ir deriv.sites=5 deriv.inano=noinano native.labels='IMEAN SIGIMEAN' deriv.labels='IMEAN SIGIMEAN' I get the error **************************************** AutoSol Input failed For SIR datasets please enter two datafiles or datasets.(native +deriv) Please treat MIR as a series of SIR datasets ...to specify a particular set of data you can specify one of the following (command-line format shown, for a script take out the '=' and use the keyword 'group_labels_list' instead): native.labels='IMEAN SIGIMEAN' deriv.labels='IMEAN SIGIMEAN' native.labels='I(+) SIGI(+) I(-) SIGI(-)' deriv.labels='I(+) SIGI(+) I(-) SIGI(-)' **************************************** Any ideas? thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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combining models from multi-start simulated annealing
by James Whittle 30 Jul '09

30 Jul '09

Is there a way to use AutoBuild to combine a set of models created by multi-start simulated annealing? I've used a random number generator to seed different SA runs at two temperatures, as suggested on this bulletin board before ... but can combine the best parts of these models automatically? --James

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Integrating Phenix with Torque
by Jeremy Mann 29 Jul '09

29 Jul '09

A new user of mine wants to run Phenix on two of our clusters. We use Torque/Maui as our batch scheduler and would like to integrated their usage of Phenix. They want to run something like: phenix.autobuild data=data.hkl seq_file=seq.dat model=model.pdb multiple_models=True multiple_models_number=20 n_cycle_rebuild_max=5 nbatch=20 nproc=20 The documentation mentions briefly the ability to use batch schedulers but doesn't give examples of submission scripts. -- Jeremy Mann jeremy(a)biochem.uthscsa.edu University of Texas Health Science Center Bioinformatics Core Facility http://www.bioinformatics.uthscsa.edu Phone: (210) 567-2672

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Phaser RMS - What happens when it is too high
by Peter Grey 29 Jul '09

29 Jul '09

Hi all, In Phaser RMS is a crucial parameter. I had several cases where underestimation of RMS resulted in negative LLG. The cure was simply increasing the RMS. But I wonder, are there negative effects to a too high RMS. What are the dangers of giving Phaser a too high RMS ? Are there any indications in the output for that. This is also important with EM maps as models since in that case estimation of RMS is difficult. Many thanks in advance for your advice and insight, Peter.

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phenix.refine issue
by Dennis Wolan 27 Jul '09

27 Jul '09

I am having an issue with running a simple phenix.refine that I have never encountered before. I get a list of issues and the program quits with: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/ refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 231, in __init__ reflection_file_server = self.reflection_file_server() File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/ command_line.py", line 566, in reflection_file_server err=self.log) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in __init__ force_symmetry=self.force_symmetry)) File "/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in as_miller_arrays base_array_info=base_array_info) File "/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in as_miller_arrays and flex.min(column_group.sigmas()) > 0): RuntimeError: min() argument is an empty array I have no idea if the issue is with my pdb or mtz. I'm sure it's something very simple that I just am not identifying. Thanks in advance, Dennis

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phaser MR
by sbiswas2＠ncsu.edu 27 Jul '09

27 Jul '09

Hi all, I was trying to solve a structure by molecular replacement. I scaled the data in P4222 space group (resolution 2.7A) with two molecules in the assymmetric unit (molecule A and B) I ran phaser with my model and got a Zscore of 5.1. When I look at the map that I got from phaser I could easily see good electron density for both molecules, However upon inspection of the electron density map there were considerable interaction or clashes with molecule B and a symmetry atom. Molecule A had no clashes however with the symmetry atoms. I was wondering if anyone knows how to resolve this. Could it be a problem of space group. The statistics are good for space group P4222 and the I/sigI was good till 2.7A. Any advice is appreciated, Shya

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