- phenixbb - phenix-online.org

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)

6 7

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

1 0

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

9 13

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

2 1

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

2 1

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 >> > >

1 0

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 | > >

1 0

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

2 3

ruthenium parameters
by Terry Lang 25 Aug '09

25 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

2 1

phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 24 Aug '09

24 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

5 8