January 2009 - phenixbb - phenix-online.org

Unmasking cavities
by Frank von Delft 24 Jan '09

24 Jan '09

Hi After being through phenix.refine, I see in my hydrophobic core a big space (a few atoms wide) that is filled with strong negative difference density. I suspect the culprit is the bulk solvent mask, which is defined too tightly. The online manual mentions three parameters, but not what they do. solvent_radius, shrink_truncation_radius, grid_step_factor What *exactly* do they do? (I thought I'd elicit a contribution for the online docs this way :) Cheers phx

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geometry of disulfide and NAG
by Li-Zhi Mi 23 Jan '09

23 Jan '09

Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,

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HL A B C D
by Raja Dey 22 Jan '09

22 Jan '09

Hello, If I want to use F, SigF and HLA, B, C and D in the phenix refinement, should I use the same command like phenix.refine data.mtz model.pdb, where data.mtz contains FREER, F, SIGF, HLA, HLB, HLC and HLD? How do I check that phenix.refine used the HL coefficients? Looking forward to hearing from you... Thanks... Raja

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Disappearing side chains after autobuilding
by Katya Heldwein 22 Jan '09

22 Jan '09

Hi, I ran phenix.autobuild with default setting (rebuild_in_place), and noticed that some side chains were gone in the resulting overall_best.pdb. That is, let's say, I started with Phe as residue 10. After rebuilding, the Phe10 is still called Phe in the output file, but the side chain atoms are gone, leaving residue 10 as Ala. This happened for several side chains, and I am at a loss for why this happened. Is this some kind of a bug? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 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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missing map coefficients
by Anne Mølgaard 16 Jan '09

16 Jan '09

I am new to Phenix, so there might be an easy explanation for this problem, though I have not been able to find a solution in the documentation. I am using phenix version 1.3b-rc4, intel-linux-2.6. I have solved a structure using phenix.automr, followed by phenix.autobuild (run from command line using "phenix.autobuild data=fromXDS_unique.mtz model=AutoMR_run_2_/MR.1.pdb seq_file=sequence.fas"). The program runs succesfully, and I get the output files I should expect. However, the overall_best_refine_map_coeffs.mtz does not contain the map coefficients 2FOFCWT PH2FOFCWT for the 2mFo-DFc map and FOFC and PHFOFC for the Fo-Fc difference map. mtzdmp gives me the following columns: 1 ASC 0 28 0 100.00 10.6 10.6 28.28 1.85 H H 2 NONE 0 35 0 100.00 13.3 13.3 28.28 1.85 H K 3 NONE 0 71 0 100.00 26.6 26.6 28.28 1.85 H L 4 NONE 1.0 1888.8 0 100.00 148.71 148.71 28.28 1.85 F FP 5 BOTH 1.0 1.0 0 100.00 1.00 1.00 28.28 1.85 Q SIGFP 6 NONE -180.0 180.0 0 100.00 2.08 90.23 28.28 1.85 P PHIM 7 BOTH 1.000 1.000 0 100.00 1.000 1.000 28.28 1.85 W FOMM 8 NONE .0 19.0 0 100.00 9.50 9.50 28.28 1.85 I FreeR_flag 9 BOTH .0 .0 0 100.00 .00 .00 28.28 1.85 F FC What should I do to get these map coefficients? Thanks for your help! Best regards, Anne

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Will phenix.refine read CNS *.cv files?
by Scott Classen 15 Jan '09

15 Jan '09

Hi all, I'm embarking on a collaboration with someone who is providing me with CNS cross validated data files. They look something like this. NREFlection= 92086 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 SIGI= 735.200 TEST= 0 INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 SIGI= 1531.800 TEST= 0 INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 SIGI= 35.700 TEST= 1 INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= 0.182215E+06 SIGI= 7507.000 TEST= 0 INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= 0.169206E+06 SIGI= 6999.000 TEST= 0 INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 SIGI= 233.200 TEST= 0 When I try to run phenix.refine --dry_run my_model.pdb my_CNS_cv_file.cv I get the following error: Processing inputs. This may take a minute or two. Sorry: Unknown file format: my_CNS_cv_file.cv Any ideas? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [phenixbb] Will phenix.refine read CNS *.cv files?
by Scott Classen 15 Jan '09

15 Jan '09

Hi Nick, I think I tried that at some point, but the problem lies in the IOBS. Some are regular float fortran format: INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 while other IOBS are large and for some reason CNS decided to put them in scientific notation such as INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 As far as I can tell this requires two sets of fortran format statements for f2mtz to work properly. format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,E15.3,/,24X,F10.3,6X,F10.0)' or format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,F10.3,/,24X,F10.3,6X,F10.0)' I'm playing around with with grep to separate the original cv file into reflections with IOBS in F10.3 format and those with IOBS in E15.3 format, convert with f2mtz, then CAD them together, but this is bloody cumbersome. I was hoping phenix.refine would just automagically figure it all out. Scott On Jan 14, 2009, at 5:35 PM, Noinaj, Nicholas (NIH/NIDDK) [F] wrote: > Scott, > > <not sure if anyone has remedied your problem yet> > > I don't know if you can read cns file directly into phenix.refine. > but > here is another option....convert the cns file to *.mtz using CCP4. > If > you use the CCP4i GUI --> Reflection Data utilities --> Convert > to/modify/extend MTZ. You can also retain the original flagged > reflections here also. You can then use the *.mtz file in > phenix.refine. > > If you need further help, just drop me a quick email. I can also > try it > here if you supply me with the data file, but this may be too 'top > secret' (lol). Best of Luck! > > > > > > Cheers, > Nick > > > > -----Original Message----- > From: Scott Classen [mailto:[email protected]] > Sent: Wednesday, January 14, 2009 8:06 PM > To: PHENIX user mailing list > Subject: [phenixbb] Will phenix.refine read CNS *.cv files? > > Hi all, > I'm embarking on a collaboration with someone who is providing me with > CNS cross validated data files. They look something like this. > > > NREFlection= 92086 > ANOMalous=FALSe { equiv. to HERMitian=TRUE} > DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END > INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 > SIGI= 293.800 TEST= 0 > INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 > SIGI= 735.200 TEST= 0 > INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= > 0.242506E+06 > SIGI= 17098.000 TEST= 0 > INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 > SIGI= 1531.800 TEST= 0 > INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 > SIGI= 35.700 TEST= 1 > INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= > 0.182215E+06 > SIGI= 7507.000 TEST= 0 > INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= > 0.169206E+06 > SIGI= 6999.000 TEST= 0 > INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 > SIGI= 233.200 TEST= 0 > > When I try to run phenix.refine --dry_run my_model.pdb > my_CNS_cv_file.cv > > I get the following error: > > Processing inputs. This may take a minute or two. > Sorry: Unknown file format: my_CNS_cv_file.cv > > > Any ideas? > > Thanks, > Scott > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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f_prime and f_double_prime in MIRAS/SIRAS
by Leo Sazanov 15 Jan '09

15 Jan '09

Hi, how can one enter f_prime and f_double_prime values for SIRAS/MIRAS experiments in phenix.autosol? Could not find any examples of that in manual, only for MAD. Just putting them in as f_prime=... and f_double_prime=... does not work, it then assumes MAD experiment. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Jan 15th deadline - User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 Jan '09

14 Jan '09

Dear Users, /Deadline for March/April 2009 proposals will be Jan 15, 2009. / Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects 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 submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for March/April 2009 allocation period, proposals must be submitted by January 15, 2009. The deadline for CC proposals for the time period May/June 2009 will be March 15, 2009. Regards, Banumathi Sankaran

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Fwd: Refinement using new Phenix causes electron density/model mismatch
by Miles Pufall 13 Jan '09

13 Jan '09

The bb bounced my email back because the enclosures were too big - let me know if you'd like them. Thanks - Miles Begin forwarded message: > From: Miles Pufall <mpufall(a)cmp.ucsf.edu> > Date: January 12, 2009 12:16:06 PM PST > To: phenixbb(a)phenix-online.org > Subject: Refinement using new Phenix causes electron density/model > mismatch > > Hi Guys - > > I am having a very puzzling problem using the new Phenix (1.4-3). I > have about 20 structures that I am preparing to deposit with an > accepted manuscript, and decided to do a final refine using the > phenix.refine_gui not only to see if I got better numbers, but to > use the integrated validation tools, which I love. Unfortunately, > often, but not always, when I refine the pdb against the > *_refine_data.mtz the statistics are a bit worse, and when I open > the resulting *.map_coeffs.mtz in Coot it appears to be shifted with > tons of negative electron density. Needless to say, this is making > my nervous, so I've tried a few things: > > 1) Tried refining the same .pdb and .mtz files in Refmac - I seem > to get the same shifting. > 2) Try using the old .def file left over from the final run (just > to make sure I didn't screw up some setting) - and I get the same > shifting. > 3) Try refining against the original .sca file - and I get the same > shifting. > 4) Try molecular replacement of the refined .pdb against the > original .sca file - and sometimes, but not always, get a shift. > > I am nervous and concerned - can you help me figure out what > happened? I am enclosing an example - > > refine_001.pdb = pdb I refined in new phenix > refine_001map_coeffs.mtz = mtz output from new phenix refinement > (lots of red) > oste44a_output.sca = original scale file from HKL2000 > MR.1_refine_data.mtz = data from which I am refining > sgk_ost_temp_H_refine_004.pdb > > Thanks - > > Miles > > Miles Pufall > Postdoctoral Scholar > Yamamoto Lab > UC San Francisco > Cellular and Molecular Pharmacology > Mail Stop 2280 > 600 16th Street, Genentech Hall S-574 > San Francisco, California 94158-2517 > (415)476-4480 > > Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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