- phenixbb - phenix-online.org

phenix.real_space_refine
by Heather L Condurso 23 Aug '13

23 Aug '13

I tried to run the phenix.real_space_refine that was discussed in the CCN but I get the following error. import mmtbx.refinement.real_space.driver ImportError: No module named driver I downloaded the latest nightly build dev-1463. Even when asking for the help I get the same error. I did however successfully create some FEMs which look lovely. Heather Condurso UF-Department of Chemistry condurso(a)ufl.edu

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Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Aug '13

23 Aug '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line at the MAX-II ring. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E. More information can be obtained from Tomás Plivelic (tomas.plivelic(a)maxlab.lu.se<mailto:[email protected]>). Information about the MAX IV laboratory can be obtained at the homepage www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Find peaks and holes documentation
by Morten Grøftehauge 22 Aug '13

22 Aug '13

Hi, I wanted to try phenix.find_peaks_holes with anomalous structure factors from XPREP but I ran into a few problems. And then I tried to fix them by reading the manual and that was really hard too. So first the missing manual. If I google it I get this page http://www.phenix-online.org/documentation/find_peaks_holes.htm which is for the GUI. When I go back to the documentation http://www.phenix-online.org/documentation/phenix_documentation.html I can't find the link for it (which is also why I was using Google to find it in the first place). I also checked the source to see if the link was somehow misnamed. Anyway, running it from the command line with default settings is not hard. phenix.find_peaks_holes model.pdb reflections.hkl but I run into this error message Sorry: Unresolved amplitude/intensity ambiguity: /path/path/path/reflections.hkl SHELX reflection files may contain amplitudes or intensities. Please append =amplitudes or =hklf3 or =intensities or =hklf4 to the file name argument or parameter to resolve the ambiguity. and I don't how to do that. If I add .hklf3 at the end of the file name I get the same error. If I go reflections.hkl=hklf3 I just get a message that I need to supply a reflection file. What is the syntax? Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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coot add residue issue
by Heather L Condurso 21 Aug '13

21 Aug '13

Dear all, I have been trying to add a residue to my model in coot for hours now. The add terminal residue function adds a residue far from the end of my chain and I've tried moving it manually and it keeps going back and it never makes a bond between the two amino acids. Is there a trick in coot or a better way to do this in phenix? Thanks, Heather Condurso UF-Department of Chemistry

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peptide ligand refinement problems
by Mengbin Chen 20 Aug '13

20 Aug '13

Dear Phenix Users, My colleague has got into trouble when he was refining a peptide ligand with a coumarin ring attached via a peptide bond. The peptide part is composed of natural amino acids, which does not require a cif file. On the other hand, a cif file has been created for the coumarin ring. Unfortuantely, after the refinement run, the peptide and the coumarin ring fell apart, and we could not figure out why this is happening. We are using the Phenix-dev-1370 version. Any help would be appreciated! Thank you in advance, Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Re: [phenixbb] HKL2000 behaved weirdly
by Mengbin Chen 20 Aug '13

20 Aug '13

Sorry for being late in replying, but thank you all for your suggestions! The resolution is ~3 angstroms, so it was quite easy to pick more than 100 peaks for indexing. So I tried to index ~5-6 images at the same time as you suggested, the Bravais Lattice window appeared (and I reset the beam center too), but the unit cell dimensions were ~10 angstroms along one axis, which was not appropriate since the protein is around 40 kDa. I tried to manually pick peaks for indexing, still cell dimensions were too small to be properly assigned. I feel the crystal has got severe problems of multiple lattices and high mosaicity at the same time, which made it hard to index. I am still playing around with the dataset to see if I can get any luck with it, so I'll let you know if I can work this out. Mengbin On Fri, Aug 16, 2013 at 12:18 PM, Noinaj, Nicholas (NIH/NIDDK) [F] < noinajn(a)niddk.nih.gov> wrote: > Mengbin, > > > This happens in HKL2000 with tough datasets. The data can sometime appear > to be very nice, possibly some high mosaicity, but still not process > properly. I have seen this many times. As mentioned already, the next > step is to start trying different things to get the data to process. > WIthout knowing more about resolution, etc, here is a few things to try. > > 1- Check and the double check the beam center. Then, check it again! > With troublesome datasets, this is EXTREMELY important. In HKL2000, > everytime you hit Abort Refinement, you have to reset the beamcenter again. > SO monitor the beam center and everytime it gets too far away from the > actual numbers, reset it. > > 2- you want to try to have roughly 100 peaks for indexing at minimum (if > possible), so change the resolution limits to 15 ang - 4 ang, then retry > indexing. IF this does not work, try 15-5ang, then 12-5, then 10-5, etc. > > 3- If #2 doesn't work, then you can alway try indexing using multiple > frames, esp if you don't have a enough peaks on the first frame. To do > this, please see the HKL2000 manual, or let me know, i can send you some > screenshots or give you a call to guide you via phone. here, you can use > 5-10 frames for indexing if needed. > > 4- as a last option, you can always manually select your peaks. i have had > this work nicely in the past, but again, last option. > > 5- you could try other data processing programs too such as MoSFLM, XDS, > Xia2, etc. > > If you still don't get it working, i am more than happy to take a quick > look. Just send me one of your frames to analyse. Of course, everything > will be strictly confidential. Thanks in advance and good luck! > > > > > Cheers, > Nick > > > > ________________________________ > From: Mengbin Chen [mengbinc(a)sas.upenn.edu] > Sent: Thursday, August 15, 2013 3:12 PM > To: PHENIX user mailing list > Subject: [phenixbb] HKL2000 behaved weirdly > > Dear All, > > I used HKL2000 to index my data, but weird things happened: after I hit > peak search, the data were selected to index, and I chose primitive > triclinic to continue. After I hit refine, the circles for peak search > disappeared, and if I hit "Bravais Lattice", the table would not show up, > which meant that I could not proceed to refine in the potentially correct > Bravais Lattice. I don't know if anyone else has encountered this problem > before, so any suggestions would be greatly appreciated! > > Thank you in advance, > Mengbin > > -- > Mengbin Chen > Department of Chemistry > University of Pennsylvania > -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Preferred treatment of residues with no electron density
by Mark Saper 20 Aug '13

20 Aug '13

What is the preferred method for handling missing residues or residues with zero occupancy, in terms of PBD submission? I see three options: Remove them from the model set occupancy=0 and flag in REMARKs 475 and 480 keep occupancy=1 and allow the temperature factors to climb I have a disordered region in my molecule which I am restraining to a portion of a structure in which that region is well resolved. There are several residues that have no density in the current refinement, yet I want to keep them in the model. Suggestions? Mark _______________________________________________ Mark A. Saper, Ph.D. Department of Biological Chemistry, University of Michigan Medical School 3040 Chemistry Building | saper(a)umich.edu | +1 (734) 764-3353

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a question on LSTc refinement
by fn1＠rice.edu 20 Aug '13

20 Aug '13

Hi all, I read some previous post on LSTc [SIA(alpha2-6)GAL(beta1-4)NAG] refinement, but i still cannot figure out how to refine it in PHENIX. In the current version of phenix, i still could not find the ALPHA2-6 link. Does anybody have such experience? Another question is that, sialic acid (SIA) is in the monomer library of phenix. But when i run on the pdb directly, it will give the error information like, "unknown bond type for O1A and O1B". Though this error could be solved by provided the cif file generated by phenix.elbow. Thank you very much! Fengyun

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Ensemble refinement, starting water structure and alternative conformations
by Joseph Noel 19 Aug '13

19 Aug '13

Is it important (or at least useful) to remove any waters before initiating ensemble refinement wherein the waters are located in what is obvious electron density for alternative conformations of side chains? Would the presence of such waters possibly result in ensemble refinement NOT modeling the alternative conformations? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Density modification using partial model phase
by Yi xing 17 Aug '13

17 Aug '13

Does mtz file from phenix.refine report FOM? If not, is there a way to have FOM listed in the mtz file. I am trying to use the mtz from the phenix refined model as the input of the ccp4 density modification (DM) or Dmmulti. For example, mtz file from Phaser molecular replacement has all the columns to run the DM. Many thanks for any help or comments! Best, yi

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