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Re: [phenixbb] NAG-NAG description
by Chris Ulens 02 Jun '10

02 Jun '10

Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122" Thanks. -Chris On 31 May 2010, at 21:34, Georg Mlynek wrote: > Dear Chris, this did it for me. > > > Create a file which you can call whatever you want even the extension > doesn't matter. E.g.: cif_link.params > > Put in this file your links: (Which Atom of residue1 will be > connected to > which Atom in residue2 is already defined in mon_lib_list.cif) > > > > refinement.pdb_interpretation.apply_cif_link { > data_link = NAG-ASN > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname ASN and resid 297 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname NAG and resid 501 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 501 > residue_selection_2 = chain A and resname BMA and resid 502 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = ALPHA1-3. > > residue_selection_1 = chain A and resname BMA and resid 502 > residue_selection_2 = chain A and resname MAN and resid 503 > } > > 4) add this file in the GUI > > > Or run % phenix.refine model.pdb data.hkl cif_link.params > > > 5)Trouble shooting > > a)run iotbx.phil cif_link.params (this checks if the syntax is > right) > > b) check .eff file the links should be added there. You can also > check the . > geo file if you see anything strange. > > c)Having unknown to phenix.refine item in PDB file (novel ligand, > etc... > (BMA is also not there) ). phenix.refine uses the CCP4 Monomer > Library as > the source of stereochemical information for building geometry > restraints > and reporting statistics. If phenix.refine is unable to match an > item in > input PDB file against the Monomer Library it will stop with "Sorry" > message > explaining what to do and listing the problem atoms. If this > happened, it is > necessary to obtain a cif file (parameter file, describing unknown > molecule) > by either making it manually or having eLBOW program to generate it: > > phenix.elbow model.pdb --do-all --output=all_ligands > > this will ask eLBOW to inspect the model_new.pdb file, find all > unknown > items in it and create one cif file for them all_ligands.cif. > Alternatively, > one can specify a three-letters name for the unknown residue: > > phenix.elbow model.pdb --residue=MAN --output=man > > !Check the file if everything is ok! > > > Please correct if this is not ok, or there is an easier way now. > > Kind regards George. > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org > [mailto:[email protected]] Im Auftrag von Chris Ulens > Gesendet: Monday, May 31, 2010 9:14 PM > An: PHENIX user mailing list > Betreff: Re: [phenixbb] NAG-NAG description > > Dear glycobiologists and phenixfriends. > > I am trying to refine a NAG-NAG chain attached to an Asn122 in my > (pentameric) structure. > What is the proper description in the cif_link.params that is the > equivalent of the pdb description pasted below that phenix so kindly > ignores? > Also, what is the proper way to define the cif_link.params file in the > GUI? > > Thank you. > -Chris > > > LINK ND2 ASN A 122 C1 NAG A 834 1555 > 1555 1.37 > LINK O4 NAG A 834 C1 NAG A 835 1555 > 1555 1.43 > LINK ND2 ASN B 122 C1 NAG B 834 1555 > 1555 1.37 > LINK O4 NAG B 834 C1 NAG B 835 1555 > 1555 1.43 > LINK ND2 ASN C 122 C1 NAG C 834 1555 > 1555 1.37 > LINK O4 NAG C 834 C1 NAG C 835 1555 > 1555 1.43 > LINK ND2 ASN D 122 C1 NAG D 834 1555 > 1555 1.37 > LINK O4 NAG D 834 C1 NAG D 835 1555 > 1555 1.43 > LINK ND2 ASN E 122 C1 NAG E 834 1555 > 1555 1.37 > LINK O4 NAG E 834 C1 NAG E 835 1555 > 1555 1.43 > > --------------------------------------------------- > Chris Ulens, Ph.D. > Lab of Structural Neurobiology > Department of Molecular Cell Biology > Campus Gasthuisberg, ON1 > Herestraat 49, PB 601 > B-3000 Leuven > Belgium > e chris.ulens(a)med.kuleuven.be > t +32 16 345812 > f +32 16 345699 > w http://www.xtal.be > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

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segmentation fault
by Harry M. Greenblatt 01 Jun '10

01 Jun '10

BS"D Dear All, We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix. The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt(a)weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Weight optimization
by Jianghai Zhu 28 May '10

28 May '10

Hi, I am using the optimize_wxc=true and optimize_wxu=true in my last refinement. The R and Rfree went down but the RMSDs were way too large. I wonder if phenix.refine still targets the geometry when it optimizes the R and Rfree. Here are the results from almost two identical runs except the weight optimization. 1) optimize_wxc = False optimize_wxu = False wxc_scale=0.08 wxu_scale=1.66 results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006 2) optimize_wxc = True optimize_wxu = True wxc_scale=0.08 wxu_scale=1.66 results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033 I am using the dev-412 version. Thanks. -- Jianghai

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offtopic: Problem with Pymol showing maps
by Tatyana Sysoeva 28 May '10

28 May '10

Hi all, if somebody is still not on the memorial day weekend, I have a short question off-topic for Pymol-users I have several maps from Phenix and want to draw some pictures in Pymol. I am opening the files, renamed to ccp4 or map, or not, and all I am getting is just a box, which is not even a unit cell boundary. If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please! Sincerely Tanya

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Super: Rotation and translation
by J. Fleming 28 May '10

28 May '10

Hello, I've been using 'super' to align the c-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the rotation and translation of model B's second domain as it moves away from A's second domain. I can output a matrix after running super using: print cmd.get_object_matrix("A") How do I go from the matrix to an angle and distance? Thanks for any thoughts, Jon

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Re: [phenixbb] Autobuild submitted jobs
by Mark A Saper 27 May '10

27 May '10

Tom -- It turns out that each of the omit region's jobs submits another job, but that latter job is only the "test run_command" job. Why test the run_command if no subsequent jobs are submitted? Our solution, thanks to an extremely savvy cluster manager, was to install the qsub (Torque?) package on each of the computing nodes (117). Also we ran the top-level process on the head (scheduler) node, so as not to tie up a computing node while it waits for its sibling jobs (the omit regions) to finish the calculation. Overall wall-time with a separate node allocated for each omit region was about 50 minutes. Interestingly, although each node has 8 processors, the OMIT region jobs seems to only use one processor! Interestingly when phenix.refine jobs are run on my Macbook Pro, the operating system is savvy enough to spread it over 2 processors. -Mark ______________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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How to turn off mask optimization
by Schubert, Carsten [PRDUS] 26 May '10

26 May '10

Hi, Is there a way to turn off the mask optimization step in 393? I tried 'main.optimize_mask = False' but that does not work. The program spends a substantial amount of time in repeated mask optimizations and I am trying to shave off a couple minutes for each run... Cheers, Carsten

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Autobuild submitted jobs
by Mark A Saper 26 May '10

26 May '10

Dear Tom and colleagues, We're running Autobuild composite omit on a large cluster, each node has 8 processors. Autobuild submits jobs with the "run_command". And it appears that each of those jobs submit other jobs. Are the latter jobs necessary? That is, are there situtations where they wouldn't be submitted as separate jobs but run as subprocesses? Currently nodes in our cluster don't have capability of qsubing new jobs, but we are in the process of changing this. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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atom selection syntax for ALT atoms?
by Scott Classen 25 May '10

25 May '10

This is the selection for the atom I'm interested in: atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 160" I want to try a refinement with an alternate conformation at GLU160 . Can someone please help me with the proper syntax. 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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PDB Deposition Question
by Alexander Hirschi 25 May '10

25 May '10

Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated. -Alex

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