- phenixbb - phenix-online.org

elbow.builder
by William Scott 03 Jun '07

03 Jun '07

Hi folks: I've been playing around a bit with elbow.builder, and found the following: -------------- elbow.builder --opt --smiles c1ccccc1 gives me a nice, flat, hexagonal benzene elbow.builder --gamess --smiles c1ccccc1 gives me a benzene that is slightly bent out of plane and has other small distortions with respect to 6-fold symmetry. Is this a problem with elbow, a problem with gamess, or a Jahn-Teller effect? ------------ Also, I noticed elbow.doc requires a mozilla or netscape executable. Since both of these are obsolete, maybe a firefox executable should be an option? On OS X, "open" should open a URL in the user's favorite browser, but it doesn't seem to work right with Safari (which stupidly opens a Finder window of the directory containing the html file). My workaround was to make a shell script called "mozilla" that invokes Camino: #!/bin/zsh -f /usr/bin/open -a Camino "$@" HTH someone. ------------------ Bill William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott

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Binary file not executable during installation?
by lkemp＠mrc-lmb.cam.ac.uk 01 Jun '07

01 Jun '07

Hello BB I am trying to install Phenix on Suse 9.3. I went for the 2.6 version as i got this: 2.6.11.4-21.17-smp i686 when i typed uname. However it required libtermcap.so.2 so i switched to the 2.4 version as suggested on a previous BB query. This however also goes wrong: This time the binary.log file says that python in /common is not executable I checked and this was due to the need for libstdc++.so.6. I made a softlink directing this to the .5 version but it doesnt like this. Does anyone have any ideas??? Thank you in advance for any help Lauris

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AssertionError & TLS
by Kanchan Anand 01 Jun '07

01 Jun '07

Hello everybody, I am a new user of Phenix and presently trying to refine 3.6 A data of a protein-RNA complex. whenever i add tls into my .def file for the next run, i get this problem: Traceback (most recent call last): File "/data/software/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5 , in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/data/software/phenix-1.3b/phenix/phenix/refinement/command_line.py", li ne 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/data/software/phenix-1.3b/phenix/phenix/refinement/driver.py", line 130 8, in run log = log) File "/data/software/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 887, in refinement_machine h_params = h_params) File "/data/software/phenix-1.3b/mmtbx/mmtbx/refinement/adp_refinement.py", li ne 160, in __init__ tools.split_u(fmodel.xray_structure, tls_selections, offset) File "/data/software/phenix-1.3b/mmtbx/mmtbx/tls/tools.py", line 468, in split _u assert (u_iso < 0.0).count(True) == 0 AssertionError I have downloaded the new 1.3b version and without tls the program runs fine! could you please help Thanks in advance Regards kanchan

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textal problem
by Daniele de Sanctis 31 May '07

31 May '07

Dear all, I'm running textal.build to build a model in a 3.2 A map, and I'm using the option --input_model and --sequence. It seems to run ok until finishing the lookup but then i got the error message: doing sequence alignment against: ../pippo.seq sh: Syntax error: Bad fd number error: [Errno 2] No such file or directory: 'phentx-lookup-correct.pdb' indeed the file is not there, but i guess that is not there because o the previous Syntax error. any clue? thanks d -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartato 127 2781-901 Oeiras Portugal

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Re: [phenixbb] how to add phase info to the autosol wizard
by Tom Terwilliger 31 May '07

31 May '07

Hi Chuanbing, I'm sorry, that option isn't there yet! It is one that is on my list of to-do's. -Tom T At 01:51 AM 5/31/2007, CB Bian wrote: >Dear all, > > I am trying to add phase info from externally calculated > phases to the autosol wizard with S-SAD data. But I can not find > the option to do it in the running. Can someone help me? > > >Thanks in advance > >Chuanbing > >-- >ChuanBing Bian, Ph.D Student >Structural biology group >State Key laboratory of Structural Chemistry >Fujian Institute of Research on the Structure of Matter, >Chinese Academy of Sciences >155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China >E-mail: ><mailto:[email protected]>cbbian(a)gmail.com ><mailto:[email protected]>cbbian(a)fjirsm.ac.cn >Tel:(office)+86-591-8370-5814 ><http://protein.fjirsm.ac.cn/>http://protein.fjirsm.ac.cn >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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how to add phase info to the autosol wizard
by CB Bian 31 May '07

31 May '07

Dear all, I am trying to add phase info from externally calculated phases to the autosol wizard with S-SAD data. But I can not find the option to do it in the running. Can someone help me? Thanks in advance Chuanbing -- ChuanBing Bian, Ph.D Student Structural biology group State Key laboratory of Structural Chemistry Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002 P. R. China E-mail: cbbian(a)gmail.com cbbian(a)fjirsm.ac.cn Tel:(office)+86-591-8370-5814 http://protein.fjirsm.ac.cn

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Re: [phenixbb] Death by Big-ass structure
by Petrus H Zwart 30 May '07

30 May '07

Hi Ulrich, Frank, Ralf has just placed a new version of cci_apps on our download sites (www.phenix-online.org). It contains a new application named phenix.xmanip (or mmtbx.xmanip if you only download the cctbx). It is basically a rewritten version of the reindex.py script I once wrote as an example jiffy. xmanip can read in various reflection files or mtz/cns data columns which subsequently can be used in reindexing or other tasks. The parameter file I send Frank a couple of days ago should still work, even though some rearrangements have been made . Typing phenix.xmanip reindex.def should do the trick. Other options are available as well. One could - generate map coefficients from a model (plain FC,PHIC, or sigmaA style maps if observed data is available) - get anomalous / isomorphous differences - scale two datasets together - generate symmetry mates of a model - the 'custom' option allows you to pass in a snippet of python code and have it executed. One has access to all datasets and molecular model read in. You could for instance add two datasets or multiply them if it makes you happy. Full documentation is under way. If you have any question, please let me know. Peter

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Re: [phenixbb] phenix.refine questions: weights, docs, etc.
by Ralf W. Grosse-Kunstleve 29 May '07

29 May '07

Hi Dale, > The sets of parameters that can be refined simultaneously is a result of the > choice of optimization method, not the choice of the function being optimized. > The crucial difference is how the second derivatives are handled. In the > methods used in Phenix and CNS the seconds derivatives of all parameters are > assumed to be equal and uncorrelated. This is true only for the first iteration of a minimization in a phenix macro cycle. After that the L-BFGS method builds up an approximation of the second derivative information. > To ensure that this assumption is true > only parameters of the same category can be varied in a single cycle. This > means that the coordinates can be varied, but the B factors and scale factors > have to be held fixed. When the B factors are varied the coordinates and > scale factors must be constant. When the scale factors are varied everything > else must be fixed. > > Other refinement programs use second derivatives in a more explicit way > than Phenix and do vary more types of parameters in a single cycle. Shelxd is > the most powerful and, by default, varies all parameters of all classes each > cycle. Refmac, to the best of my knowledge, refines both coordinates and ADPs > together, but does refine TLS parameters in a separate step. As far as I know, Shelx doesn't use second derivatives at all. Shelx is shaped completely by the least-squares approach, using the Jacobian. You couldn't plug another target function into Shelx as you can do in the common macromolecular programs. I.e. there is in fact a link between the minimization method and choice of the target function. REFMAC uses a block-diagonal approach that only takes the correlations of the parameters of one atom into account. phenix approximates these with the L-BFGS method. We have not actually tried to refine coordinates and B-factors simultaneously since we've been too busy with other priorities. In theory it should be possible, but I'm sure it will take a lot of fine-tuning. > Since all the parameters of our models are correlated with one another, it > is better to refine as many of them at once as possible. Implementing > the join refinement of all these kinds of parameters is difficult, so to save > programmers' time approximations are sometimes made. We'll spend the time when we find it. :-) But I don't expect spectacular gains, no matter how long we beat on the second derivatives. Ralf

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phenix.refine questions: weights, docs, etc.
by Frank von Delft 29 May '07

29 May '07

Hi, four questions on phenix.refine: 1) What's the reason for refining bss, xyz and adp in separate cycles? CNS does that too while refmac (I believe) refines them simultaneously. I suspect I missed something, but I thought the power of ML refinement is that no refinable parameters are held constant if they're not supposed to be. (At least, wasn't that the big deal in Sharp when it came out?) 2) How does one figure the right restraint weights? (wxc and wxc). In refmac, I've always calibrated the weight with rmsd(bonds), tightening it until rmsd(bonds) is ~0.018 (or below for lower reso); invariably this is where Rfree will decrease furthest and smoothly as well (i.e. without that silly rise at the end.) With phenix.refine I'm finding that I only get Rfree to drop monotonously when I tighten the weights (both wxc and wxu) so much that rmsd(bonds) goes down to ~0.002. Would there be a different way to do this? 3) There isn't currently torsional refinement, is there? For high-temperature simulated annealing, I mean. I'm having the same weight-adjustment question for SA, except is harder to fiddle with because jobs take so long, but with torsional that becomes moot. Or should one always put very tight weights on for SA? 4) Is there good documentation for all the loads and loads of keywords? The names themselves are just descriptive enough to be interesting, but obviously not enough to be informative if I don't just want the black box. Nice program, though, got to say... phx.

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Death by Big-ass structure
by Frank von Delft 25 May '07

25 May '07

Hi, we get the memory error below for a structure of 30603 atoms 273217 reflections 2.1A H3 193.868 193.868 352.223 90.00 90.00 120.00 10x NCS Anything I said? It's not THAT large a problem, I'd have thought, or should we go to the rhombohedral setting instead? (Hmmmm, this rings a bell, wasn't there a posting about this 3 days ago? Nothing in the archives, was it CCP4bb?) Cheers phx Traceback (most recent call last): File "/usr/local/phenix/phenix-1.26b/phenix/phenix/command_line/refine.py", line 5, in ? command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/command_line.py", line 75, in run refine_object.run( File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/driver.py", line 1236, in run log = log) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/strategies.py", line 273, in refinement_machine log = log) File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/weight_xray_chem.py ", line 111, in __init__ self.fmodel_copy = self.fmodel.deep_copy() File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1003, in deep_copy map_types = self.map_types File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/twin_f_model.py", line 888, in __init__ self.update_f_mask() File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/twin_f_model.py", line 1370, in update_f_mask self.f_mask_array = mask.structure_factors( self.miller_set ) File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/masks.py", line 103, in structure_factors flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) MemoryError

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