- phenixbb - phenix-online.org

optional bits of the CCI Apps installion?
by Ben Eisenbraun 03 Jun '08

03 Jun '08

Hi Phenix Developers, When I install CCI Apps, I end up with a directory that looks like this: $ ls -1 1NSF.pdb cci_apps_build cci_apps_fedora3_py251.selfx cci_apps_install_script.csh cci_apps_sources nsf_d2_peak.sca test_apps Which of the bits are optional and can be deleted without affecting the installation? It seems like the selfx install file is fine to delete. How about the sources directory? $ du -k --max-depth=1 62584 ./cci_apps_sources 125840 ./cci_apps_build 225012 . If the sources directory is not needed, that would save me about 30% of the disk use for the installation, and since I have 2-3 concurrent versions installed, and those versions get pushed around to ~75 machines across the network, every bit I can trim helps. As a side note, I think it might be clearer to refer to the "Opteron" builds of the CCI Apps as AMD64 or x86_64. I didn't see anything on the download page that makes this explicit. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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Group ADP not working
by alebus＠pasteur.edu.uy 03 Jun '08

03 Jun '08

Dear all, I am refining a structure (2.9angs res; P21) with phenix (Version: 1.3b; Release tag: rc6; linux platform) I want to carry on group_ADP refinement, according to the ('lengthy') command line : phenix.refine eden_unique1.hkl hlcoeff_blur.hkl abril28_phenix.pdb input.experimental_phases.labels="PA_BLUR PB_BLUR PC_BLUR PD_BLUR" ordered_solvent=false simulated_annealing=false simulated_annealing.mode=first strategy=rigid_body+individual_sites+group_adp+tls main.ncs=tru e main.number_of_macro_cycles=10 xray_data.low_resolution=15.0 xray_data.high_resolution=2.7 tls_group_selections.params rigid_body_selections.params group_anomalous_1.params elbow.acp_A_pdb.001.cif restraints_edits.params convert_to_isotropic=true everything works just fine (including correct handling of an 'unusual' ligand; selected NCS restraints; TLS; etc)...except for the group ADP : phenix keeps doing individual atom B-factor refinement (e.g. these are some pertinent remarks in the output pdb REMARK ****************** REFINEMENT STATISTICS STEP BY STEP ****************** REMARK leading digit, like 1_, means number of macro-cycle REMARK 0 : statistics at the very beginning when nothing is done yet REMARK 1_bss: bulk solvent correction and/or (anisotropic) scaling REMARK 1_xyz: refinement of coordinates REMARK 1_rbr: rigid body refinement REMARK 1_gbr: group B-factor refinement REMARK ------------------------------------------------------------------------ REMARK R-factors, x-ray target values and norm of gradient of x-ray target REMARK stage r-work r-free xray_target_w xray_target_t REMARK 0 : 0.3951 0.4346 -6.345353e+00 -6.295977e+00 REMARK 1_bss: 0.3189 0.3519 -6.182904e+00 -6.132416e+00 REMARK 1_rbr: 0.3199 0.3553 -6.164872e+00 -6.111524e+00 REMARK 1_bss: 0.3197 0.3548 -6.158236e+00 -6.106543e+00 REMARK 1_xyz: 0.3145 0.3612 -6.243414e+00 -6.163029e+00 REMARK 1_adp: 0.2890 0.3327 -6.111496e+00 -6.011406e+00 REMARK 2_bss: 0.2862 0.3290 -6.107396e+00 -6.004629e+00 REMARK 2_xyz: 0.2801 0.3278 -6.104559e+00 -5.995221e+00 REMARK 2_adp: 0.2783 0.3213 -6.062947e+00 -5.954846e+00 REMARK 3_bss: 0.2783 0.3214 -6.063301e+00 -5.955103e+00 REMARK 3_xyz: 0.2755 0.3218 -6.065099e+00 -5.950739e+00 REMARK 3_adp: 0.2751 0.3218 -6.062715e+00 -5.947567e+00 ... and so on, always doing 'X_adp' (and not 'X_gbr') on the different steps... starting from a single value on the B-factor column in the input pdb, of course I end up having individually varied figures in the end, which I don't want I will greatly appreciate any help on what am I doing wrong. Thanks, Alejandro

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phenix.elbow
by Morten Grøftehauge 02 Jun '08

02 Jun '08

Dear Phenix.BB, I wrote a mail earlier about some problems I had with phenix.elbow but it didn't seem to get through. I've solved two of the problems now but also found a new one so I'll try posting again. When you set the --xyz option along with --clean then your .xyz file is deleted. Of course the easy solution is simply to not use --clean but I imagine that it is a minor bug since it doesn't happen with --tripos. Secondly I have a slightly larger problem. When an isoSMILES with more than one molecule is inputted then phenix.elbow joins them up to a single molecule (or places them so closely that all programs, including phenix.elbow, interprets them as one molecule when converting to a format such as mol2 with explicit bonds). For an example try phenix.elbow --output=009_3085017 --write_hydrogens=false --overwrite --clean --tripos --smiles='C=CCN.C1C(O1)CCl' The period is supposed to designate two seperate molecules. Remember to use elbow.become_expert before running that line. I hope someone can help me. Sincerely, -- Morten K Grøftehauge PhD student Department of Molecular Biology Gustav Wieds Vej 10 C 8000 Aarhus C - Denmark Phone: +45 89 42 52 61 Fax: +45 86 12 31 78 www.bioxray.dk

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shell variable SSH_Path not set
by shivesh kumar 02 Jun '08

02 Jun '08

Dear all, We have installed Phenix in Red Hat Linux enterprises 5. It takes a long time for the GUI to appear with the following message-- Shell variable SSH_Path not set What is the solution of this problem. Thanx in advance for suggestions. shivesh

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Error running cci_apps
by JENDREK 29 May '08

29 May '08

Hi, I've encountered following error running cci_apps (25.05.08 build): Sorry: Error reading CIF file: "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/monomer_library/mod_rnaC2.cif" (IOError: [Errno 2] No such file or directory: '/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/monomer_library/mod_rnaC2.cif') I thought it might be my data fault but the same error appears during test_apps script. I'm running cci_apps on the Mac (Tiger 10.4.11). Funny thing that Phenix 1.3rc2 is running without the problem. I hope someone can help me solve the mystery... Andrzej -- alnyds[at]gmail[dot]com

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prosthetic group
by Bryan W. Lepore 29 May '08

29 May '08

should prosthetic groups be attached to proteins by those LINK or CONNECT records as found in typical PDB files? e-LBOW seems for _ligands_ only. -bryan

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BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY
by Cyndi Salbego 28 May '08

28 May '08

BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. Focused beam size 20x80micron Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalbego(a)anl.gov for further details. See http://necat.chem.cornell.edu for information on our beamlines and a calendar of available days.

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syntax and alternate conformations
by Mark Collins 28 May '08

28 May '08

Hi I have an unexpected result, my syntax must be incorrect. The relevant script commands are below, the problem is residues A113 and B143 have alternate conformation occupancies that sums to 0.98 to 1.06 respectively. Clearly alternate conformations of a single residue should sum to 1 (or less than 1 possibly). Any suggestions please? Thank you, Mark refine { strategy = *individual_sites \ rigid_body \ *individual_adp \ group_adp \ tls \ individual_occupancies \ *group_occupancies \ group_anomalous \ occupancies { individual = None group = chain A and resid 113 and altid A group = chain A and resid 113 and altid B group = chain B and resid 143 and altid A group = chain B and resid 143 and altid B } }

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Re: [phenixbb] problem with high Rfree
by Christina Bourne 28 May '08

28 May '08

Thank you very much for your help. I just wanted to follow up in how I'm progressing with this. I tried the things you suggested, as well as a variety of others, with no luck. It turns out that my 4mol/AU P41 twinned data is ACTUALLY 8mol/AU P212121. The packing in the AU has an almost 41 screw relating 4 mols to the other 4. When this operation is carried out, 2 mols overlay 2 others almost perfect, while the other 2 overlay the other 2 by 180 degrees. So my AU packing is a pseudo-41 with apparent twinning. (The b dimension did not need halving, so my cell is 2x the size, if that makes sense). The data refines very well as P212121, and Rfree drops like a rock. Again, thank you so much for your suggestions, and Phenix is really wonderful! Christina ----- Original Message ---- From: Pavel Afonine <pafonine(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Sent: Tuesday, May 20, 2008 1:51:42 AM Subject: Re: [phenixbb] problem with high Rfree Hi Christina, I usually observe similar R/Rfree behavior when I use LS target instead of maximum-likelihood. In fact, twin refinement in phenix.refine is based on LS target function. This is just to share my observations; it's not necessarily happening in your case. - How many of test reflections you have and how they are distributed in resolution bins? - Just out of curiosity: did you try to ignore twinning and run refinement with default target? - What if you don't run SA? - Did you try to play with target weights (try different values for wxc_scale and wxu_scale) to see how this affect the R-factors? - Are you using the latest (or one of) phenix.refine? - Did you try to fill in water? Could you send a log file: may be we could spot something outstanding... Pavel. On 5/19/2008 1:32 PM, Christina Bourne wrote: Hello BB, I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A. I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density. I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong. Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell. Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina ________________________________ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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OXT
by Rife, Christopher L 23 May '08

23 May '08

Should phenix.refine be able to handle OXT? I find it is moving the OXT atom ~2A from where it should be. Do I need to rename it or add a separate definition to the refinement? Thanks, Chris

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