- phenixbb - phenix-online.org

Strange negative density when refining at low resolution
by Andrew Purkiss-Trew 20 Feb '09

20 Feb '09

Dear Phenixers I've been helping a colleague with a dataset at ~3.8 Angstroms (phases and map from AutoSharp using SAD phasing). At the moment he has an incomplete polyALA model consisting of two chains related by NCS and a few extra sections. Refinement seems to proceed OK using phenix.refine version 1.4-3, but the resultant maps have blobs of negative density in the core of the protein. I am assuming that these are a side-effect of the bulk-solvent correction part of the refinement which is confusing the region where the protein sidechains would be as solvent. There are no corresponding negative peaks on the surface of protein, but some positive peaks where larger sidechains may be. Is this interpretation likely to be correct and if so, which parameter should be altered in the Bulk Solvent section of the input to allow for a bigger mask around the protein. I see that it isn't recommended to change the parameters, but the refinement.mask.solvent_radius=1.0 looks like an obvious candidate. If necessary, I can get an image made showing the maps. Thanks Andrew Purkiss-Trew This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England & Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so.

2 1

2 Wonderings: adding H atoms and overcoming overfitting problem
by Young-Jin Cho 19 Feb '09

19 Feb '09

Hi, my current wonderings are as below: First, how can I add H atoms into nucleotide ligands in pdb file? I did 'phenix.reduce model.pdb > model_h.pdb', but as I see it didn't add H's of sugar (1', 2', 3' 4' and 5'). Once I had this kind of problem before, I was suggested to use phenix.ready_set command but seemingly this does not work any longer with last version that I am using now. Also, is it possible to add H into phosphate group? The second very general question is about getting over overfitting problem. My phenix runs gave me too much difference between R and Rfree about .7 w/o adding H atoms. I assume it came from water molecules because it(huge gap) just starts to happen after 1_bss stage. If anybody can suggest a good way to get over this problem, you will save my tremendous times and useless efforts. Big thanks in advance, Young-Jin

3 4

optimizing target weights in phenix
by Yusuf Akhter 19 Feb '09

19 Feb '09

*Hi Everybody, I am using phenix-1.3b. When i tried to use "Optimizing target weights" utility by typing following command line * *phenix.refine data.hkl model.pdb optimize_wxc=true optimize_wxu=true I got following error. * Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/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 "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given) *May anybody tell me please how can i fix these errors?? Thanks in advance. yusuf *

3 3

maintenance release of CCI Apps
by Pavel Afonine 17 Feb '09

17 Feb '09

PHENIX users: A maintenance release of CCI Apps is available: http://www.phenix-online.org/download/ See "Changes" section for the list of problems fixed: http://www.phenix-online.org/download/cci_apps/ Pavel.

1 0

phenix.refine GUI freezes when using Coot or Pymol
by Derek Logan 17 Feb '09

17 Feb '09

Hi, I've been using the phenix.refine GUI for a few days now and find it a very valuable addition. However I notice that when I choose to display the results of refinement in Pymol or Coot, it freezes the GUI until I exit the chosen graphics program. Is this a bug or a feature? If nothing else, it makes it hard to analyse the MolProbity results in Coot. I'm using Mac OS X 10.5.6. Thanks Derek __________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics mob: +46 76 8585 707 Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden

2 1

Re: [phenixbb] individual plus group adp's
by Pavel Afonine 17 Feb '09

17 Feb '09

Hi Emmanuel, why don't you just do combined TLS + individual ADP refinement, which is the best option in most of cases? Anyway, here is the answer to your question. If you are running phenix.refine from the command line, the following command phenix.refine model.pdb data.hkl params.txt where the file "params.txt" contains these lines refinement.refine { strategy = *individual_sites rigid_body *individual_adp *group_adp tls \ *occupancies group_anomalous adp { individual { isotropic = chain A or chain B } group_adp_refinement_mode = one_adp_group_per_residue \ two_adp_groups_per_residue *group_selection group = chain C } } will refine: - individual coordinates for all atoms; - individual isotropic B-factors for all atoms in chain A and B; - group B-factor for chain C (one B-factors per whole chain C); - occupancies for all atoms in alternative conformations (if any present in your structure). Also should be able to do this using phenix.refine GUI. Please let me know if you have any questions! Pavel. On 2/17/2009 7:47 AM, Manolis Saridakis wrote: > Dear Colleagues, > I have a question that I guess has a simple answer which however I haven't been able to > find in the manual. I am using phenix.refine version 1.4. > > My model has 3 chains + solvent and I would like to refine individual adp's for > everything except one of the chains, for which I would like to keep a group adp > refinement option. > > My attempts have failed so far: depending on what exactly I do (which I guess there is > no point detailing here), I am either refining my other chains as groups too (i.e. the > same number is added to all adp's of the chain) or nothing stays grouped. However, in > the manual it does say if I am not mistaken that one can do what I want (but there is > no example of that situation). > > Many thanks for your help! > > Best wishes, > > Emmanuel Saridakis > >

1 0

LINK records, sugars, and a question in two parts
by Engin Ozkan 14 Feb '09

14 Feb '09

Hi everyone, I was wondering if phenix.refine does or does not write out LINK records in the output pdb. Also, are carbohydrate groups written out as ATOM or HETATMs? The reason I am asking is that I was trying to use a sugar group geometry/naming validation tool called pdbcare (at glycosciences.de), and the program is failing to read out the sugar groups from the pdb. One reason I can see is that the sugars are written out with ATOM cards, while the program possibly expects HETATM, and the other is that this program might be looking for LINK cards (These pdb files were written put by phenix 1.3rc6, so maybe if I rerefined them with 1.4.3, I might get a different result). By the way, I can get these files to be read properly by pdb2linucs at the same webpage (after telling it to use both ATOM and HETATM, and telling it to calculate linkages itself). If there is anyone out there who has used the pdbcare successfully on phenix.refine pdb files, please let me know. It would also be great to add carbohydrate validation tools to the army of great modules in phenix (such as phenix.xtriage and phenix.ramalyze). Engin

2 1

phenix.automr ensemble/component question
by Scott Classen 13 Feb '09

13 Feb '09

Hi Phenixers, I'm a bit confused about the proper syntax for my phenix.automr job. This is probably a simple concept, but I'm running on 3 hours of sleep as my kid was up all night, and my synapses aren't working so good. I expect 2 copies of my protein per AU My protein is composed of two domains I have a single PDB search model for each domain is either of these commands correct? phenix.automr data=mydata.sca \ ensemble_1.coords=domain1.pdb \ ensemble_1.identity=95 \ ensemble_1.copies_to_find=2 \ component_1.mass=40579 \ component_1.component_copies=2 \ ensemble_2.coords=domain2.pdb \ ensemble_2.identity=95 \ ensemble_2.copies_to_find=2 \ component_2.mass=13410 \ component_2.component_copies=2 or phenix.automr data=mydata.sca \ ensemble_1.coords=domain1.pdb \ ensemble_1.identity=95 \ ensemble_1.copies_to_find=1 \ component_1.mass=40579 \ component_1.component_copies=2 \ ensemble_2.coords=domain2.pdb \ ensemble_2.identity=95 \ ensemble_2.copies_to_find=1 \ component_2.mass=13410 \ component_2.component_copies=2 essentially I'm not really using an ensemble of search models, I only have a single PDB for each domain. So should ensemble_1.copies_to_find and ensemble_2.copies_to_find be set to 1 or 2? 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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

1 0

Error
by Knapp, Mark 11 Feb '09

11 Feb '09

This occurs when running phenix.refine_gui with twin mode turned on. A Python error was detected. This is almost certainly a bug; please send an email containing this message to phenixbb(a)phenix-online.org so we can fix it. Thanks! TypeError : float argument required, not NoneType Traceback: Traceback (most recent call last): File "/protos/package/strucbio/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 269, in OnUpdate self.notebook.run_tab.OnStatsUpdate(event) File "/protos/package/strucbio/phenix-1.4-3/phenix/wxGUI2/RefineNotebook.py", line 277, in OnStatsUpdate self.xyzerr_val.SetLabel("%.2f" % f_info.ml_coordinate_error) TypeError: float argument required, not NoneType Mark Knapp Structural Chemistry NIBR 4560 Horton Street M/S 4.4 Emeryville, CA 94608 510-923-6926

2 1

wx._core.PyDeadObjectError?
by TC Hu 11 Feb '09

11 Feb '09

Dear all, I got the "wx._core.PyDeadObjectError" when using Phenix 1.4-3 GUI under OS X 10.5.6 for a SAD run. The program stuck at the blue window after the first step of AutoSol. Attached is the log file. Could anyone help me find out what is wrong? Thanks very much in advance! Cheers, Tiancen Hu Shanghai Institute of Materia Medica Chinese Academy of Sciences " PHENIX distribution located in /usr/local/phenix-1.4-3/phenix Project Details Project Name: phenix2 Date Stamp : Thu Feb 12 01:08:25 2009 Machine : htcdemacbook-pro.local Directory : /Users/htc/xtal/subjects/cd147se/phenix2 PDS Server Details User : htc Machine : 192.168.1.3 Directory : /Users/htc/xtal/subjects/cd147se/phenix2 Port : 47702 PID : 4863 WIZARD: AutoSol ************************************************************ PHENIX AutoSol Thu Feb 12 01:19:23 2009 ************************************************************ PHENIX VERSION: 1.4 of 08-12-2008 PHENIX RELEASE_TAG : 3 PHENIX MTYPE : mac-intel-osx PHENIX MVERSION : osx-10.5.6 LOCAL INIT: Readdatabase: True SetUpInputs: True AutoSol Thu Feb 12 01:19:23 2009 Gathering defaults from ['AutoBuild', 'ImportRawData', 'LigandFit', 'AutoMR'] WORKDIR: /Users/htc/xtal/subjects/cd147se/phenix2 Checking for KnownWizards: ['AutoSol', 'AutoBuild', 'ImportRawData'] Running start first time through Setting default value of 2.5 for resolution Setting default value of 0.5 for solvent_fraction Setting default value of 200 for residues Guessing sequence file is cd147_21a.seq application method: AutoSol_start Getting inputs on first pass... SUMMARY Input files dataset #1 amom360_p41212_31A.sca Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 522, in OnGoButton try: self.parent.OnGo() File "/usr/local/phenix-1.4-3/phenix/wxGUI/Dialogs.py", line 470, in OnGo gp.RunStrategy() File "/usr/local/phenix-1.4-3/phenix/wxGUI/BMPTaskCanvas.py", line 1170, in RunStrategy self.RunRemotely() File "/usr/local/phenix-1.4-3/phenix/wxGUI/BMPTaskCanvas.py", line 1380, in RunRemotely remote = frame.RemoteHostName, File "/usr/local/phenix-1.4-3/phenix/phenix/pds_server/StrategyUtils.py", line 124, in RunStrategy LastStrategy File "/usr/local/phenix-1.4-3/phenix/phenix/server/PhenixClient.py", line 87, in StartProcessMaster return self._remote_call('StartProcessMaster',arg,kw) File "/usr/local/phenix-1.4-3/phenix/phenix/server/PhenixClient.py", line 466, in _remote_call raise result AssertionError: No user for ssh to machine 192.168.1.3 Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 892, in OnTableKillFocus self.OnTableTextEnter(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 861, in OnTableTextEnter (grid, cbox, ctrl, t_param, ir, ic) = self.get_event_table(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 1204, in get_event_table (ctrl, group_list, key_list, winszr) = self.get_ctrl_context(evtwin) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 1173, in get_ctrl_context result = self.RootWinSzr.FindInParentSizer(ctrl) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 159, in FindInParentSizer result = child.FindInParentSizer(window, child_groups, child_keys) File "/usr/local/phenix-1.4-3/phenix/wxGUI/wxtask.py", line 143, in FindInParentSizer if (child.GetId() == SearchWinId): File "/usr/local/phenix-1.4-3/build/mac-intel-osx/base/Python.framework/Versions/2.6/lib/python2.6/site-packages/wx-2.8-mac-ansi/wx/_core.py", line 14522, in __getattr__ raise PyDeadObjectError(self.attrStr % self._name) wx._core.PyDeadObjectError: The C++ part of the Panel object has been deleted, attribute access no longer allowed. "

2 1