- phenixbb - phenix-online.org

Re: [phenixbb] Please help with neutron composite SA-omit
by Thomas C. Terwilliger 23 Feb '09

23 Feb '09

Hi Anna, Try putting your cmmand "scattering_table=neutron" in a "refine.eff" file and then run phenix.autobuild including the keyword refine_eff_file=refine.eff (note that you may need to specify the scope of scattering_table just as if you were using the command directly for phenix.refine) That is the way you can put any phenix.refine parameters into autobuild. Let me know if that doesn't do it! -Tom T > Hello. > > I am attempting to create an SA-omit composite map with neutron > scatterers. > > Unfortunately, > > phenix.autobuild data= "neutron.mtz" model="neutron_004.pdb" > composite_omit_type=sa_omit scattering_table=neutron > > results in an error: > > "Sorry, unknown file or keyword: scattering_table=neutron > Possibilities... (use 'phenix.autobuild --help all' to get full help): > general.resolve_pattern_command_list=neutron > density_modification.use_resolve_pattern=neutron > decision_making.semi_acceptable_r=neutron > decision_making.acceptable_r=neutron > multiple_models.multiple_models_starting_resolution=neutron > " > > Can someone here help, please? > > (For what it's worth: I'd use nCNS, but while CNS 1.21 (precompiled > binaries) works on my computer, CNS 1.1 version seems to compile, it > will not run. When I apply the nCNS patch to CNS 1.1, again it seems > to compile, but will not run. ) > > Regards, > Anna Gardberg > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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DTT at special position
by Nikos Pinotsis 23 Feb '09

23 Feb '09

Dear all, even though I checked the documentation and previous threads I didn't find something relative to my problem: I have an elongated e-density that looks like DTT and appears to be located on a special position (there is actually an axis betwenn C2 and C3 atoms of DTT). Refining with phenix.refine using either 0.5 or 1.0 occupancy, I am getting the DTT molecule outside the density (and the symmetry related DTT from the other side and still in the middle the strong difference density. thanks in advance for any suggestions-solutions Nikos -- --------------------------------- Dr. Nikos Pinotsis Section of Structural Biology Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London SW3 6JB, UK Tel: +44 20 7153 5453 / 5447 --------------------------------- The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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ADP refinement
by Katya Heldwein 20 Feb '09

20 Feb '09

Hi, I would like to use TLS refinement for protein (I have selected TLS groups) and individual isotropic refinement for water. How can I specify this in phenix.refine? Thanks, Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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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.

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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

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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 *

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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.

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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

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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 > >

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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

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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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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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

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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. "

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Constrained occ refinement -- sum not equal 1
by Schubert, Carsten [PRDUS] 10 Feb '09

10 Feb '09

Hi, I am trying to sort out some issues with the constrained occupancy refinement in phenix 1.4.3. The structure I am working on is fairly high resolution ~1.4A and it looks as if a couple of the alternative conformations would benefit from occupancy refinement, no hydrogens are present yet. I defined the constrained groups like this: occupancies { individual = None remove_selection = None constrained_group { selection = chain A and resid 66 and altid A selection = chain A and resid 66 and altid B } .... I expected that the sum of occupancies would be restrained to 1, which they should according to the manual, but the refinement gives me occupancies of 0.7 for altid A and 0.34 for altid B, starting values were both 0.5. Similar discrepancies were also present in other groups, like 0.5 A, 0.37 B etc. The latter is the largest deviation from 1 I have seen in thus far. The alternate conformations were generated in coot, by splitting at the CA position. Is this a rounding error I just have to contend with or is there some other parameter I need to tweak? Cheers, Carsten

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phenix.ready_set and SS bond
by dziuba＠amu.edu.pl 09 Feb '09

09 Feb '09

Hi, Is it possible to prevent phenix.ready_set (or actually phenix.reduce) from . adding hydrogen atoms to Cys SG atoms if they are involved in disulphide bonds? Karolina

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phenix.superpose_pdbs_1.4
by David Garboczi 07 Feb '09

07 Feb '09

The default unit cell and symmetry for the "fitted" model (the one that was moved) is the unit cell and symmetry of the "fixed" pdb. As I am superimposing the same model from several space groups to study the differences in packing, I need the "fitted" pdb to keep its own unit cell and symmetry. How might I do this? When is the current default of altering the unit cell and symmetry of the moving model useful? thanks, Dave --

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TLS in phenix.refine_gui
by Miles Pufall 03 Feb '09

03 Feb '09

Hi Guys - Is there a way to load the TLS groups, generated so kindly by TLSMD in old phenix format, into the new gui? It would save a lot of typing. Thanks! Miles Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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modification of nonbonded geo restraints between symmetry mates
by Alejandro Buschiazzo 03 Feb '09

03 Feb '09

Dear PHENIX users, I wonder what is the 'correct' way of (re)defining geometric restraints among atoms. Here's what I need to do : I have several cations that are chelated by protein residues; some of them involve residues from the same monomer, yet others involve atoms from both the ASU monomer as well as crystal neighbors (i.e. symmetry mates). I see that in the .geo file, these parameters are taken into account as nonbonded simple and nonbonded asu respectively ... how can I change the ideal distances to get proper Zn+2 coordination bonds for both kind of partners? Thank you in advance for your help! -- Alejandro Buschiazzo, PhD Research Scientist Laboratory of Protein Crystallography Pasteur Institute of Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +5982 5220910 int. 120 Fax: +5982 5224185

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map coeffs?
by Walter Novak 03 Feb '09

03 Feb '09

Hi all, I am doing joint X-ray neutron refinement, and in the 1.4-3 version I now get twice the number of choices of map coefficients when opening the mtz. Half now have "no_fill" with them. I am assuming that the difference between maps has something to do with missing Fobs, is that right? Which maps should I be looking at then? Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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TLS + anisotropic ADP mixed refinement
by Scott Classen 02 Feb '09

02 Feb '09

I am trying to perform refinement on a model with three chains (two protein and one DNA... plus water, Cl, and a few other solventy things). The B factors for chain A are generally better than for the other two and I am thinking that the resolution (1.8Å) warrants attempting anisotropic individual adp refinement for at least chain A, and then using TLS for the other two. So my strategy is: *individual_sites *individual_adp *tls *occupancies adp.individual.isotropic = "not Chain A" adp.individual.anisotropic = "Chain A" adp.tls = "Chain B" adp.tls = "Chain D" Previously the model had only been refined with individual isotropic adp (no TLS). The starting model has an r_work=0.2079 and r_free=0.2427. With this new aniso/TLS strategy in the first macrocycle when it gets to the initial TLS refinement it completely blows up with r_work and r_free both going up to 60% have I specified my refinement with bad syntax? or is this even possible with phenix.refine? I can submit more of the log file if you're interested. 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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can phenix.refine calculate r_work and r_free without doing refinement?
by Scott Classen 02 Feb '09

02 Feb '09

Hi all, I was wondering if phenix can calculate r_work and r_free without refinement, sort of like the model_stats from CNS. 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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phenix version 1.4-3: problem with bulk solvent scaling
by Oliv Eidam 30 Jan '09

30 Jan '09

Hi, I am currently refining a good 1.6 Angstroem data set using Phenix. Thereby I noticed a significant difference of R-free (>3%) depending on whether I used phenix version 1.3-rc6 (installed on my Mac laptop) or phenix version 1.4-3 (installed on my linux work station). Rfree differs by more than 3% (!) although I am using the same starting model, the same reflection file and the same refinement protocol (shown at the end of this email with detailed R and R-free factors for the 3 steps). In my opinion, my phenix 1.4-3 installation has a problem in the "bulk solvent modeling and scaling" steps. Indeed, I find in the log file that the "overall anisotropic scale matrix" shows all values set to zero. Analogous the "maximum likelihood estimate for coordinate error". This is true in all steps where an "overall anisotropic scale matrix" is calculated. Here is one example during 1.4-3 refinement: ====================== bulk solvent modeling and scaling ====================== |--(resolution: 1.61 - 29.59 A; n_refl. = 99535)------------------------------| | | | r_work= 0.3419 r_free= 0.3358 ksol= 0.39 Bsol= 19.12 scale= 1.247 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: -0.00 A | | x-ray target function (ml) for work reflections: 5.981207 | |-----------------------------------------------------------------------------| The same example during 1.3-rc6 refinement: ===================== bulk solvent correction and scaling ===================== |-macro cycle = 1-(resolution: 1.61 - 29.59 A; n_refl. = 99537)---------------| | | | r_work= 0.3153 r_free= 0.3064 ksol= 0.40 Bsol= 43.79 scale= 1.087 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-4.01,-5.36,-8.20,-0.00,2.74,0.00); trace/3= -5.86 | | | | maximum likelihood estimate for coordinate error: 0.33 A | | x-ray target function (ml) for work reflections: 5.946583 | |-----------------------------------------------------------------------------| I am asking now: Did something go wrong during my Phenix installation? I already re-installed Phenix (no errors): same result. Do I have to change something in my input files? I should probably mention that "bulk_solvent_and_scale = True" in my input .def files. Any help appreciated. Many thanks, Oliv -------------------------------------------------------------------------------- Refinement protocol and development of R and Rfree during each refinement round: -------------------------------------------------------------------------------- 1)Rigid body refinement 2) Simulated annealing (5000K) 3) Ordered solvent (plus annealing @ 2000K) phenix version 1.3-rc6: 1) R=31.5, Rf=30.6 2) R=23.9, Rf=25.8 3) R=19.8, Rf=22.0 phenix version 1.4-3: 1) R=31.6, Rf=30.6 2) R=27.8, Rf=29.8 3) R=23.7, Rf=25.2 -- Oliv Eidam, Ph.D. Postdoctoral fellow University of California, San Francisco Dept. of Pharmaceutical Chemistry 1700 4th Street, Byers Hall North, Room 501 San Francisco, CA 94158 - Box 2550 Phone: 415-514-4253 Fax : 415-514-4260 Email: eidamo(a)blur.compbio.ucsf.edu

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joint xn refinement question
by Walter Novak 30 Jan '09

30 Jan '09

Hi, I am new to the list, but I didn't see this issue in the list archive. I am doing a joint refinement using x-ray and neutron data (each set is ~2.0 Å). I added H positions using reduce and have been switching to Ds as the density suggests for exchangeable positions. My problem is that I cannot seem to get the H (or D) positions to refine into the neutron density. Perhaps I need an additional command, so I am attaching my refinement script. I can provide a few pictures from coot to demonstrate if helpful. Thanks! Wally phenix.refine prot_joint4_r8_001.pdb \ neutron_data.file_name=prot_best_mcH_D2O_2_data.mtz \ xray_data.file_name=prot_best_mcH_D2O_2_data.mtz \ output.prefix=prot_joint4_r9 \ strategy=rigid_body+individual_sites+individual_adp \ simulated_annealing=False \ input.xray_data.labels=F-obs input.neutron_data.labels=F-obs-neutron \ input.xray_data.r_free_flags.label=R-free-flags \ input.xray_data.r_free_flags.file_name=prot_best_mcH_D2O_2_data.mtz \ input.xray_data.r_free_flags.test_flag_value=1 \ input.neutron_data.r_free_flags.label=R-free-flags-neutron \ input.neutron_data.r_free_flags.file_name=prot_best_mcH_D2O_2_data.mtz \ input.neutron_data.r_free_flags.test_flag_value=1 \ main.number_of_macro_cycles=5 \ restraints_edits.params \ refinement.hydrogens.refine=individual \ find_and_add_hydrogens=True \ switch_to_isotropic_high_res_limit=2.5 \ optimize_wxc=true \ optimize_wxu=true \ --overwrite Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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Site-wide defaults for phenix.refine parameters
by Stephen Graham 29 Jan '09

29 Jan '09

Hi all, Apologies if I've missed this in the documentation, but is there any way to set 'site-wide' defaults for, say, phenix.refine? That is, I'd like to modify the default parameters for phenix.refine so that occupancy refinement is turned off by default, the output.serial_format is different, geo files aren't created, always use F/SIGF not I/SIGI, etc. Cheers, Stephen P.S. I know I can change this by hand in my .def file and then propagate the .def file through subsequent rounds of refinement for a given project. It would just be nice to have my default personal preference parameters set (~/.phenix?) so I don't need to change them each time I start a new project... -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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occupancy refinement
by Nicole Bischoff 29 Jan '09

29 Jan '09

Dear all, in my electron density I can see negative difference density (fo-fc) for the carboxyl groups of some aspartates or glutamates. Assuming that this is a result of partial decarboxylation due to radiation damage, I wanted to refine the occupancies of these carboxyl groups. To this end, I set the occupancy of these atoms to 0.99 in Coot so that they would be picked up by occupancy refinement in phenix.refine (using version 1.4-3). Phenix however just put the value back to one. It looks like the occupancy refinement in phenix is meant for alternative conformations where the sum of the occupancies of the different conformations is 1. How can I make phenix refine partially decarboxylated acidic side chains? It does not seem appropriate to me to make alternative conformations, one with and one without the carboxyl group. That would look funny at my resolution (2.7 Angstrom) and might not fix the problem. Any hints are appreciated. Thank you, Nicole ---- Nicole Bischoff, M. Sc. PhD student in the Gruetter lab Department of Biochemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland +41 44 635 5556 nbischoff(a)bioc.unizh.ch

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TLS question
by Jeffrey Chao 27 Jan '09

27 Jan '09

hello all- i apologize if this question has previously been posted, but i was not able to track down an answer by google. i am refining a 2.75A structure that has three copies of the protein in the asu with phenix 1.4-3 and using NCS with each chain as an NCS group. after molecular replacement, i set all of the b-factors to the wilson b-factor and then performed four different refinements: grouped b-factor (1 group per residue) : Rwork 22.6 Rfree 27.0 individual b-factor : Rwork 21.4 Rfree 26.6 grouped b + tls ( : Rwork 21.9 Rfree 25.2 individual + tls : Rwork 21.2 Rfree 24.8 i defined the tls groups with the following: adp { tls = chain A tls = chain B tls = chain C } after grouped b-factor the atoms of each residue all have the same b- factor as i expected. after grouped b-factor+tls, however, each atom of a residue has a unique b-factor, which i did not expect. i realize that this confusion is likely caused by me not fully understanding how tls refinement is implemented. if someone could explain this to me, i will be able to sleep better. thank you for your time, jeff Jeffrey Chao, PhD 1300 Morris Park Ave ASB-Golding 601 Bronx NY 10461 jchao(a)aecom.yu.edu 718-430-8597

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rmsd: phenix vs refmac
by Frank von Delft 25 Jan '09

25 Jan '09

Hi I thought that a while ago, I read somewhere that rmsd(bonds) had not been calculated the same way in phenix as in refmac. I believe it was in connection with automated weights, and that rmsd(bonds) always much lower in phenix. I understood too that this had been adjusted since to match refmac. But we're still seeing some much lower rmsd(bond) from phenix: in particular, when we take a refmac model and plug it straight into phenix, the rmsd for cycle zero is already much lower than what it was at the end of refmac. Could someone enlighten...? (Yup, latest version of phenix.) Thanks! phx

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bond and angle rmsds: phenix.refine, Refmac, hydrogens, ...
by Pavel Afonine 24 Jan '09

24 Jan '09

For all who asked about observed differences in bond rmsd reported by phenix.refine and Refmac, H atoms included in statistics calculation and more... 1) First, I wanted to check bond rmsd reported by phenix.refine. I made up a PDB file containing just one residue (SER, no H atoms) and I wrote a crystal-clear and simple Python script that computes bond rmsd for this residue. Here are the numbers: Bond length rmsd: Script: 0.148 phenix.pdbtools: 0.148 phenix.refine: 0.148 Refmac_5.5.0070: 0.152 Both programs are using the Monomer Library. Since both of these very different ways of computing bond rmsd: this simple script and phenix.refine, give the identical values, I tend to think that the PHENIX implementation is actually correct. I have no idea why Refmac gives a different value and I think it's now up to Refmac developers (or any other enthusiast) to find it out or show that I'm wrong in my calculations. It well could also be me who's incorrectly using Refmac - today was my second time I tried it (the first was 3 or 4 years ago) -:) As for the bond angles rmsd, I didn't bother to include it into the script, but for the rest of tools in question, the numbers are: phenix.pdbtools: 16.628 phenix.refine: 16.628 Refmac_5.5.0070: 16.628 so all results seem to be in-sync. 2) Some people reported that the geometry statistics for the exact same structure with and without hydrogens seems to be reported different in phenix.refine. To find out, I did the same test as above, where I used the same one residue model with all hydrogens added. Unfortunately, I failed to make Refmac accept a PDB file containing H atoms so I gave up after 20 minutes of struggle. Here are the numbers: Bond length rmsd: Script: 0.155 phenix.pdbtools: 0.155 phenix.refine: 0.155 So, it seems like the hydrogens are included... I have to fix it. Well at least those who are doing refinement using neutron data or both X-ray and neutron data, were not concerned, since in that case I presume the H and D atoms should be included. Anyway, I'm fixing it right now, I'm making a corresponding regression test (to make sure the fix stays there forever) and the fixed version will be available in the next release. By the way, the new tool, phenix.model_vs_data is and was smart about this: it automatically excludes H and D atoms if X-ray data is used. And this proves it: phenix.model_vs_data: 0.148 which is the exact same number as in "1)", where H were not present. Thanks to all who raised this issue (Frank von Delft, Jianghai Zhu, Karolina Michalska and others)! Pavel. PS> All files used and the script are here: http://cci.lbl.gov/~afonine/rmsd_issue/ Use "phenix.python run.py" to run the script.

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IAS causes phenix.refine to die
by Anna Gardberg 24 Jan '09

24 Jan '09

Dear phenix list, My 0.75 A refinement has some problems in its higher resolution bins, so I thought I might try adding in IAS scatterers. However, the phenix.refine (version 2008_09_13_0905) crashed when I set "ias = True". I hope someone here can help me figure out the problem. I include snippets of output below, as the entire error message was very lengthy. Am I misusing the command, is there a problem with my system setup, or what? Regards, Anna Gardberg ----------Building IAS model---------- >>> Adding IAS.......... Total number of covalent bonds = 895 show_stack(1): /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(438) _ _init__ show_stack(2): /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(371) s et_peaks show_stack(3): /home/a1g/downloads/cci_apps_sources/mmtbx/ias/__init__.py(616) _ _init__ show_stack(4): /home/a1g/downloads/cci_apps_sources/mmtbx/model.py(494) add_ias show_stack(5): /home/a1g/downloads/cci_apps_sources/phenix/phenix/refinement/str ategies.py(409) refinement_machine show_stack(6): /home/a1g/downloads/cci_apps_sources/phenix/phenix/refinement/dri ver.py(1082) run <snip pages of output> /home/a1g/downloads/cci_apps_build/lib/cctbx_maptbx_ext.so(boost::python::obje cts::make_holder<4>::apply<boost::python::objects::value_holder<cctbx::maptbx::o ne_gaussian_peak_approximation>, boost::mpl::vector4<scitbx::af::const_ref<doubl e, scitbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::a f::trivial_accessor> const&, bool const&, bool const&> >::execute(_object*, scit bx::af::const_ref<double, scitbx::af::trivial_accessor> const&, scitbx::af::cons t_ref<double, scitbx::af::trivial_accessor> const&, bool const&, bool const&)+0x 75c) [0x2a9d79598c] /home/a1g/downloads/cci_apps_build/lib/cctbx_maptbx_ext.so(cctbx::maptbx::find _gaussian_parameters::find_gaussian_parameters(scitbx::af::const_ref<double, sci tbx::af::trivial_accessor> const&, scitbx::af::const_ref<double, scitbx::af::tri vial_accessor> const&, double const&, double const&, double)+0x3fe) [0x2a9d7827f e] /lib64/tls/libm.so.6 [0x32ee506263] /lib64/tls/libc.so.6 [0x32ee22e300] Floating-point error (Python and libc call stacks above) [1]+ Done gedit newscale-ias.eff

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Unmasking cavities
by Frank von Delft 23 Jan '09

23 Jan '09

Hi After being through phenix.refine, I see in my hydrophobic core a big space (a few atoms wide) that is filled with strong negative difference density. I suspect the culprit is the bulk solvent mask, which is defined too tightly. The online manual mentions three parameters, but not what they do. solvent_radius, shrink_truncation_radius, grid_step_factor What *exactly* do they do? (I thought I'd elicit a contribution for the online docs this way :) Cheers phx

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geometry of disulfide and NAG
by Li-Zhi Mi 22 Jan '09

22 Jan '09

Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,

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HL A B C D
by Raja Dey 21 Jan '09

21 Jan '09

Hello, If I want to use F, SigF and HLA, B, C and D in the phenix refinement, should I use the same command like phenix.refine data.mtz model.pdb, where data.mtz contains FREER, F, SIGF, HLA, HLB, HLC and HLD? How do I check that phenix.refine used the HL coefficients? Looking forward to hearing from you... Thanks... Raja

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Disappearing side chains after autobuilding
by Katya Heldwein 21 Jan '09

21 Jan '09

Hi, I ran phenix.autobuild with default setting (rebuild_in_place), and noticed that some side chains were gone in the resulting overall_best.pdb. That is, let's say, I started with Phe as residue 10. After rebuilding, the Phe10 is still called Phe in the output file, but the side chain atoms are gone, leaving residue 10 as Ala. This happened for several side chains, and I am at a loss for why this happened. Is this some kind of a bug? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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missing map coefficients
by Anne Mølgaard 15 Jan '09

15 Jan '09

I am new to Phenix, so there might be an easy explanation for this problem, though I have not been able to find a solution in the documentation. I am using phenix version 1.3b-rc4, intel-linux-2.6. I have solved a structure using phenix.automr, followed by phenix.autobuild (run from command line using "phenix.autobuild data=fromXDS_unique.mtz model=AutoMR_run_2_/MR.1.pdb seq_file=sequence.fas"). The program runs succesfully, and I get the output files I should expect. However, the overall_best_refine_map_coeffs.mtz does not contain the map coefficients 2FOFCWT PH2FOFCWT for the 2mFo-DFc map and FOFC and PHFOFC for the Fo-Fc difference map. mtzdmp gives me the following columns: 1 ASC 0 28 0 100.00 10.6 10.6 28.28 1.85 H H 2 NONE 0 35 0 100.00 13.3 13.3 28.28 1.85 H K 3 NONE 0 71 0 100.00 26.6 26.6 28.28 1.85 H L 4 NONE 1.0 1888.8 0 100.00 148.71 148.71 28.28 1.85 F FP 5 BOTH 1.0 1.0 0 100.00 1.00 1.00 28.28 1.85 Q SIGFP 6 NONE -180.0 180.0 0 100.00 2.08 90.23 28.28 1.85 P PHIM 7 BOTH 1.000 1.000 0 100.00 1.000 1.000 28.28 1.85 W FOMM 8 NONE .0 19.0 0 100.00 9.50 9.50 28.28 1.85 I FreeR_flag 9 BOTH .0 .0 0 100.00 .00 .00 28.28 1.85 F FC What should I do to get these map coefficients? Thanks for your help! Best regards, Anne

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Will phenix.refine read CNS *.cv files?
by Scott Classen 14 Jan '09

14 Jan '09

Hi all, I'm embarking on a collaboration with someone who is providing me with CNS cross validated data files. They look something like this. NREFlection= 92086 ANOMalous=FALSe { equiv. to HERMitian=TRUE} DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 SIGI= 735.200 TEST= 0 INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 SIGI= 1531.800 TEST= 0 INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 SIGI= 35.700 TEST= 1 INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= 0.182215E+06 SIGI= 7507.000 TEST= 0 INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= 0.169206E+06 SIGI= 6999.000 TEST= 0 INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 SIGI= 233.200 TEST= 0 When I try to run phenix.refine --dry_run my_model.pdb my_CNS_cv_file.cv I get the following error: Processing inputs. This may take a minute or two. Sorry: Unknown file format: my_CNS_cv_file.cv Any ideas? 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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Re: [phenixbb] Will phenix.refine read CNS *.cv files?
by Scott Classen 14 Jan '09

14 Jan '09

Hi Nick, I think I tried that at some point, but the problem lies in the IOBS. Some are regular float fortran format: INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 SIGI= 293.800 TEST= 0 while other IOBS are large and for some reason CNS decided to put them in scientific notation such as INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= 0.242506E+06 SIGI= 17098.000 TEST= 0 As far as I can tell this requires two sets of fortran format statements for f2mtz to work properly. format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,E15.3,/,24X,F10.3,6X,F10.0)' or format '(6X,3F5.0,6X,F10.3,7X,F10.3,6X,F10.3,/,24X,F10.3,6X,F10.0)' I'm playing around with with grep to separate the original cv file into reflections with IOBS in F10.3 format and those with IOBS in E15.3 format, convert with f2mtz, then CAD them together, but this is bloody cumbersome. I was hoping phenix.refine would just automagically figure it all out. Scott On Jan 14, 2009, at 5:35 PM, Noinaj, Nicholas (NIH/NIDDK) [F] wrote: > Scott, > > <not sure if anyone has remedied your problem yet> > > I don't know if you can read cns file directly into phenix.refine. > but > here is another option....convert the cns file to *.mtz using CCP4. > If > you use the CCP4i GUI --> Reflection Data utilities --> Convert > to/modify/extend MTZ. You can also retain the original flagged > reflections here also. You can then use the *.mtz file in > phenix.refine. > > If you need further help, just drop me a quick email. I can also > try it > here if you supply me with the data file, but this may be too 'top > secret' (lol). Best of Luck! > > > > > > Cheers, > Nick > > > > -----Original Message----- > From: Scott Classen [mailto:[email protected]] > Sent: Wednesday, January 14, 2009 8:06 PM > To: PHENIX user mailing list > Subject: [phenixbb] Will phenix.refine read CNS *.cv files? > > Hi all, > I'm embarking on a collaboration with someone who is providing me with > CNS cross validated data files. They look something like this. > > > NREFlection= 92086 > ANOMalous=FALSe { equiv. to HERMitian=TRUE} > DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END > DECLare NAME=TEST DOMAin=RECIprocal TYPE=INTE END > INDE 3 0 0 FOBS= 100.142 SIGMA= 1.478 IOBS= 10028.400 > SIGI= 293.800 TEST= 0 > INDE 4 0 0 FOBS= 158.996 SIGMA= 2.329 IOBS= 25279.600 > SIGI= 735.200 TEST= 0 > INDE 5 0 0 FOBS= 492.449 SIGMA= 17.677 IOBS= > 0.242506E+06 > SIGI= 17098.000 TEST= 0 > INDE 7 0 0 FOBS= 246.492 SIGMA= 3.127 IOBS= 60758.400 > SIGI= 1531.800 TEST= 0 > INDE 8 0 0 FOBS= 32.790 SIGMA= 0.549 IOBS= 1075.200 > SIGI= 35.700 TEST= 1 > INDE 9 0 0 FOBS= 426.866 SIGMA= 8.886 IOBS= > 0.182215E+06 > SIGI= 7507.000 TEST= 0 > INDE 10 0 0 FOBS= 411.347 SIGMA= 8.597 IOBS= > 0.169206E+06 > SIGI= 6999.000 TEST= 0 > INDE 11 0 0 FOBS= 87.275 SIGMA= 1.346 IOBS= 7617.000 > SIGI= 233.200 TEST= 0 > > When I try to run phenix.refine --dry_run my_model.pdb > my_CNS_cv_file.cv > > I get the following error: > > Processing inputs. This may take a minute or two. > Sorry: Unknown file format: my_CNS_cv_file.cv > > > Any ideas? > > 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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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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f_prime and f_double_prime in MIRAS/SIRAS
by Leo Sazanov 14 Jan '09

14 Jan '09

Hi, how can one enter f_prime and f_double_prime values for SIRAS/MIRAS experiments in phenix.autosol? Could not find any examples of that in manual, only for MAD. Just putting them in as f_prime=... and f_double_prime=... does not work, it then assumes MAD experiment. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-dunn.cam.ac.uk Tel: +44-1223-252910 Fax: +44-1223-252915

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Jan 15th deadline - User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 13 Jan '09

13 Jan '09

Dear Users, /Deadline for March/April 2009 proposals will be Jan 15, 2009. / Through the Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source, scientists can send protein crystals to Berkeley Center for Structural biology (BCSB) staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the regular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography ============= How To Apply: To submit a proposal, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html Click on "protein crystallography" to begin proposal. For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for March/April 2009 allocation period, proposals must be submitted by January 15, 2009. The deadline for CC proposals for the time period May/June 2009 will be March 15, 2009. Regards, Banumathi Sankaran

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Fwd: Refinement using new Phenix causes electron density/model mismatch
by Miles Pufall 12 Jan '09

12 Jan '09

The bb bounced my email back because the enclosures were too big - let me know if you'd like them. Thanks - Miles Begin forwarded message: > From: Miles Pufall <mpufall(a)cmp.ucsf.edu> > Date: January 12, 2009 12:16:06 PM PST > To: phenixbb(a)phenix-online.org > Subject: Refinement using new Phenix causes electron density/model > mismatch > > Hi Guys - > > I am having a very puzzling problem using the new Phenix (1.4-3). I > have about 20 structures that I am preparing to deposit with an > accepted manuscript, and decided to do a final refine using the > phenix.refine_gui not only to see if I got better numbers, but to > use the integrated validation tools, which I love. Unfortunately, > often, but not always, when I refine the pdb against the > *_refine_data.mtz the statistics are a bit worse, and when I open > the resulting *.map_coeffs.mtz in Coot it appears to be shifted with > tons of negative electron density. Needless to say, this is making > my nervous, so I've tried a few things: > > 1) Tried refining the same .pdb and .mtz files in Refmac - I seem > to get the same shifting. > 2) Try using the old .def file left over from the final run (just > to make sure I didn't screw up some setting) - and I get the same > shifting. > 3) Try refining against the original .sca file - and I get the same > shifting. > 4) Try molecular replacement of the refined .pdb against the > original .sca file - and sometimes, but not always, get a shift. > > I am nervous and concerned - can you help me figure out what > happened? I am enclosing an example - > > refine_001.pdb = pdb I refined in new phenix > refine_001map_coeffs.mtz = mtz output from new phenix refinement > (lots of red) > oste44a_output.sca = original scale file from HKL2000 > MR.1_refine_data.mtz = data from which I am refining > sgk_ost_temp_H_refine_004.pdb > > Thanks - > > Miles > > Miles Pufall > Postdoctoral Scholar > Yamamoto Lab > UC San Francisco > Cellular and Molecular Pharmacology > Mail Stop 2280 > 600 16th Street, Genentech Hall S-574 > San Francisco, California 94158-2517 > (415)476-4480 > > Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Deadline for ALS PX beamtime this Thursday, Jan 15.
by Peter Zwart 12 Jan '09

12 Jan '09

Dear All, The deadline for general user proposals for PX beamtime at the ALS is coming up soon (Jan 15)! At the BCSB, we have 5 beamlines for which you can apply for beamtime. At the Berkeley Center for Structural Biology (BCSB) we have recently completed a number of upgrades: Sector 8: Recent improvements include: * A high-accuracy microdiffractometer on BL 8.2.1, allowing for centering and viewing of very small crystals * Robotic automounters which can increase the screening throughput at the beamlines, and allows for the implementation of remote data collection. * A new large format (315mm active surface area) CCD detector on BL 8.2.1, facilitating data collection on large unit cell crystals Sector 5: Beamlines (5.0.1 and 5.0.3) now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. Beamline 5.0.2 (the tunable beamline) generates a peak flux of 8x10^11 photons per second, and the energy range of 5.0.2 has been extended to 17 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. Remote data collection for general users on sector 5 is currently being tested for a limited number of users. Please contact beamline staff for details. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to apply for next round of beamtime (March-April) at the Advanced Light Source, please submit a General User proposal by Januari 15, 2009. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] TLS in phenix.refine_gui
by Pavel Afonine 10 Jan '09

10 Jan '09

Hi Miles, > Thanks for the info. I see where I can load a parameter file in the > gui (File => Open parameter file) but I don't think I have it with the > right extension (.eff or .param). I'll give it a whirl tomorrow. Oh good, I'm glad to hear that this exists! I'm not sure if it relies on the file extension (it wouldn't be right if it does). I think we should have this option (to load a parameters file) right next to the prompt for PDB, data and CIF files. Best, Pavel.

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Scratch last help request
by Miles Pufall 10 Jan '09

10 Jan '09

As it turns out there were some problems with my .pdb file - missing chain label somehow. Once I fixed it everything works - sorry for the trouble. Miles Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Error running refine_gui
by Miles Pufall 10 Jan '09

10 Jan '09

Hi Guys - I was running the phenix_gui ad had just started a refinement run with tls, adp, occupancy, individual sites, simulated annealing, update waters and add hydrogen when the run stop and this error popped up: RuntimeError : mean_weighted() argument is an empty array Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 259, in OnExcept raise event.data RuntimeError: mean_weighted() argument is an empty array CHeers - M Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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Postdoc Crystallographer Position - Berkeley
by Paul Adams 09 Jan '09

09 Jan '09

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 22539 Division: Physical Biosciences Date Opened: 1/5/2009 Summary: A postdoctoral position is immediately available to study structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position is joint between the Center for Protein Folding Machinery (www.proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). Robotic hardware for performing crystallization trials and imaging results are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. The biological systems to be studied are: - Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells. - Glycosyl transferases responsible for the synthesis of hemicellulose in plants. - Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. Duties: Using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Qualifications: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Note that this is a one-year appointment with renewal based on performance and continued funding. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. To apply visit http://cjo.lbl.gov/ and search for the job number 22539 or visit: http://jobs.lbl.gov/LBNLCareers/details.asp?jid=22539&p=1 -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Kristine Sawyer [ KKSawyer(a)lbl.gov ][ 1-510-486-4151 ] --

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phenix v1.4-3 and NX
by Jesper Lykkegaard Karlsen 09 Jan '09

09 Jan '09

Hi, After upgrading our workstations to phenix v1.4-3, the user started having problems connecting to the machines through nxclient. The login ended up with a black screen on the client and absolutely no error messages on neither client nor server. The problem seemed to come from setting up the global environment for phenix (phenix_env.sh). I narrowed the problematic statement down to this: /if [ "$PHENIX_MTYPE" = "unknown-unknown" ]; then exit 1 fi/ Although "$PHENIX_MTYPE" = "intel-linux-2.6-x86_64" when logged in, somehow the "nx user" gets "$PHENIX_MTYPE" = "unknown-unknown" when it logs in, through it's authorization key, to establish the users session. To make a already to long story short. The problem can be fixed by commenting out the problematic statement above. And one question to the developers: Could this be avoided in the future? Perhaps give a warning instead off exiting completly! Sincerely Jesper -- Jesper L. Karlsen Scientific Computing Centre for Structural Biology Department of Molecular Biology University of Aarhus Gustav Wieds Vej 10C 8000 Aarhus C Phone: +45 8942 5268 E-mail: jelka(a)bioxray.au.dk

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Re: [phenixbb] phenix v1.4-3 and NX
by Jesper Lykkegaard Karlsen 09 Jan '09

09 Jan '09

Hi Paul, > what happens if you change the statement to say: > > exit 0 > > instead of exit 1? No did not help, still get black screen on the nxclient. Only out-commenting/deleting helps. Cheers, Jesper > > On Jan 9, 2009, at 3:52 AM, Jesper Lykkegaard Karlsen wrote: > >> Hi, >> >> After upgrading our workstations to phenix v1.4-3, the user started >> having problems connecting to the machines through nxclient. The >> login ended up with a black screen on the client and absolutely no >> error messages on neither client nor server. >> >> The problem seemed to come from setting up the global environment for >> phenix (phenix_env.sh). I narrowed the problematic statement down to >> this: >> >> if [ "$PHENIX_MTYPE" = "unknown-unknown" ]; then >> exit 1 >> fi >> >> Although "$PHENIX_MTYPE" = "intel-linux-2.6-x86_64" when logged in, >> somehow the "nx user" gets "$PHENIX_MTYPE" = "unknown-unknown" when >> it logs in, through it's authorization key, to establish the users >> session. >> >> To make a already to long story short. The problem can be fixed by >> commenting out the problematic statement above. >> >> And one question to the developers: >> >> Could this be avoided in the future? >> Perhaps give a warning instead off exiting completly! >> >> Sincerely >> Jesper >> >> -- Jesper L. Karlsen Scientific Computing Centre for Structural >> Biology Department of Molecular Biology University of Aarhus Gustav >> Wieds Vej 10C 8000 Aarhus C Phone: +45 8942 5268 E-mail: >> jelka(a)bioxray.au.dk_______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >

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fixing a partial solution of mol. rep.
by chern 06 Jan '09

06 Jan '09

I am doing a molecular replacement. There are two types of protein molecules in the crystal. One type is forming a hexameric core; there are 6 molecules of the second type that I need to locate. I found a solution for the hexameric core, but the other 6 molecules are difficult to find. 1. Can I fix the solution for the core, so that I don't have to find it every time. The other inconvenience with that is that the origine is different for every new run. If I fix the hexamer, then I fix the origine. It's important to me to compare different runs of MR. 2. Some of the six other molecules that MR finds are not the closest to the core. How can I request to output the closest molecules? Maia

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TRIED resolve ...NEED A BIGGER VERSION... message
by Ben Eisenbraun 05 Jan '09

05 Jan '09

Howdy Phenixians, One of my users is running phenix.autobuild, and while it seems to run okay, the output contains this warning: TRIED resolve ...NEED A BIGGER VERSION... Looking through phenix/phenix/autosol/run_resolve.py, it seems like this is an informational message, but I'm not sure, so I figured I'd ask. Is this actually an error? This is phenix-1.3-final on OS X 10.5. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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question about xn joint refinement
by crystallogrphy 02 Jan '09

02 Jan '09

Deall all: I have a question about xray and neutron joint refinement. When I start phenix joint refinement like this, phenix gave the wrong message: phenix.refine dhfr-mtx-rt-xray.hkl neutron_data.file_name=newdhfr_un_change.hkl xn_easy_080326a.pdb input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn xray_data.r_free_flags.generate=True neutron_data.r_free_flags.generate=True refine_default.params ===================== joint neutron/xray refinement start ===================== Traceback (most recent call last): call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/driver.py", line 1031, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/strategies.py", line 184, in refinement_machine * assert not neutron_refinement AssertionError* I guess in my default parameters, something is wrong, particularly the bold word I highlighted. But I do not know how to fix. Does any one have a clue?\ Thanks and Happy New Year! main { bulk_solvent_and_scale = True simulated_annealing = False ordered_solvent = False ncs = False ias = False number_of_macro_cycles = 3 max_number_of_iterations = 25 use_form_factor_weights = False tan_u_iso = False use_convergence_test = False target = *ml mlhl ml_sad ls min_number_of_test_set_reflections_for_max_likelihood_target = 50 max_number_of_resolution_bins = 30 reference_xray_structure = None use_experimental_phases = None compute_optimal_errors = False random_seed = 2679941 *scattering_table = wk1995 it1992 *n_gaussian neutron* use_normalized_geometry_target = True target_weights_only = False use_f_model_scaled = False max_d_min = 0.25 fake_f_obs = False -- Qun Wan Department of Pharmacology, Case Western Reserve University 10900 Euclid Avenue, Cleveland, OH 44106 email: qunwan1(a)gmail.com lab phone: 216-368-3337

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Error
by Miles Pufall 27 Dec '08

27 Dec '08

Hi - It appears there was a problem with the NCS flag being on, and when I took it off I received this error. Let me know if you'd like data to recreate this. Cheers - Miles RuntimeError : OpenGL: invalid operation Traceback: Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 188, in run self.check_params_and_run() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Refine.py", line 229, in check_params_and_run self.model.add_hydrogens() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 369, in add_hydrogens self.update_from_interface() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 181, in update_from_interface self.update_viewer() File "/usr/local/phenix-1.4-3/phenix/wxGUI2/Model.py", line 317, in update_viewer self .viewer_frame.glview.update_structure_from_files(self.get_all_files()) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 166, in update_structure_from_files self.update_structure(pdb_hierarchy, atomic_bonds, redraw=True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 180, in update_structure self.OnUpdate(recenter=True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 208, in OnUpdate self.update_view(True, True) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 566, in update_view self.OnRedraw() File "/usr/local/phenix-1.4-3/gltbx/wx_viewer.py", line 473, in OnRedraw self.OnRedrawGL(event) File "/usr/local/phenix-1.4-3/phenix/wxGUI2/GLViewer.py", line 118, in OnRedrawGL wx_viewer.wxGLWindow.OnRedrawGL(self, event) File "/usr/local/phenix-1.4-3/gltbx/wx_viewer.py", line 476, in OnRedrawGL gltbx.util.handle_error() RuntimeError: OpenGL: invalid operation Miles Pufall Postdoctoral Scholar Yamamoto Lab UC San Francisco Cellular and Molecular Pharmacology Mail Stop 2280 600 16th Street, Genentech Hall S-574 San Francisco, California 94158-2517 (415)476-4480

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