- phenixbb - phenix-online.org

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 > >

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

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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 03 Feb '09

03 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 31 Jan '09

31 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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