- phenixbb - phenix-online.org

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] 11 Feb '09

11 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 03 Feb '09

03 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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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 25 Jan '09

25 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 24 Jan '09

24 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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