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metal ion
by chene＠umbi.umd.edu 20 Feb '10

20 Feb '10

Dear Phenix users, My question may have been asked before. I am refining a structure containing calcium ions. I am wondering if the program considers it to be divalent Ca++ or neutral calcium atom. It seems that the ion and neutral atom have different atomic scattering factors. Thanks Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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Re: [phenixbb] riding model and deposition
by Alex Theodossis 19 Feb '10

19 Feb '10

Dear Pavel, thank you for your comments. Alex

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omit map with twinning?
by Kelly Daughtry 18 Feb '10

18 Feb '10

Hello all, The omit_map in the new gui (version 1.5) is great, but I can not include a twin law when calculating the omit map, thus the result is very messy unclear maps. I do not know if 1.6 has the solution or not, I am still lobbying our computer guy to upgrade to it... Is there a way from the command line i can include the twin law in autobuild so I can calculate the omit map, or can I just add it into the eff file? My other solution has been to use the create maps function with my data and pdb with ligand removed. This works, giving me a nice Fo-DFc map, but it would be nice to be able to show a true omit map for the ligand, as is customary in most structure papers I have run across. Thanks in advance for any help you can provide! Kelly ******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 *******************************************************

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riding model and deposition
by Alex Theodossis 18 Feb '10

18 Feb '10

Dear phenixbb, I have refined a 1.3A structure using individual anisotropic B-factors (Rfactor, 15.5%; Rfree, 17.7%). Additional use of the riding model during refinement has improvement the R values (Rf, 14.5%; Rfree, 16.6%), although bond length and angle outliers did increase (anyone know why that would be?). I have decided to deposit the model obtained using the riding model, but am unsure whether to include the hydrogen coordinates in the deposition. The Phenix.refine documentation advises that they are left in, as they are needed to reproduce the refinement statistics. However, reviewing the high resolution structures in the PDB I found that: 1. In the case of structures refined using REFMAC or SHELX, the riding model does not seem to be included, although its use during refinement is mentioned in the pdb header. 2. In the case of structures refined using PHENIX, use of the riding model is sometimes indicated in the header, but hydrogen coordinates only appear to be included in the pdb in the case of structures refined to a resolution better than 1.3A. As far as I can understand the purpose of the riding model is to provide additional restraints for refinement, so as long as its use is made evident in the pdb header (and maybe the methods section of the publication) that should be enough. Inclusion of hydrogens in the model, when you can't see them seems inappropriate. Nevertheless, I would appreciate a more authoritative perspective on this issue. Thank you in advance, Alex Theodossis

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refinement error with ligand
by Christian Roth 17 Feb '10

17 Feb '10

Dear all, I started a refinement of one of my structures using the GUI of phenix (Version 1.6). I used the options of adding hydrogens and dis a suimulated annealing. I used the output file and corrected it manually using Coot. I incorporated a few Ethylenglycol Monomers which might have bound. I merged everything wrote the file out and loaded this pdb in the GUI. I got an error which might be du to the fact that I didnt specify a CIF file for the ligand. I started ready set from the GUI to check the pdb and used REEL to create a CIF File. I added the CIF-File to the File list and tried to start again phenix.refine using the hydrogen option but no sim. annealing. However I got always the following error log: # Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s) #phil __OFF__ Command line arguments: "/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff" "-- overwrite" HOST = bbzws339 HOSTTYPE = i486-linux VENDOR = intel USER = roth PID = 29983 ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 1.6 Release tag: 289 Platform: intel-linux-2.6 linux User: roth ------------------------------------------------------------------------------- phenix.refine: Macromolecular Structure Refinement Monomer Library directory: "/software/linuxsoft/phenix-1.6-289/chem_data/mon_lib" Total number of atoms: 16881 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1575 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 87} and so on for other chains Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'EDO': 1} Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1} Classifications: {'undetermined': 1} Number of atoms with unknown nonbonded energy type symbols: 16 "HETATM16821 HO2 EDO K 1 .*. H " "HETATM16826 HO1 EDO K 1 .*. H " "HETATM16828 HO2 EDO L 1 .*. H " "HETATM16834 HO1 EDO L 1 .*. H " "HETATM16836 HO2 EDO M 1 .*. H " "HETATM16840 HO1 EDO M 1 .*. H " "HETATM16842 HO2 EDO N 1 .*. H " "HETATM16848 HO1 EDO N 1 .*. H " "HETATM16850 HO2 EDO O 1 .*. H " "HETATM16857 HO1 EDO O 1 .*. H " ... (remaining 6 not shown) I looked in the pdb for this atoms, but I cannot find them. When I use a cif file created directly by phenix elbow using command line and when I did not use the update hydrogen button the refinement works. But the new residues as well as the EDO molecules have no hydrogens in riding positions. Do I have to remove all hydrogens and attach them again for every cycle? One Refinement runs for more then 5 hours regardless I use sim annealing or not. This seems to be very long for me. Maybe I want too many optimization steps? Could anyone explain me what goes wrong here. I am no so much experienced with phenix and now I run out of ideas. Thanks in advance Christian

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phenix.elbow and compound refinement
by YS. Chung 16 Feb '10

16 Feb '10

Dear all, I am having some difficulties in refining my compound within my structure. I was able to create the compound and the cif file using PRODRG and was able to fit it in coot perfectly fine. However, as pointed out by many users of phenix.refine, the cif file from PRODRG does not work well with phenix.refine. I have created a cif file using phenix.elbow and the refinement itself works fine. However, when I try to use the cif file from phenix elbow in coot, it pulls apart my compound and it's extremely difficult to work with. This still happens when I create the cif file using the --final_geometry option. Is there a way around this or is there something I can do? Any help will be much appreciated. Thank you, Yu Seon Chung

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refinement at 4.4 A => side chains or not
by jonathan elegheert 12 Feb '10

12 Feb '10

Dear bb, could anyone please share his/her opinion on following matter; I am refining a 4.4 A protein complex structure which I could solve using MR with the high resolution models of the separate components. I also have another 3.5 A crystal form of the complex. My question is whether or not to rebuild/leave "positionally known" side chains in the 4.4 A structure, because of course 2/3 of the time there is of course no density for it. However, a review of the PDB learnes that almost all models deposited between 4 and 5 A contain full side chains! Personally my opinion is not to include them because a model should be a representation of the information content of the experiment and thus density, but maybe that deviates from the consensus. On a more technical note: until now the trimming procedure has only sporadically led to Fo-Fc 'blobs' in the hydrophobic protein interior; are there proven modifications one has to apply to the bulk solvent model mask to avoid these even more? Thanks a lot for your insights, Jonathan -- Jonathan Elegheert Ph.D. Student Unit for Structural Biology& Biophysics http://www.lprobe.ugent.be/xray.html Lab for Protein Biochemistry and Biomolecular Engineering Department of Biochemistry& Microbiology Ghent University, Belgium e-mail: jonathan.elegheert(a)ugent.be

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multiple model refinement
by chene＠umbi.umd.edu 12 Feb '10

12 Feb '10

Hi, PHENIX users, Does anyone know if multiple model refinement is implemented in the latest version? I am using version 1.3. It was not implemented yet in that version. Thanks Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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iMosflm .mtz
by anon 11 Feb '10

11 Feb '10

Hi, i was under the impression Phenix (AutoSol) could handle .mtz files from iMosflm, however when i input the .mtz file into AutoSol, no labels appears in the pull-down menu, and pressing Run results in a dialogue box appearing stating you must select a column label for the reflection file, if no labels are present it may not be a valid format. If i input the iMosflm .mtz file into phenix.reflection_file_editor, and copy over the I, SIGI, M_ISYM columns, i get the following error; A Python error was detected. This is probably a bug; click "OK" to send a bug report to the PHENIX developers. TypeError : not all arguments converted during string formatting Traceback (most recent call last): File "/usr/local/phenix-1.6-289/phenix/wxGUI2/MainWindow.py", line 880, in OnRun self.run() File "/usr/local/phenix-1.6-289/phenix/wxGUI2/Programs/ HKLTools.py", line 81, in run symmetry_callback=None) # TODO File "/usr/local/phenix-1.6-289/cctbx_project/iotbx/ reflection_file_editor.py", line 358, in __init__ "related reflections are not identical.)" % array_name) TypeError: not all arguments converted during string formatting When i use the scaled .mtz file produced by scala, AutoSol works fine. Just wondering what's going on! Also, how do you delete individual Jobs in the Job History window (ie jobs that have failed or you no longer want to keep etc) Thanks for the help

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phenix.refine frozen
by Roberto Steiner 11 Feb '10

11 Feb '10

Hi there, I would appreciate some feedback on the following: I am playing around with phenix.refine which comes with Phenix distro 1.6-289 for Mac-Intel. When running a normal refinement job (ind site + grouped ADPs + ncs+TorsionSimulatedAnnealing) phenix.refine gets stuck after bulk solvent modelling and scaling. The last things I see in the log page are: ====================== bulk solvent modeling and scaling ====================== |--(resolution: 3.50 - 58.55 A; n_refl. = 55140)------------------------------| | | | r_work= 0.2687 r_free= 0.2800 ksol= 0.38 Bsol= 10.09 scale= 1.148 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (-2.67,-2.67,5.34,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.41 A | | x-ray target function (ml) for work reflections: 7.216427 | | -----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= and that's it. For completeness, I must report that I changed the defaults of wxc_scale and wxu_scale (but surely that cannot be the problem...). Switching off the TorsionSimAnnealing does not help. Additionally, if I click on the abort button on the bottom-left of the page nothing happens. On the other hand if I click on the abort icon at the top of the page I get the message "You are not currently running any calculations. Do you want to close this window?" If I say Ok the following message appears: "There is at least one process running; are you sure you want to exit before it is finished" Other tasks (phenix.xtriage for example) seem to run fine. Any suggestion? Best Roberto

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