September 2012 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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links in phenix summary
by Christian Roth 04 Apr '13

04 Apr '13

Dear all, thanks to the phenix team which helped me a lot to resolve all issues regarding the correct link definitions. I have summarised a few things which one might consider if nonstandard links are necessary. Try phenix ready set to get your links out of the pdb. Do not forget to change the possible LINKR to LINK! Inspect the links and decide if they are useful! Peptide links are automatically incorporated if residues are close (inspect geo file) Non standard peptide links could be created using using an now available alpha release script: elbow.ligand_linking model.pdb Inspect the generated cif file and correct angles and incorporate dihedrals and so on if necessary. Sugar links which exists in the mon_lib.cif should be incorporated using the apply_cif link option like refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-4 residue_selection_1 = chain B and resname GLC and resseq 1 residue_selection_2 = chain B and resname GLC and resseq 2 } According to the link definition the C1 oxygen of the following sugar with the higher number must be removed. The automatic incorporation of sugar links will be probably soon available in phenix. Nigel is already working on this. If one want use hydrogens in the refinement, they have to be added previously with ready_set and afterwards the OH4 sugar hydrogen has to be removed before the refinement. For links with symmetry related atoms the symmetry operator must be included in a custom bond definition efinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } The operator can be obtained using iotbx.show_distances your.pdb > all_distances Search for keyword "sym" or from Coot clicking on the symm option. Coot print out the operator and the translation term separately. Both has to be merged in the final operator used in phenix! Christian

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Memory and CPU usage
by Jon Agirre 05 Mar '13

05 Mar '13

Dear community, I'm planning on buying a new macbook for my first abroad postdoc venture, and I'm currently trying decide what amount of RAM & CPU to choose. My question is a little bit intricate: is there any rule of thumb to estimate the needed RAM versus the number of input atoms for any particular refinement type? I'm planning on tackling some big (18,000 residues/asu) refinements but I don't have any estimation as to how many GBs of RAM they might require. The maximum amount of RAM I can install is 16GB, but it is a non-standard configuration that might void Apple's warranty. About the CPU: how scalable are typical phenix processes? Would it be sensible to invest in a quad-core machine with HT? In this particular case, and since HT would present 8 logical cores, would I get any speed up from launching phenix tasks configured for 8 processors instead of 4? Thanks in advance! Jon

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use of the file find_ncs.resolve
by Fred. Vellieux 29 Jan '13

29 Jan '13

Hi all, I do not understand how the file "find_ncs.resolve" has to be fed into the "resolve" part of Phenix. Can it be used in the GUI for an autobuild procedure? Can anyone help on this? Ta very much in advance, F. Vellieux -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605 Fax: +33 438785494

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OS X 10.8 Mountain Lion
by Alexander Batyuk 10 Oct '12

10 Oct '12

Dear all, Could anybody confirm that Phenix does or does not run on OS X 10.8 Mountain Lion, please? Best wishes, Alex -- Alex Batyuk The Plueckthun Lab www.bioc.uzh.ch/plueckthun

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point-n-click installer is bjorking OS X Dock
by Scott Classen 26 Sep '12

26 Sep '12

Hello, After running the OS X point-n-click installer for the 1.8.1-1160 nightly build, the dock becomes unresponsive and I can no longer command+tab to switch between applications. I've reproduced this on 2 Macs. One running 10.8.2 and the other running 10.7.5 Relaunching Finder does not fix the proton dock/app switching Logging out and then logging back in fixes the problem. Scott

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den refinement with multiple reference files
by Andreas Förster 26 Sep '12

26 Sep '12

Dear all, I've started DEN refinement on a structure obtained by MR from data optimistically going to 3.8A. There are several chains of two kinds in the structure. High-resolution structures exist for both. How do I use two reference files for DEN refinement, and how do I assign which chain corresponds to which reference? (Currently, I'm using reference_file = None.) Thanks. Andreas -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk

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Phenix cut out density labels choice
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following issue with running Phenix.cutout density either on command line or in GUI. I have multiple columns in the mtz.file and I want to choose map coefficients FOFCWT_d1-8,PHFOFCWT_d1-8 for the difference map to be cut around pdb selection. I run a command: phenix.cut_out_density model.pdb my.mtz cutout_fix_position=True cutout_model_radius=10 cutout_type=model \ map_coeff_labels=FOFCWT_d1-8,PHFOFCWT_d1-8 Problem: The output cutout.mtz has FWT and PHWT (which I did not have at all in the input) and not my difference map coefficients, and obviously the map is not my difference map. In GUI is the same problem, I choose columns I need but it outputs FWT and PHWT again. Please, let me know what I am doing wrong. Thank you very much! Mikalai

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Combine map labels
by Mikalai Lapkouski 21 Sep '12

21 Sep '12

Hello, I have a following question. I have generated several Fo-Fc sa omit maps (FOFCWT, PHFOFCWT) for different portions of a DNA molecule. Now that I have each omit map as a separate file to display the whole DNA omit map I have to load them in coot one by one. Is there a way of how to combine all this maps into one file and have a single name for label columns so that the whole map will open at once? I managed to put them all in one file but column labels are separate: FOFCWT_1, PHFOFCWT_1 FOFCWT_2, PHFOFCWT_2...... Can they all go under FOFCWT, PHFOFCWT? Thank you very much for any suggestion Mikalai

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Specifying union of two chains in pdb_atom_selection
by Francis E Reyes 20 Sep '12

20 Sep '12

Hi all, I issue the following command to pdb_atom_selection but I get 0 atoms selected at the end? $ phenix.pdb_atom_selection refine_to_submit.pdb "chain X and chain B" refine_to_submit.pdb Monomer Library directory: "/usr/local/phenix-1.8-1069/chem_data/mon_lib" Total number of atoms: 3817 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} Chain: "X" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1800 Classifications: {'RNA': 84} Modifications used: {'rna3p_pyr': 26, 'rna2p_pur': 5, 'rna3p_pur': 44, 'rna2p_pyr': 9} Link IDs: {'rna3p': 70, 'rna2p': 13} chain X and chain B 0 atoms selected Thanks! F --------------------------------------------- Francis E. Reyes PhD 215 UCB University of Colorado at Boulder

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