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phenix.refine python error !!
by john kryst 12 Oct '07

12 Oct '07

Hi all !!! I have recently updated phenix version to phenix-1.3b-rc3. After that when i run phenix.refine it runs properly. But while writing the pdb file it is giving the following error. Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc3/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc3/phenix/phenix/refinement/command_line.py", line 89, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.3b-rc3/phenix/phenix/refinement/driver.py", line 1101, in write_refined_pdb pdb_header.write_remark_3(info = m_info, out = f) File "/usr/local/phenix-1.3b-rc3/mmtbx/mmtbx/pdb_header.py", line 21, in write_remark_3 info.show_remark_3(out = out) File "/usr/local/phenix-1.3b-rc3/mmtbx/mmtbx/model_statistics.py", line 483, in show_remark_3 self.data_x.show_remark_3(out = out) File "/usr/local/phenix-1.3b-rc3/mmtbx/mmtbx/f_model.py", line 2034, in show_remark_3 bin.n_work, bin.n_free, bin.r_work*100., bin.r_free*100.) TypeError: unsupported operand type(s) for *: 'NoneType' and 'float' I am using fedora 5, python 2.4.2. I have used phenix-installer-1.3b-rc3-intel-linux-2.4.tar. It was working fine in the last build. Google'ing the error didn't help much. Thanks for your inputs. regards John

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Hires input file problem
by Troy E Messick 12 Oct '07

12 Oct '07

Hi all, I seem to be having a problem specifying the labels for the Hires dataset for an Autobuild run. Here is my input script: input_data_file sharp.mtz input_labels 'Fdm' 'SIGFPsha' 'PHIdm' 'FOMdm' 'HLAdm' 'HLBdm' 'HLCdm' 'HLDdm' 'FreeR_flag' input_pdb_file ab.pdb input_seq_file seq.dat input_hires_file output.native.sca Here is the error from the AutoBuild.log file: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ I've tried to use the mtz file from the ImportRawData_run directory and specify the columns by substituting the last line in my input script file with: input_hires_file output_PHX.mtz input_hires_labels 'output.native' 'SIGoutput.native' which are the only labels I could find from mtzdump and that doesn't work either. What am I missing here? Any suggestions would be greatly appreciated. Thanks, Troy

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"Aromatic" question
by Claudia Scotti 11 Oct '07

11 Oct '07

Dear list, I've refined a protein at 2.0 A resolution with its ligand, a small molecule which includes a phenyl group. For this, I used elbow to generate the cif file, and in this file the atoms of the phenyl ring are correctly defined as "aromatic". However, the pdb output of the refinement shows a boat configuration for the 6 carbon atoms ring, with a very nice fit to the electron density. This would suggest a flexible cyclohexyl- substituent instead of the expected, typically planar phenyl ring. As my chemistry is poor, I'd really need some suggestions on where I'm wrong: did I give the wrong cif file or does phenix recognise a better fitting in a boat structure, indicating that my ligand phenyl moiety has been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the phenyl group not so planar as I've supposed it to be until now? Any help would be very appreciated. Many many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=…

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Confused with ANAISOU in PDB
by Partha Chakrabarti 10 Oct '07

10 Oct '07

Hi, I am bit confused with two things. First I did specify individual isotopic, as following, still see ANAISOU in PDB. Is it from TLS strategy? I have used TLS in refmac, don't see it there. Second thing is, I want to tighten the water picking. How can I do that? adp { individual { isotropic = "all" anisotropic = None } group = None one_adp_group_per_residue = True tls = "chain A" tls = "chain B" Best, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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planarities definition help
by Francis E Reyes 10 Oct '07

10 Oct '07

I need to specify a group of residues/atoms that must exist on the same plane for refinement. I think the keyword is refinement.geometry_restraints.planarities may be the right keyword, but I'm unsure as to the syntax for defining the selection? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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R free set in twinned dataset
by Jianghai Zhu 09 Oct '07

09 Oct '07

Hi, Can I use phenix.refine to generate R-free flag in the case of twinning? Will phenix.refine consider the twinning operator in the process? I couldn't find this information in the manual. Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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NAG-ASN link
by Jianghai Zhu 08 Oct '07

08 Oct '07

Hi, I got the following error when I added a NAG-ASN link in the def file. /nfs/home/jzhu/xiao/x61b/phenix6/temp/x61b.pdb Monomer Library directory: "/nfs/home/jzhu/phenix-1.3b-rc3/ext_ref_files/mon_lib" Total number of atoms: 46651 apply_cif_link: data_link: NAG-ASN mod_id_1: DEL-O1 mod_id_2: DEL-HD22 residue_selection_1: chain S and resname NAG and resid 1001 residue_selection_2: chain A and resname ASN and resid 15 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 46651 Number of chains: 8 Number of residues, atoms: 909, 13713 Unexpected atoms: {'ASN%DEL-HD22,HD22': 1} Classifications: {'peptide': 909} Modifications used: {'DEL-HD22': 1, 'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 847, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 601, 8947 Classifications: {'peptide': 601} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 569, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 898, 13559 Classifications: {'peptide': 898} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 59, 'TRANS': 836, 'PCIS': 2} Chain breaks: 3 Number of residues, atoms: 602, 8954 Classifications: {'peptide': 602} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 28, 'TRANS': 570, 'PCIS': 3} Chain breaks: 2 Number of residues, atoms: 642, 642 Classifications: {'water': 642} Link IDs: {None: 641} Number of residues, atoms: 31, 780 Unusual residues: {'MAN': 7, 'NAG%DEL-O1': 1, 'NAG': 23} Classifications: {'undetermined': 31} Modifications used: {'DEL-O1': 1} Link IDs: {None: 30, 'NAG-ASN': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen chiralities: 30 Number of residues, atoms: 16, 16 Unusual residues: {' MG': 2, ' CA': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Number of residues, atoms: 4, 40 Unusual residues: {'IMD': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Number of atoms with unknown nonbonded energy type symbols: 1 "HD22 ASN A 15 " Time building chain proxies: 32.54, per 1000 atoms: 0.70 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 1 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary (see phenix.refine documentation). Also note that phenix.elbow is available to create restraint definitions for unknown ligands. Couldn't figure out what went wrong. Can somebody help me? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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twin fraction
by Jianghai Zhu 06 Oct '07

06 Oct '07

Hi, I am using the phenix 1.3 beta rc3 to refine a twinned structure. In the old version, phenix.refine would report a twin fraction for each cycle of refinement. I could not find the twin fraction anymore in either the log file or the output pdb file. Where is it now? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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Hinge movement for refine?
by Partha Chakrabarti 05 Oct '07

05 Oct '07

Hiya, I have used rigid body refinement in phenix.refine as suggested: refinement.refine.sites { rigid_body = chain A rigid_body = chain B } If I have a multidomain protein like kinases, or G proteins which have flexible switches, how can I define the region within a given chain? Best, Partha -- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: pchakra(a)nimr.mrc.ac.uk Phone: + 44 208 816 2515

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Re: [phenixbb] Question about strategy in phenix.refine
by Pavel Afonine 05 Oct '07

05 Oct '07

Hi, this figure from phenix.refine manual illustrates the refinement protocol the best (although it's a bit sketchy): http://phenix-online.org/documentation/refinement.htm#anch8 Pavel. > 2007/10/4, Partha Chakrabarti <ppchak(a)gmail.com>: > >> I am just trying to figure out certain details. For example, if one chooses >> multiple options in the strategies, how does the program decide if step 1 >> is nearly done and it can go to step 2? Of course I guess the whole process >> is iterative (macro cycle?) but having a bit control so to say.. >>

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