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problems with map quality, refinement and R/Rfree
by Joe Smith 19 Oct '07

19 Oct '07

Hi all, We have data sets for a protein-RNA complex at 3.2 A resolution. . The data belong to the space group I4122 and contains one molecule of Protein-RNA complex (300AA and 16nt; 66% solvent content) in the asym unit. We have managed to get phases using Se-SAD and the present model contains 60% of the protein atoms (250 residues many of them build as Ala) and almost complete RNA (16nt). We could not locate ~20 % of the residues (present in various loops as well as at N- and C-terminal ends). First 120 residues present at N-terminal end seem to have poor relatively main-chain density and almost no side chain density. RNA and 130 residues present at the C-terminal end have good electron density for main-chain as well as side chain. The solution seems to be correct as molecular replacement trials with this model gave same solution in Phaser, Molrep and AMoRe. Solution seems to be also correct because as expected one RNA strand present in asym unit pairs with another one coming from symmetry related molecule. We have checked data in space group I4122 with CCP4 (SFCHECK, cumulative intensity distribution), Yeates server as well as Phenix.xtriage. In all the cases it indicates no twinning. However if I process the data in lower symmetry space group it does indicate presence of almost perfect twin. We realize that this could be just because of processing data in lower symmetry space group and data in all probability may still be fine. The problem is now with refinement and model building. Refinement with CNS and Refamc gave considerably higher value of R and R free. In CNS1.1, refinement with small changes in the model some time leads to large shift in R and R-free value. Refmac: R=36; Rfree=47 CNS1.1: R=40-59; R-free=45-63 However in both the cases map looks more or less same (with reasonably good density for the main-chain as well as RNA) I tried refining with phenix.refine and there is some improvement in the R(34%) and Rfree(40%) values. I think may be robust bulk solvent correction incorporated in phenix.refine has helped in this case. However, I still see no improvement in the map quality for the first 120 residues. In the absence of any clear density I am unable to build any further. I feel N-terminal domain is bit flexible and may have overall poor density. I have used Se position as well as predicted secondary structure in assigning the amino acid in the map but due to few breaks in the N-terminal domain as well as poor density I am unable to assign any amino acid into the poly ala main chain. Frankly speaking, I do not know how to proceed further. I welcome any kind of suggestions which could help us in this case. Regards Joe

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1.3 beta rc3 version FC2 gui error
by Balasundaresan 12 Oct '07

12 Oct '07

Dear Author, I downloaded and installed the 1.3 beta rc3 version(GUI) in FEDORA CORE 2.0 and everything went well during installation and sourced it in .cshrc. while typing phenix in the command line I faced the below error, Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc3/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b-rc3/build/intel-linux-2.6/base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b-rc3/build/intel-linux-2.6/base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libstdc++.so.6: cannot open shared object file: No such file or directory any opinion or suggestions are welcome... regards Bala -- Balasundaresan <d-bala(a)aist.go.jp>

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phenix.refine python error !!
by john kryst 11 Oct '07

11 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 11 Oct '07

11 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 10 Oct '07

10 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 09 Oct '07

09 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 09 Oct '07

09 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 08 Oct '07

08 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 07 Oct '07

07 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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