- phenixbb - phenix-online.org

broken bonds in the substrate
by houjin zhang 11 Jul '08

11 Jul '08

Hi: I am trying to use phenix.elbow to generate restrains for a substrate. I notice that the PDB file produced by elbow contains some broken bonds. So I ran the elbow with the internal strings ATP. The output PDB file also harbors broken bonds. The --opt did help a little. But some bonds still look weird. I am wondering if this a bug or I just didn't install phenix right. I use the latest version of phenix and default setting. Thank you very much!! Houjin

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Reminder: Crystallographic Computing School registration deadline approaching
by Ralf W. Grosse-Kunstleve 11 Jul '08

11 Jul '08

The registration deadline for the 2008 Crystallographic Computing School is in two weeks: *** July 25 *** The schedule of the program including abstracts from all speakers is available here: http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/program.html This program puts a strong weight on fostering one-on-one interactions. There will be only 16 lectures of 45 minutes each (12 hours total) but more than 20 hours of tutorials and demonstrations. Don't miss this unique opportunity for close interaction with the developer community! On behalf of the organizing committee: A. L. Spek (Utrecht University , Netherlands) R. Grosse-Kunstleve (LBNL, USA) M. Yao (Hokkaido University, Japan) A. Nakagawa (Osaka Institute of Protein, Japan) H. Powell (MRC, UK) L. Cranswick (NRC , Canada)

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PHENIX on OS X Intel 10.5 "need access to screen" error
by Ben Eisenbraun 10 Jul '08

10 Jul '08

Howdy, I have PHENIX 1.3-rc2 built on an OS X Intel 10.4 machine. It runs fine there, but using the same installation mounted via NFS, I get this error: This program needs access to the screen. Please run with 'pythonw', not 'python', and only when you are logged in on the main display of your Mac. I dug around in the program a bit to see if there was a script testing for the DISPLAY setting, but this seems to be generated in the wx-python bits: build/mac-intel-osx/base/Python.framework/Versions/2.5/lib/python2.5/site-packages/wx-2.8-mac-ansi/wx/_core.py contains the error message, as do a couple of other files in the /wx/ hierarchy. The PHENIX 1.3-rc2 I built on OS X 10.4 PPC works fine on the 10.5 PPC machines, so I'm a bit surprised it's failing on the Intel side. Does anyone know if a PHENIX built on 10.5 will work on a 10.4 machine? If it was really necessary, I could install versions built on both 10.4 and 10.5, but I'd prefer to avoid it if possible. Any insight on fixing this would be much appreciated. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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Re: [phenixbb] phenix.autobuild: command not found
by Paul Adams 09 Jul '08

09 Jul '08

Hi, Please install the latest version of Phenix (1.3-rc2) from the web page. Cheers, Paul On Jul 8, 2008, at 6:45 PM, Vinayak Agarwal wrote: > Hello, > > I installed Phenix 1.24 on Fedora 8 and get the following error > message while trying to use phenix.autobuild command on the command > line: > > bash: phenix.autobuild: command not found > > Could you please help me to rectify this? > > When I try to run the GUI by typing in phenix at the command line, I > get the following warning messages, though the GUI does open: > > Shell variable SSH_PATH not set > > Shell variable RSH_PATH not set > > Thanking you, > > Sincerely, > > Vinayak Agarwal -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Administrator: Delia Clark [ DNClark(a)lbl.gov ][ 1-510-486-6331 ] --

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sugar chain cif file
by Daniele de Sanctis 08 Jul '08

08 Jul '08

Dear all, I have a trisaccharide in my structure, and I generate the cif file with elbow (see below). Unfortunately phenix.refine seems not recognizing the bonds C5-O1 between different units and is not keeping the chain together. As far as I could understand I should also use the keyword "apply_cif_link", but I couldn't find which syntax i should use. Thanks for the help Daniele # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version 1.3b (Mon Nov 20 17:20:00 2007) # - file written: Mon Jul 7 18:19:22 2008 # # Input file: a3.pdb # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level AHR AHR 'Unknown ' ligand 15 9 . # data_comp_AHR # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z AHR 'C5'' C CH3 . 61.3311 15.7148 36.7946 AHR 'C4'' C CR5 . 60.1817 16.4682 36.1126 AHR 'O4'' O O . 60.3257 17.5507 35.0934 AHR 'C3'' C CR5 . 58.6911 16.2438 36.3556 AHR 'O3'' O OC . 58.1296 15.2877 37.2130 AHR 'C2'' C CR5 . 57.9427 17.1885 35.4852 AHR 'O2'' O OC . 56.5500 17.3383 35.4371 AHR 'C1'' C CR5 . 58.9640 18.0045 34.6971 AHR 'O1'' O OH1 . 58.6701 18.9985 33.7515 AHR 'H5'1' H HCH3 . 61.2131 14.6537 36.6320 AHR 'H5'2' H HCH3 . 61.3175 15.9201 37.8548 AHR 'H5'3' H HCH3 . 62.2726 16.0401 36.3773 AHR 'H3'1' H H . 57.7021 15.7812 38.0734 AHR 'H2'1' H H . 56.1521 16.7529 34.6214 AHR 'H1'1' H HOH1 . 59.4063 19.7861 33.8153 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd AHR 'C5'' 'C4'' single 1.53429 0.02 AHR 'C4'' 'O4'' aromatic 1.49380 0.02 AHR 'C4'' 'C3'' aromatic 1.52685 0.02 AHR 'O4'' 'C1'' aromatic 1.48900 0.02 AHR 'C3'' 'O3'' double 1.40168 0.02 AHR 'C3'' 'C2'' aromatic 1.48663 0.02 AHR 'C2'' 'O2'' double 1.40154 0.02 AHR 'C2'' 'C1'' aromatic 1.52635 0.02 AHR 'C1'' 'O1'' single 1.40306 0.02 AHR 'H5'1' 'C5'' single 1.08000 0.02 AHR 'H5'2' 'C5'' single 1.08000 0.02 AHR 'H5'3' 'C5'' single 1.08000 0.02 AHR 'H3'1' 'O3'' single 1.08000 0.02 AHR 'H2'1' 'O2'' single 1.08000 0.02 AHR 'H1'1' 'O1'' single 1.08000 0.02 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd AHR 'O4'' 'C4'' 'C5'' 125.93952 3.0 AHR 'C3'' 'C4'' 'C5'' 126.05117 3.0 AHR 'H5'1' 'C5'' 'C4'' 109.48717 3.0 AHR 'H5'2' 'C5'' 'C4'' 109.48699 3.0 AHR 'H5'3' 'C5'' 'C4'' 109.47730 3.0 AHR 'C1'' 'O4'' 'C4'' 108.31507 3.0 AHR 'O3'' 'C3'' 'C4'' 126.06060 3.0 AHR 'C2'' 'C3'' 'C4'' 107.75208 3.0 AHR 'C3'' 'C4'' 'O4'' 108.00930 3.0 AHR 'C2'' 'C1'' 'O4'' 108.15545 3.0 AHR 'O1'' 'C1'' 'O4'' 125.92746 3.0 AHR 'H3'1' 'O3'' 'C3'' 109.52327 3.0 AHR 'O2'' 'C2'' 'C3'' 126.02920 3.0 AHR 'C1'' 'C2'' 'C3'' 107.76809 3.0 AHR 'C2'' 'C3'' 'O3'' 126.15656 3.0 AHR 'H2'1' 'O2'' 'C2'' 109.52075 3.0 AHR 'O1'' 'C1'' 'C2'' 125.91301 3.0 AHR 'C1'' 'C2'' 'O2'' 126.15898 3.0 AHR 'H1'1' 'O1'' 'C1'' 109.51700 3.0 AHR 'H5'2' 'C5'' 'H5'1' 109.46605 3.0 AHR 'H5'3' 'C5'' 'H5'1' 109.45474 3.0 AHR 'H5'3' 'C5'' 'H5'2' 109.45508 3.0 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period AHR CONST_01 'C2'' 'C1'' 'O4'' 'C4'' 0.00000 0.0 0 AHR CONST_02 'C1'' 'C2'' 'C3'' 'C4'' -0.00000 0.0 0 AHR CONST_03 'C2'' 'C3'' 'C4'' 'O4'' 0.00000 0.0 0 AHR CONST_04 'C3'' 'C2'' 'C1'' 'O4'' -0.00000 0.0 0 AHR CONST_05 'C1'' 'O4'' 'C4'' 'C3'' -0.00000 0.0 0 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd AHR plan-1 'C4'' 0.020 AHR plan-1 'O4'' 0.020 AHR plan-1 'C1'' 0.020 AHR plan-1 'C2'' 0.020 AHR plan-1 'C3'' 0.020 AHR plan-1 'C5'' 0.050 AHR plan-1 'O1'' 0.050 AHR plan-1 'O2'' 0.050 AHR plan-1 'O3'' 0.050 AHR plan-2 'C4'' 0.100 AHR plan-2 'O4'' 0.100 AHR plan-2 'C5'' 0.100 AHR plan-2 'C3'' 0.100 AHR plan-3 'C3'' 0.100 AHR plan-3 'O3'' 0.100 AHR plan-3 'C4'' 0.100 AHR plan-3 'C2'' 0.100 AHR plan-4 'C2'' 0.100 AHR plan-4 'O2'' 0.100 AHR plan-4 'C3'' 0.100 AHR plan-4 'C1'' 0.100 -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartado 127 2781-901 Oeiras Portugal

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using TLS files from Refmac
by nihmayerm 02 Jul '08

02 Jul '08

Hi, I've just started to learn how to use PHENIX. I'd like to continue a refinement started with REFMAC for which I already have refined TLS parameters initially generated using the WUSTL TLSMD server. Can I use the .tls file as input to PHENIX or do I have to redefine the TLS groups and tensors. Thanks

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Re: [phenixbb] distance restraints
by Ralf W. Grosse-Kunstleve 02 Jul '08

02 Jul '08

Hi Oliver, > I am about to define distance restraints for a metal coordination site > using a refinement.geometry_restraints.edits entry. Unfortunately, > two of the four ligand side chains come from a symmetry-related > molecule! What is the syntax to properly refer to a symm in such > a case? You have to use the "symmetry_operation" keyword in this input block: refinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None slack = None } } With phenix.refine --show-defaults=all.help you get: symmetry_operation = None .help = "The bond is between atom_1 and symmetry_operation * atom_2, " "with atom_1 and atom_2 given in fractional coordinates. " "Example: symmetry_operation = -x-1,-y,z" The symmetry_operation must produce the fractional coordinates of atom_2 exactly (within floating-point precision). I.e. depending on where the atoms are, you may need -x+2,-y-3,z or similar. Let me know if you need help figuring out the fractional coordinates. Ralf

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special positions
by o.h.weiergraeber＠fz-juelich.de 02 Jul '08

02 Jul '08

Hello, a very simple question (although I could not find *anything* about this in the documentation!): What does phenix.refine expect as occupancy for an atom on a special position: reduced occupancy (like refmac) or full occupancy (like cns_solve)? Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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Re: [phenixbb] special positions
by o.h.weiergraeber＠fz-juelich.de 02 Jul '08

02 Jul '08

Adding to my previous post, I have found another strange issue (possibly a bug?) concerning special positions: In my case, the "special" atom (a cation on a three-fold in sg I23), while being considered during refinement, seems to be completely omitted (or heavily downweighted) for map calculations! The 2fo-fc map shows a "hole" at this position, while there is huge difference density in the fo-fc map (largely irrespective of whether or not the occupancy is reduced in the input.) The same pdb file, used in cns just for map calculation, gives a beautiful density at the cation position, while the rest of the map is more or less identical. At the moment I cannot think of any error in the input since refinement of the atom does take place, with the proper restrictions due to the three-fold axis. But something is going seriously wrong. Any ideas? Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ----- Original Message ----- From: o.h.weiergraeber(a)fz-juelich.de Date: Wednesday, July 2, 2008 2:55 pm Subject: [phenixbb] special positions > Hello, > > a very simple question (although I could not find *anything* about > this in the documentation!): > What does phenix.refine expect as occupancy for an atom on a > special position: reduced occupancy (like refmac) or full occupancy > (like cns_solve)? > > Oliver > > > > ------------------------------- > Dr. Oliver H. Weiergraeber > Institute of Neurosciences and Biophysics > Molecular Biophysics > Research Centre Juelich > D-52425 Juelich > Germany > Phone: +49-2461-612028 > Fax: +49-2461-612020 > ------------------------------- > > > > ------------------------------------------------------------------- > ------------------------------------------------------------------- > Forschungszentrum Juelich GmbH > 52425 Juelich > > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, > Dr. Sebastian M. Schmidt > ------------------------------------------------------------------- > ------------------------------------------------------------------- > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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Fwd: [COOT] Using Coot with PHENIX
by Stephen Graham 02 Jul '08

02 Jul '08

Below is an email from Kevin Cowtan (posted on the COOT bb) that may be of interest to people who use COOT for building. Stephen ---------- Forwarded message ---------- From: Kevin Cowtan <cowtan(a)ysbl.york.ac.uk> Date: Jul 2, 2008 9:31 AM Subject: [COOT] Using Coot with PHENIX To: COOT(a)jiscmail.ac.uk There are some issues which may be affecting some people using Coot with PHENIX. If you try and use the two together in the wrong way, then you may get unexpected results. (Problems hashed out with help from Dirk). phenix.refine produces two different sets of output files. I quote from the documentation: At the end of refinement the program generates: ... two maps: likelihood weighted mFo-DFc and 2mFo-DFc. These are in ASCII X-PLOR format. A reflection file with map coefficients is also generated for use in Coot or XtalView (e.g. lysozyme_refine_001_map_coeffs.mtz); There are some CNS maps, which may be used in conventional graphics programs, and there is an MTZ file, which may be used in Coot or XtalView. The difference is important. Coot and XtalView have a fundamentally different concept of what a map is to other graphics programs. As a result they require different information. Phenix.refine recognises this and provides appropriate information for each type of program. In the last year we incorporated the ability to read CNS files into coot. As a result, some users have started reading the CNS map files into coot instead of the MTZ file. Unfortunately, this does not always work the way you would expect, because the map files has not been generated with Coot in mind. This may lead to misleading sigma levels, or, if the map is modified or masked in any way before giving it to Coot, much more serious artifacts. The solution is simple: When using Coot, use the MTZ file which the phenix developers have provided for that purpose, *not* the CNS map files. In addition to giving the right answers, there are some other benefits: - The MTZ is much smaller, in case you want to archive it. - Using auto-open mtz, you get both maps at once, and the difference map is automatically displayed as such, saving mouse clicks. - The spacegroup and cell information are in the file, so it works even if you don't open the PDB file first. .. You can stop reading here, the rest is detail for those who are interested: Coot and XtalView use a different representation of electron density, a continuous crystal representation. Most other graphics programs use a bounded box representation. The continuous crystal representation means that the electron density is everywhere, it is omnipresent. "If I scroll up to the heavens, density is there; if I place my ligand in the depths, density is there. If I drag over to the far side of the solvent, even there the density will guide my fitting." (*) To generate a continuous crystal representation, you need a complete and consistent description of the electron density over the asymmetric unit (any asymmetric unit - it doesn't matter where in space). The bounded box representation need the electron density over the volume of the molecule. It is not always possible to get the asymmetric unit representation from the bounded box representation, because in creating the bounded box some information may have been lost. However, you can always get it from an MTZ file, or from a map file on the condition that the map file is appropriately bounded. Kevin (*) Psalm 139 v8-10 -- 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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distance restraints
by o.h.weiergraeber＠fz-juelich.de 02 Jul '08

02 Jul '08

Hello, I am about to define distance restraints for a metal coordination site using a refinement.geometry_restraints.edits entry. Unfortunately, two of the four ligand side chains come from a symmetry-related molecule! What is the syntax to properly refer to a symm in such a case? Oliver ------------------------------- Dr. Oliver H. Weiergraeber Institute of Neurosciences and Biophysics Molecular Biophysics Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 ------------------------------- ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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tlsanal
by john kryst 01 Jul '08

01 Jul '08

Hi all !! I have coupls of questions regarding TLS in phenix. 1. Has anyone tried using program tlsviewer with phenix refined pdb. It is not able to detect TLS groups unless you modify your residue range in the pdb to refmac convention. Is there any other program available to visualize the TLS movements. 2. I would like to use tlsanal to see how much is the contibution from TLS to the ADP. Is there any utility availble in TLS to do it. If i need to use tlsanal.. what should i modify in the pdb. thanks regards John

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Postdoctoral Position - Chemical Imaging of Plant Biomass with Micro- and Nano-Raman Spectroscopy
by Paul Adams 30 Jun '08

30 Jun '08

Postdoctoral Researcher Chemical Imaging of Plant Biomass with Micro- and Nano-Raman Spectroscopy Job ID: UCB-013 Institution: Energy Biosciences Institute, Berkeley California Date Opened: 5/10/2008 Position Description: Development of computational tools for the analysis of chemical imaging data. Computational construction of three- dimensional maps of plant cell wall material from Raman spectroscopy measurements. Position Responsibilities: Development of algorithms to indentify chemical species from Raman spectroscopy measurements. Processing of data to generate two-dimensional images of chemical components in plant cell wall material. Use of tomographic methods to construct three-dimensional images. Development of maximum likelihood methods to extract information from weak spectroscopic data. Position Qualifications: Strong computational skills with experience in their practical application to imaging or complex data analysis. Preference will be given to candidates with experience in the analysis of spectroscopic data or imaging of biological samples. Experience with programming languages: C/C++ and scripting languages: Python/ Perl. Demonstrated publication record in the computational analysis of data and algorithm development. Ability to work in a team environment and good communication skills. Ph.D. in physical chemistry, biology, physics, computer science or related field. See the program description for more details: http://energybiosciencesinstitute.org/index.php?option=com_content&task=vie… How to Apply: Submit a Letter of Interest, CV, and three (3) contacts for references via email to: Paul Adams Lawrence Berkeley Lab, BLDG 64R0121 1 Cyclotron Road Berkeley, CA 94720 510-486-4225 pdadams(a)berkeley.edu The University of California, Berkeley is an Equal Opportunity Employer committed to diversity in its staff, faculty, and student body, and invites all qualified people to apply, including minorities and women, veterans and individuals with disabilities. -- Paul Adams Adjunct Professor, Department of Bioengineering, U.C. Berkeley Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul --

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Fwd: Re: help with refinement in Phenix
by hosur＠barc.gov.in 30 Jun '08

30 Jun '08

Hi PHENIX developers, I am forwarding herewith my correspondence with Dr. Pavel Afonine regarding a reinement issue in PHENIX. I would appreciate if other developers can help me with the solution before Pavel comes back on June 25th. Thanks. The requirement is to be able to refine a model in which a piece of electron density is interpreted as partial occupancy protein residue and a set of water molecules. Hosur M.V. ----- Forwarded message from Pavel Afonine <pafonine(a)lbl.gov> ----- Date: Sat, 14 Jun 2008 21:57:36 -0700 From: Pavel Afonine <pafonine(a)lbl.gov> Reply-To: Pavel Afonine <pafonine(a)lbl.gov> Subject: Re: help with refinement in Phenix To: hosur(a)barc.gov.in Hi Hosur, I'm out of town and not regular at email, so the delay with the answer,, sorry for this. Actually, it is the best to address your questions to phenixbb (http://www.phenix-online.org/mailman/listinfo/phenixbb) so all the PHENIX developers get it and you don't hang up with the delay if a particular person is temporarily absent. I will be back in office on June 25. Regarding your question: > In my case, the set of 4 water molecules has to have the same occupancy, and > this occupancy with the occupancy of a side chain must make up unity. That is > the sum of two occupancies must be unity. > This particular feature is currently not available in phenix.refine. I will add this option once I'm back in office. > If I understand correctly, if i identify each of the four water molecules by a > different altloc label, then the sum of 5 occupancies will be adjusted to one, > with the possibility of each water occupancy converging to different value. > Yes, this is expected behavior. > Further, the final occupancy would be close to 0.25 of the required value. The > complication, in my opinion, is because the set of four water molecules is not > like set of atoms that make one residue which can be assigned a single altloc > label. I hope I have been able to convey what I mean. Let me have the suitable > PDB, which I can try out. > Yes, this is very clear for me and like I said above I will add this feature to PHENIX as soon as I get back to office. All the best, Pavel. ----- End forwarded message ----- -------------------------------------------------

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refinement with several twins / modulated data / pseudo-translational symmetry
by iulek 29 Jun '08

29 Jun '08

Dear all, I have a strongly modulated dataset as can be observed in the truncate output below. Specially, the modulation is higher for L odd/even and at lower resolution: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Analysis of mean intensity by parity for reflection classes For each class, Mn(I/sig(I)) is given for even and odd parity with respect to the condition, eg group 1: h even & odd; group 7 h+k+l even & odd; group 8 h+k=2n & h+l=2n & k+l=2n or not Range Min_S Dmax Nref 1 2 3 4 5 6 7 8 h k l h+k h+l k+l h+k+l h+k,h+l,k+l 1 0.00018 20.85 519 13.2 8.9 13.9 8.2 22.3 2.4 13.3 8.9 12.5 9.6 12.9 9.0 12.6 9.5 16.5 9.2 2 0.00230 15.04 994 15.9 16.0 15.3 16.5 30.1 2.3 15.7 16.2 15.1 16.7 14.9 16.8 15.1 16.7 13.5 16.6 3 0.00442 12.36 1289 17.2 16.0 17.0 16.2 33.8 3.7 17.2 16.0 14.9 18.0 14.7 18.2 14.9 18.0 13.1 17.4 4 0.00655 10.74 1568 20.7 18.9 20.3 19.2 35.5 4.9 20.4 19.2 18.7 20.7 18.3 21.0 18.5 20.9 17.7 20.3 5 0.00867 9.63 1759 20.3 15.8 20.1 16.0 33.2 4.9 20.1 15.9 18.7 17.3 18.6 17.4 18.8 17.2 21.6 16.9 6 0.01079 8.80 2042 19.6 15.4 19.3 15.7 30.5 5.8 19.5 15.5 17.6 17.3 17.5 17.4 17.6 17.3 19.9 16.7 7 0.01291 8.15 2206 15.9 12.0 15.8 12.1 22.6 5.0 15.5 12.4 14.3 13.5 14.1 13.7 14.0 13.8 16.2 13.2 8 0.01504 7.63 2393 11.8 9.0 11.5 9.3 18.6 3.6 11.7 9.1 10.5 10.2 10.3 10.3 10.4 10.3 12.0 9.9 9 0.01716 7.20 2526 9.8 6.5 9.8 6.5 13.8 3.2 9.8 6.6 9.0 7.3 9.0 7.3 9.0 7.4 11.6 7.1 10 0.01928 6.83 2747 11.1 7.5 11.0 7.6 15.7 3.0 10.8 7.8 10.0 8.5 9.9 8.6 9.8 8.6 12.3 8.3 11 0.02141 6.52 2867 10.3 7.3 10.2 7.3 14.4 3.0 10.3 7.3 9.4 8.1 9.4 8.1 9.4 8.2 11.7 7.9 12 0.02353 6.24 3122 8.6 5.8 8.5 5.8 11.6 3.0 8.4 5.9 7.3 6.9 7.3 6.9 7.2 7.0 8.8 6.6 13 0.02565 6.00 3124 7.9 5.7 7.7 5.9 11.1 2.9 7.7 5.9 6.8 6.7 6.8 6.8 6.8 6.7 7.8 6.5 14 0.02777 5.78 3346 9.8 6.7 9.7 6.7 12.7 3.5 9.6 6.8 8.8 7.7 8.7 7.8 8.6 7.9 10.7 7.5 15 0.02990 5.59 3428 9.0 5.6 8.9 5.7 11.2 3.1 8.8 5.8 7.9 6.7 7.8 6.8 7.7 6.9 9.9 6.4 16 0.03202 5.41 3633 8.3 5.5 8.2 5.5 10.9 3.5 8.2 5.6 7.1 6.6 7.1 6.6 7.1 6.6 8.8 6.2 17 0.03414 5.25 3658 9.6 6.2 9.4 6.3 12.4 3.7 9.4 6.4 8.4 7.3 8.4 7.3 8.2 7.5 10.6 7.0 18 0.03627 5.10 3696 10.2 6.4 10.1 6.5 12.5 4.3 9.8 6.7 8.8 7.8 8.7 7.9 8.6 7.9 10.8 7.4 19 0.03839 4.97 3955 10.1 6.9 9.9 7.0 12.6 4.5 9.8 7.1 8.8 8.2 8.6 8.3 8.6 8.3 10.4 7.9 20 0.04051 4.84 3902 10.9 7.2 10.9 7.2 13.4 4.6 10.7 7.4 9.7 8.4 9.7 8.4 9.7 8.4 12.1 8.0 21 0.04263 4.73 4207 11.4 6.8 11.3 6.9 13.7 4.8 11.1 7.0 9.5 8.5 9.4 8.6 9.5 8.6 12.0 8.1 22 0.04476 4.62 4169 9.7 6.8 9.6 6.9 12.4 4.6 9.5 7.0 8.3 8.1 8.3 8.2 8.2 8.2 9.7 7.8 23 0.04688 4.52 4100 11.1 6.7 11.0 6.8 12.6 5.5 10.8 7.0 9.0 8.8 8.9 8.8 8.9 8.9 11.0 8.2 24 0.04900 4.42 4605 10.8 6.5 10.7 6.5 12.3 4.9 10.5 6.8 9.5 7.8 9.4 7.9 9.3 7.9 12.2 7.5 25 0.05113 4.33 4449 9.6 6.1 9.5 6.2 11.1 4.6 9.4 6.3 8.3 7.4 8.2 7.5 8.2 7.5 10.2 7.0 26 0.05325 4.25 4528 9.1 5.8 9.1 5.8 10.0 4.8 8.8 6.0 7.6 7.2 7.5 7.3 7.5 7.3 9.2 6.8 27 0.05537 4.17 4782 8.6 5.3 8.6 5.3 9.7 4.6 8.5 5.4 7.5 6.5 7.4 6.5 7.4 6.5 9.5 6.1 28 0.05749 4.10 4774 8.3 5.2 8.2 5.3 9.6 3.9 8.0 5.4 7.0 6.4 7.0 6.4 6.9 6.5 8.6 6.1 29 0.05962 4.02 4837 8.1 5.6 8.1 5.7 9.7 4.4 7.9 5.8 7.2 6.6 7.2 6.6 7.2 6.6 8.6 6.4 30 0.06174 3.96 5066 8.2 4.9 8.2 4.9 8.9 4.2 8.0 5.1 6.9 6.2 6.8 6.2 6.7 6.3 8.6 5.8 31 0.06386 3.89 4954 7.4 4.7 7.3 4.8 7.9 4.1 7.2 4.9 6.2 5.9 6.1 6.0 6.2 5.9 7.5 5.6 32 0.06599 3.83 5052 7.6 4.6 7.6 4.6 8.2 4.0 7.4 4.8 6.4 5.8 6.4 5.8 6.3 5.9 8.0 5.5 33 0.06811 3.77 5159 6.9 4.4 6.8 4.5 7.2 4.0 6.6 4.6 5.8 5.4 5.7 5.5 5.6 5.6 6.9 5.2 34 0.07023 3.72 5226 6.7 4.1 6.7 4.2 7.2 3.8 6.6 4.2 5.6 5.2 5.6 5.2 5.6 5.2 7.0 4.9 35 0.07236 3.66 5359 6.6 4.1 6.6 4.2 6.7 4.1 6.4 4.4 5.4 5.3 5.4 5.3 5.3 5.4 6.6 5.0 36 0.07448 3.61 5293 6.4 3.9 6.3 3.9 6.9 3.5 6.2 4.1 5.4 4.8 5.4 4.9 5.4 4.8 6.7 4.6 37 0.07660 3.56 5633 6.7 4.4 6.7 4.4 7.4 3.7 6.6 4.5 5.8 5.3 5.7 5.4 5.7 5.4 7.0 5.1 38 0.07872 3.52 5479 5.9 3.8 5.9 3.8 6.2 3.6 5.8 3.9 5.0 4.7 5.0 4.7 5.0 4.7 6.1 4.5 39 0.08085 3.47 5578 5.2 3.3 5.2 3.3 5.4 3.1 5.0 3.5 4.4 4.0 4.4 4.0 4.3 4.1 5.4 3.8 40 0.08297 3.43 5580 5.3 3.3 5.3 3.3 5.3 3.3 5.2 3.4 4.6 4.0 4.6 4.1 4.6 4.1 5.8 3.8 41 0.08509 3.39 5936 5.3 3.3 5.3 3.2 5.4 3.2 5.1 3.4 4.5 4.0 4.5 4.0 4.4 4.1 5.5 3.8 42 0.08722 3.35 5783 4.7 3.0 4.7 3.0 4.5 3.3 4.6 3.1 3.9 3.8 4.0 3.8 3.9 3.8 4.8 3.6 43 0.08934 3.31 5889 4.4 3.0 4.4 2.9 4.5 2.9 4.3 3.1 3.8 3.6 3.8 3.5 3.7 3.6 4.5 3.4 44 0.09146 3.27 5966 4.4 2.8 4.5 2.8 4.5 2.8 4.3 2.9 3.8 3.5 3.8 3.5 3.8 3.5 4.7 3.3 45 0.09358 3.23 6145 4.0 2.6 4.0 2.6 4.1 2.5 3.9 2.8 3.5 3.2 3.5 3.2 3.5 3.2 4.2 3.0 46 0.09571 3.20 6202 3.6 2.3 3.7 2.3 3.6 2.3 3.6 2.4 3.2 2.8 3.2 2.7 3.2 2.7 4.0 2.6 47 0.09783 3.16 6042 3.7 2.3 3.8 2.2 3.5 2.5 3.7 2.3 3.1 2.9 3.1 2.9 3.1 2.9 4.0 2.7 48 0.09995 3.13 6198 3.5 2.2 3.5 2.1 3.3 2.4 3.4 2.2 2.9 2.8 2.9 2.8 2.9 2.8 3.6 2.6 49 0.10208 3.10 6421 3.3 2.1 3.3 2.1 3.1 2.3 3.2 2.1 2.7 2.6 2.7 2.6 2.7 2.6 3.4 2.4 50 0.10420 3.07 6403 3.2 2.2 3.3 2.1 3.1 2.3 3.2 2.2 2.8 2.6 2.8 2.6 2.8 2.6 3.3 2.5 51 0.10632 3.04 6357 2.9 2.0 3.0 1.9 2.8 2.1 2.9 2.0 2.6 2.4 2.6 2.3 2.6 2.4 3.1 2.2 52 0.10844 3.01 6389 2.6 1.9 2.6 1.9 2.6 2.0 2.6 1.9 2.4 2.2 2.4 2.2 2.3 2.2 2.8 2.1 53 0.11057 2.98 6580 2.8 1.9 2.8 1.9 2.7 2.0 2.8 2.0 2.5 2.3 2.4 2.3 2.4 2.3 2.9 2.2 54 0.11269 2.95 6663 2.8 1.9 2.8 1.8 2.7 1.9 2.7 1.9 2.5 2.1 2.5 2.1 2.5 2.1 3.1 2.0 55 0.11481 2.92 6582 2.6 1.9 2.7 1.8 2.6 1.9 2.6 1.9 2.4 2.1 2.4 2.1 2.4 2.1 2.9 2.0 56 0.11694 2.90 6572 2.6 1.8 2.6 1.8 2.5 1.9 2.6 1.8 2.3 2.1 2.3 2.1 2.3 2.1 2.7 2.0 57 0.11906 2.87 6820 2.4 1.7 2.4 1.7 2.3 1.8 2.4 1.8 2.1 2.0 2.1 2.0 2.1 2.0 2.5 1.9 58 0.12118 2.85 6970 2.3 1.6 2.3 1.6 2.2 1.8 2.3 1.6 2.0 1.9 2.0 1.9 2.0 2.0 2.3 1.8 59 0.12330 2.82 6717 2.4 1.7 2.5 1.6 2.2 1.8 2.4 1.7 2.0 2.0 2.0 2.0 2.0 2.0 2.4 1.9 60 0.12543 2.80 5677 2.1 1.6 2.1 1.6 2.0 1.7 2.0 1.6 1.8 1.8 1.8 1.8 1.8 1.8 2.0 1.8 Totals: 277916 6.4 4.3 6.4 4.3 7.6 3.2 6.3 4.4 5.5 5.2 5.5 5.2 5.5 5.2 6.6 4.9 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! As you can imagine, I have pseudo-translation peaks , the strongest at 48 % height (of the origin peak) at 0.0 0.0 0.5, other two at ~ 30 % height at 0.0 0.5 0.0 and 0.5 0.0 0.0 (and so at 0.5 0.0 0.5, etc.). The cell is large, 229 229 72 90 90 120, data processed at several space group options with good statistics; the highest symmetry is P622. With much struggle, some solutions from molecular replacement came out. Basically, the monomers (~274 residues each) makes "strings" (pack of one monomer over the other in one dimension), then these strings seem to be able to pack themselves in parallel (within them there must be an up/down feature) and parallel to the shorter cell axis. Given the cell dimensions, it seems most probable that I have 48 mol/au, although I cannot discard 36 mol/au (or even something between, depending upon the symmetry). I attach a picture of the supposed pack in case of 48 mol/au, viewed down to the 120 angle. The packing has made me practically rule out space groups P622 and P312, yet the need for a 2-fold axis passing through both 0, 1, 0 and 1, 0 0. Whenever I process the data in a lower space group, xtriage suggests strongly twinning, and close to 50 % in almost any operation. Also, whatever space group I choose for refinement, the results are all some how alike, R-free stucks (with any twinning operation that I can use to refine) at about 40/41 %; non-twinned refinement stucks R-free around 48 %. The investigated space groups include P321, P6, P3, P2, C222, C2 and P1 (besides, of course, at the beginning, P622 and P312), with several combinations of molecules/au (I there might be screw axes, although no systematic absences). With P1, I have the lowest reason between R and R-free (because R is higher). I must add that I have already tested some refinement alternatives, such as bulk solvent models, fix these, etc., but of course not all alternatives. Much information has been produced; one other highlight I think is the fact that most of the time atomic B-factors are refined to the ground, I suppose because of the abnormal intensity distribution/data modulation. I have a couple of questions and other information which I prefer to number since from now. a) Is there a source of information for refinement of such modulated data? Or previous cases reported in the literature? b) I have not tried yet P1 with 48 molecules. I run out of chain ID's, what does phenix accept besides the alphabet and 0-9? c) For P3, with any of the 3 twin operators the result is practically the same. To my knowledge, only shelxl can deal, currently, with more that one twinned domain, but these can only be produced in a iterative fashion. So, what might be the other way round? Is this development expected for phenix? For P1, I would have 11 pseudo-merohedral twin operations... I think the kind of packing is quite prone to twinning. d) Concerning what is raised in c, how necessary is to combine the 3 possible twin operators with the 3 reindexing possibilities.... e) How can I convince phenix to use the suggested twin operation 1/2*h-1/2*k,3/2*h+1/2*k,l in C222 (and some others with the * symbol in C2)? Much more information is available; I think I could pick the main ones. Thanks for any help. Jorge

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Error when specifying anomalous scatterers in autosol.
by Francis E Reyes 27 Jun '08

27 Jun '08

------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol data=ScalAveragedSG_76_30.ref seq_file=seq_from_pdb.dat \ refine_eff_file_list=./refinement/non_default.eff sites=2 atom_type=I \ f_prime=-0.582314 f_double_prime=6.84299 res_phase=3.4 resolution_build=3.0 \ resolution=3.0 wavelength=1.5418 ha_sites_file=./ha_sites.pdb Sending output to AutoSol_run_7_/AutoSol_run_7_1.log ******************************************************************************** Failed to carry out AutoSol_build: Refinement failed...perhaps something wrong with input refinement file or data file or the column labels for them? Error message from phenix.refine: Empty atom selection: refinement.refine.anomalous_scatterers.group.selection="name I" ******************************************************************************** Cuts out in the first round of refinement (after initial Build_1.pdb) . I guess I should not have specified anomalous scatterers (at least to autosol). Does it refine anomalous automagically in the autobuild when doing a SAD via autosol? How do I recover from this error? (continue with the autobuild without anomalous scattering it now seems). 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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Twinnig
by Michael Gorman 27 Jun '08

27 Jun '08

Dear all, After over 15 years solving structures I have (knowingly) encountered my first twinned data set. Short history.. Processed synchrotron data with HKL2000 SG P 42 21 2 ( Cell 105.485, 105.485, 62.445, 90, 90, 90) Rmerge 6% to 2A Solved MR using Phaser ( 1 mol in ASU) and built using COOT Refined using Phenix to a 'final' Rwork 29.4% Rfree 31.7% The maps look good but not great. Spurious peaks in difference maps. Couldn't get R's down any further. Xtriage suggested 'Overmerging pseudo-symmetric or twinned data' Re-processed in P2 ( cell 105.299, 62.385, 105.548, 90, 90.021, 90) Two molecules in ASU Xtriage suggested the presence of 3 pseudo-merohedral twin operators (one 4-fold and two 2-folds) Refined with twin law h,-k,-l (one of the pseudo 2-folds) using Phenix Rwork 26% Rfree 28% (no further building carried out at the moment) Wondered if it was a higher space group so.... re-processed in P222 (again Rmerge 6% to 2A) and did MR with Phaser in all the alternative space groups. The highest LL-gain was for P 21 21 21 (cell 62.377 105.297 105.546 90 90 90) I re-processed the data in P 21 21 21, all the systematic absences looked 'absent'. Xtriage suggested the presence of only one 4-fold Pseudo-merohedral twin law h,l,-k, R obs 5.1% Simulated annealing and ADP refinement in Phenix with twin law h,l,-k gave Rwork 33% Rfree 40%. Here are my questions... 1) Should I go for P2 due to the low R-factors and build from my good model ( beta angle of 90.021 seems unlikely ) 2) Should I try other possible SG ( HKL2000 suggested, primitive tetragonal, primitive orthorhombic, C centred orthorhombic, and monoclinic). 3) I'm concerned that my free-R reflections will be screwed-up since I have pseudo-merohedral twinning and some Rwork reflections may be the same as Rfree ones. I have read that Phenix is rather clever and chooses the highest observed symmetry to ovoid this problem but I can't see it being reported in the log-file that, in the case of P2, pseudo P42 21 2 is used for Rfree calculations. All help is much appreciated Mike -- Michael Gorman PhD St. Vincent's Institute of Medical Research 9 Princes Street Fitzroy Victoria 3065 Australia Tel : (03) 9288 2519

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Re: [phenixbb] Rfree increases during ordered solvent filtering
by Jennifer L Ekstrom 25 Jun '08

25 Jun '08

Hi Pavel, Thanks. I don't believe that is the cause of this refinement anomaly. If I run the same job without the filter_only option, I am still seeing a very large jump in R/Rfree at the ordered solvent location/analysis/update step (before 2_xyz). ordered_solvent=true 0 : 0.1564 0.1709 2.905699e+00 3.076326e+00 1_bss: 0.1145 0.1431 2.837441e+00 3.027552e+00 1_xyz: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_adp: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_occ: 0.1155 0.1429 2.844726e+00 3.028603e+00 2_bss: 0.1154 0.1427 2.844702e+00 3.028393e+00 2_xyz: 0.1313 0.1555 2.950732e+00 3.111378e+00 2_adp: 0.1307 0.1543 2.945031e+00 3.101981e+00 2_occ: 0.1306 0.1542 2.945015e+00 3.101954e+00 3_bss: 0.1301 0.1538 2.944930e+00 3.101580e+00 3_xyz: 0.1312 0.1565 2.951306e+00 3.117549e+00 3_adp: 0.1306 0.1546 2.940355e+00 3.100448e+00 3_occ: 0.1305 0.1546 2.940347e+00 3.100439e+00 3_bss: 0.1292 0.1534 2.940856e+00 3.100060e+00 However, if I run this job with no ordered solvent manipulation, the R/Rfree are stable at their previous lower value. ordered_solvent=false 0 : 0.1564 0.1709 2.905699e+00 3.076326e+00 1_bss: 0.1145 0.1431 2.837441e+00 3.027552e+00 1_xyz: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_adp: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_occ: 0.1155 0.1429 2.844726e+00 3.028603e+00 2_bss: 0.1154 0.1427 2.844702e+00 3.028393e+00 2_xyz: 0.1151 0.1427 2.842538e+00 3.027628e+00 2_adp: 0.1151 0.1427 2.842538e+00 3.027628e+00 2_occ: 0.1151 0.1427 2.842433e+00 3.027654e+00 3_bss: 0.1151 0.1426 2.842430e+00 3.027578e+00 3_xyz: 0.1156 0.1428 2.846107e+00 3.029162e+00 3_adp: 0.1156 0.1428 2.846106e+00 3.029160e+00 3_occ: 0.1156 0.1429 2.846122e+00 3.029225e+00 3_bss: 0.1156 0.1429 2.846122e+00 3.029225e+00 I wouldn't expect to see a 1% jump in Rfree after minor tweaking of a few dozen waters. This is not a small structure. There must be something strange in the refinement protocol during the ordered water treatment. I had thought it could be a weighting issue, but subsequent refinement with optimization of wxc and wxu does not bring the R/Rfree down to the original range. Thanks, Jennifer (Running version 2008_05_03_2330) ................................................... Pavel Afonine writes: > Hi Jennifer, > > you are using "ordered_solvent.mode=filter_only". This means that the new > waters are not added but the existing ones are filtered (removed) at final > step based on selection criteria (B-factors, distances, H-bonding, > etc...). Do you really want this? If not, then do not use > "ordered_solvent.mode=filter_only" (the default is "auto" which is good in > most of cases). > > Please let me know if you have any questions! > > Pavel. > > > On 6/24/2008 2:42 PM, Jennifer L Ekstrom wrote: >> I am running phenix.refine (version 2008_05_03_2330) with the >> command-line options ordered_solvent=true >> ordered_solvent.mode=filter_only >> >> During the final step (3_bss), my R and Rfree increase significantly. >> Any thoughts on why this jump would occcur? Per the notations in the >> logfile, only 30 waters were removed in the final model. >> >> Thanks, Jennifer >> >> >> R-factors, x-ray target values and norm of gradient of x-ray target >> stage r-work r-free xray_target_w xray_target_t >> 0 : 0.1564 0.1709 2.905699e+00 3.076326e+00 >> 1_bss: 0.1145 0.1431 2.837441e+00 3.027552e+00 >> 1_xyz: 0.1159 0.1433 2.846219e+00 3.029651e+00 >> 1_adp: 0.1159 0.1433 2.846219e+00 3.029651e+00 >> 1_occ: 0.1155 0.1429 2.844726e+00 3.028603e+00 >> 2_bss: 0.1154 0.1427 2.844702e+00 3.028393e+00 >> 2_xyz: 0.1151 0.1427 2.842538e+00 3.027628e+00 >> 2_adp: 0.1151 0.1427 2.842538e+00 3.027628e+00 >> 2_occ: 0.1151 0.1427 2.842433e+00 3.027654e+00 >> 3_bss: 0.1151 0.1426 2.842430e+00 3.027578e+00 >> 3_xyz: 0.1156 0.1428 2.846107e+00 3.029162e+00 >> 3_adp: 0.1156 0.1428 2.846106e+00 3.029160e+00 >> 3_occ: 0.1156 0.1429 2.846122e+00 3.029225e+00 >> 3_bss: 0.1306 0.1512 2.943092e+00 3.079441e+00 >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >

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PI Position @ SGC-Oxford: Integral Membrane Proteins
by Frank von Delft 25 Jun '08

25 Jun '08

Hi, any ambitious membrane protein researchers, please read about the vacancy below. Thanks, phx We are seeking a Principal Investigator to lead the Integral Membrane Protein (IMP) group of the Structural Genomics Consortium (SGC), Oxford. The SGC is a charity organization that includes ~200 researchers in laboratories in the universities of Oxford, Toronto and the Karolinska Institute. Our goal, successfully pursued since 2004, is to solve structures of medically relevant human proteins and deposit them immediately in public databases. We further exploit our target proteins in downstream studies with special emphasis on Chemical Biology, using both our in-house infrastructure and a network of collaborators. In the last year, our efforts have expanded to human integral membrane proteins. The present PI of the IMP group is leaving, and we are seeking a replacement with demonstrated experience and publication record in structural biology of membrane proteins. The IMP group comprises ~8 people, and is additionally supported by the SGC's extensive infrastructure, with close collaborations with molecular biologists, crystallographers, biophysicists and informaticians in the other groups. Currently funded until 2011, the post offers an unrivalled opportunity to develop a strong research program and a reputation as a group leader. More details are available at the following links: http://www.sgc.ox.ac.uk http://www.sgc.ox.ac.uk/jobs/H908014.html

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group_adp default ? and other phenix questions?
by hari jayaram 25 Jun '08

25 Jun '08

Hi I quite new to the phenix environemnt and just ran a phenix refinement with the following command line *phenix.refine myfile.mtz mymodel.pdb simulated_annealing=true model.ncs refinement.main.ncs=true --overwrite refinement.ncs.excessive_distance_limit=None >phenix_06_18_2008_2.log * The model.ncs file is structured as follows refinement.ncs.restraint_group { reference = chain A selection = chain B selection = chain C selection = chain D } My data is good to 3.3 A ( membrane protein) and thus far I have been refining with refmac5. After the phenix run indicated above, I had a dramatic reduction in r/rfree ( post refmac 33/36 AND post phenix 28/31). This is despite relatively small changes to my model by the simulated annealing refinement. I have a few questions about the process and am hoping some phenix veterans can help me out. 1) At my resolution I guess I should at best be refining only one B-factor / ADP per residue is this the default behavior with the command line above 2) I have seen the emails about syntax for forcing group-B refinement at this location<http://www.phenix-online.org/pipermail/phenixbb/2007-March/000161.html>and this one<http://www.phenix-online.org/download/documentation/cci_apps/structure_refi…>. Basically they use strategy=group_adp . I am imagining this calculates one ADP per residue or per defined group. In my case if I force the behavior with the syntax , how is group ADP for NCS-mates handled? 3) On a general note , when I say phenix.refine --show-defaults , the section on strategy has a long list, what do the asterisks (*) in the syntax mean .Does that mean those are the defaults . Also how can I infer the syntax from this hierarchy? Sorry for the long list of questions but I am very happy with phenix and just thought I should understand the syntax better. Thanks for your help Hari Jayaram Attachments: phenix.refine --show-defaults returns refine { strategy = *individual_sites rigid_body *individual_adp group_adp tls \ individual_occupancies group_occupancies group_anomalous sites { individual = None rigid_body = None } adp { individual { isotropic = None anisotropic = None } group = None one_adp_group_per_residue = True tls = None }

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How to generate an anomalous map in PHENIX?
by Schubert, Carsten [PRDUS] 25 Jun '08

25 Jun '08

Hi, I am trying to make an anomalous map in the latest phenix. After refinement of a medium resolution structure (1.8A) with anomalous data (and signal) I used the ANOM and PHANOM columns in the map_coeffs.mtz file to generate a map. The map was created either in coot or via fft, but shows no anomalous peaks for a present Cl1 nor for SS bonds. It rather mimics a noisy protein map. Generation of an anomalous map in CNX using the same data (FOBS(+/-) and HL coeffs(calc) ) produces a nice map with the expected peaks. Am I misunderstanding the purpose of the ANOM/PHANOM columns or is this feature not implemented yet. Cheers Carsten

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Rfree increases during ordered solvent filtering
by Jennifer L Ekstrom 25 Jun '08

25 Jun '08

I am running phenix.refine (version 2008_05_03_2330) with the command-line options ordered_solvent=true ordered_solvent.mode=filter_only During the final step (3_bss), my R and Rfree increase significantly. Any thoughts on why this jump would occcur? Per the notations in the logfile, only 30 waters were removed in the final model. Thanks, Jennifer R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.1564 0.1709 2.905699e+00 3.076326e+00 1_bss: 0.1145 0.1431 2.837441e+00 3.027552e+00 1_xyz: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_adp: 0.1159 0.1433 2.846219e+00 3.029651e+00 1_occ: 0.1155 0.1429 2.844726e+00 3.028603e+00 2_bss: 0.1154 0.1427 2.844702e+00 3.028393e+00 2_xyz: 0.1151 0.1427 2.842538e+00 3.027628e+00 2_adp: 0.1151 0.1427 2.842538e+00 3.027628e+00 2_occ: 0.1151 0.1427 2.842433e+00 3.027654e+00 3_bss: 0.1151 0.1426 2.842430e+00 3.027578e+00 3_xyz: 0.1156 0.1428 2.846107e+00 3.029162e+00 3_adp: 0.1156 0.1428 2.846106e+00 3.029160e+00 3_occ: 0.1156 0.1429 2.846122e+00 3.029225e+00 3_bss: 0.1306 0.1512 2.943092e+00 3.079441e+00

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Phenix / Resolve build related..
by Partha Chakrabarti 24 Jun '08

24 Jun '08

Hi, Sorry for the slightly off the topic question. I have a three wavelength SE MAD data to 3A, which I could only solve using SHARP or BP3. It seemed to have two monomers and each having one ordered SE sites. Found the NCS using RAVE programs, AVE, NCS6d and IMP. I am wondering if it is possible to give the NCS matrix (transposed from O format) and somehow tell Resolve (or Autobuild) to build multiple chains.. in this case, a homodimer. Do I need to duplicate the sequence? Regards, 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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NCS
by john kryst 24 Jun '08

24 Jun '08

Hi all !! What is the NCS restrain energy used by default in phenix... like CNS can we restarain 100kcal/mol.... Thanks regards John

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COURSE ANNOUNCEMENT - BIOCRYS2008 - REMINDER
by Daniele de Sanctis 24 Jun '08

24 Jun '08

On behalf of the organizers, Maria Armenia Carrondo and Thomas R. Schneider COURSE ANNOUNCEMENT - BIOCRYS 2008 Fundamentals of Modern Methods in Biocrystallography - 'What you always wanted to know about crystallography but never dared to ask' http://biocrys.itqb.unl.pt 4th - 11th October 2008 at the Instituto de Tecnologia Química e Biológica, Oeiras, Portugal. The topics of the second edition of this course will run from fundamentals such as symmetry, point groups and crystal systems, basic diffraction physics, reciprocal space and the Ewalds sphere, radiation damage, data processing, structure factors, Patterson function to modern methodologies including molecular replacement, SAD, MAD, MIR and maximum likelihood phasing, density modification, refinement, model building, twinning and structure validation. The course will be organized with lectures in the mornings and interactive practicals and tutorials in the afternoons. Evening lectures on current topics will be presented by the invited speakers. Instructors and speakers (confirmed): M. Archer, I. Bento, N. Berrow, G. Bunkoczi, M. Coll, K. Cowtan, Z. Dauter, D. de Sanctis, P. Donner, C. Frazão, E. Garman, C. Hermes, E. Hough, G. Leonhard, A. Leslie, P. Matias, A. Perrakis, T. Schneider, C. Vonrhein. 36 participants will be selected with preference to scientists at the beginning of their crystallographic career and to those from Europe. A registration fee of 500 Euro for academic and of 1000 Euro for not academic applicants is requested for full board and accommodation. Selected applicants will have to pay the registration fee by bank transfer before arrival. A very limited number of grants may be available to partially cover the registration fees and will be paid upon students arrival. For application, please please fill the form on the web page http://www.embl-hamburg.de/workshops/2008/BIOCRYST08/ by the 15th of July For more information visit the course web page http://biocrys.itqb.unl.pt -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartado 127 2781-901 Oeiras Portugal

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