- phenixbb - phenix-online.org

broken bonds in the substrate
by houjin zhang 12 Jul '08

12 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

2 1

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)

1 0

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

2 3

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 ] --

1 0

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

3 2

using TLS files from Refmac
by nihmayerm 03 Jul '08

03 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

2 1

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

1 0

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 ------------------------------------------------------------------- -------------------------------------------------------------------

2 1

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 ------------------------------------------------------------------- -------------------------------------------------------------------

2 1

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

1 0