- phenixbb - phenix-online.org

Switching refinement to higher resolution
by Francis E Reyes 19 Jun '08

19 Jun '08

Hello all, I was previously refining a structures used phased (mlhl) refinement at 3.4. My dataset has a resolution range up to 2.5. The I/sig is still good at 3.0A. I tried changing the resolution cut off in the refinement .def file refinement.xray_data.high_resolution to 3.0, but I now get the error: Sorry: R-free flags not compatible with F-obs array: missing flag for 1 F-obs selected for refinement. Any advice? 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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cif mods, .def, .cifs...
by Bryan W. Lepore 19 Jun '08

19 Jun '08

using phenix 1.3b rc6 cctbx_tag 2007_11_18_2203 have a few questions : 1. can .cif modifications such as refinement.pdb_interpretation.apply_cif_modification { data_mod = 5pho residue_selection = resname GUA and name O5T } (from http://www.phenix-online.org/documentation/refinement.htm#anch281 ) be copy/pasted into the .def file so a .params file doesn't have to be given on the command line? i.e. can't _everything_ go in the .def? 2. in the example where it says "data_mod_5pho" at the top of the .cif file, is phenix looking for a file - .pdb, .params, .. - with that prefix? 3. in "data_mod = 5pho", does 5pho come from 5pho.cif? and it still needs to be on the command line? -bryan

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Ordered Solvent in phenix-1.3-rc2
by Mary Fitzgerald 12 Jun '08

12 Jun '08

I just installed the new version of of Phenix and I'm trying to use ordered solvent. I have a twinned, 3 A data set of about a 0.5 kDa protein, two in the asu. The job keeps dying during the ordered solvent, it says killed in the window the process was ran from. I think I might be running out of memory. I tried phenix refine without the ordered solvent and it didn't crash. How can I tell if it's a memory problem or a problem with the program? Thanks, Mary Mary X. Fitzgerald Postdoctoral Associate Arnold Lab

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Re: [phenixbb] constraining alpha-helical geometry in phenix
by Ralf W. Grosse-Kunstleve 11 Jun '08

11 Jun '08

Hi Pascal, > I am currently refining a structure at moderate resolution (~3.4A) > which is mainly composed of alpha-helices . Is there a way to > constrain the backbone geometry of the alpha helical regions in the > model used for refinement. Luca Jovine has kindly contributed a perl script that converts HBPLUS output to phenix geometry_restraints.edits. You can find it here: http://www.phenix-online.org/contrib/hbplus2phenix_restraints.pl We don't have much practical experience with this approach yet, other that it works at a technical level. If you get a chance to try it out, we'd be interested to know how much it helps in your case. Ralf

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After 25 years: photos from the 1983 Crystallographic Computing School on the web
by Ralf W. Grosse-Kunstleve 10 Jun '08

10 Jun '08

For those interested in the history of Crystallographic Computing, the 1983 Crystallographic Computing School, organised by Prof. Sydney Hall and Prof. Tamaichi Ashida, was held in Kyoto, Japan at the same site as the upcoming IUCr Crystallographic Computing School: the Kansai Seminar House. Thanks to Prof Atsushi Nakagawa, pictures of that 1983 Computing School are now on the IUCr Computing Commission website at: http://www.iucr.org/iucr-top/comm/ccom/1983school/ Many "young" faces can be seen in the album. The album includes not only the School itself but also the excursion to Nara and the Institute for Protein Research at Osaka University. Information, including program and registration on the upcoming IUCr Crystallographic Computing School 2008 * Sharing our knowledge * Kyoto, Japan, August 18-23 - is available on the school webpage: http://www.iucr.org/iucr-top/comm/ccom/kyoto2008/

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xtriage crash - what to do?
by Martin Moche 09 Jun '08

09 Jun '08

Dear Phenix developers, I got a crash when running phenix xtriage on a mtz-file in P3112. Error message below: The logfile prior to the crash is attached. Best regards, Martin ############# Error message ################ Traceback (most recent call last): File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/command_line/xtriage.py", line 7, in <module> xtriage.run(args=sys.argv[1:]) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/xtriage.py", line 725, in run plot_out = string_buffer ) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/xtriage.py", line 383, in __init__ additional_parameters=self.params.scaling.input.parameters.misc_twin_parameters) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 2380, in __init__ out=out, verbose=verbose) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 425, in __init__ self.show(out) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 596, in show self.suggest_new_space_groups(out=out) File "/net/fileserver/xtal/phenix-1.3b-rc4/mmtbx/mmtbx/scaling/twin_analyses.py", line 450, in suggest_new_space_groups tmp_space_group = sgtbx.space_group_info( str(tmp_space_group), space_group_t_den=t_den) File "/net/fileserver/xtal/phenix-1.3b-rc4/cctbx/cctbx/sgtbx/__init__.py", line 61, in __init__ space_group_symbols=symbols, t_den=space_group_t_den) RuntimeError: cctbx Internal Error: /net/longnose/scratch1/phenix/phenix-1.3b-rc4/cctbx/sgtbx/change_of_basis_op.cpp(70): CCTBX_ASSERT(c_.t().den() % s.t().den() == 0) failure. __________________________________________________ Martin Moche, Ph.D., M.Sc. Senior scientist Karolinska Institutet MBB/SGC Scheeles väg 2 171 77 Stockholm Sweden Phone: +46-8-524 868 43 Mob: +46-733-229327 Fax: +46-8-524 868 68 Martin.Moche(a)ki.se

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disulfides and .defs, maybe custom geom.
by Bryan W. Lepore 09 Jun '08

09 Jun '08

i can start phenix with new .pdb/.mtz, and custom geometry with satisfactory output. problem is, when i provide that output .def file (possibly w/ custom geometry in it) on the command line, phenix always sets up disulfides when it didn't before: Number of disulfides: simple=4, symmetry=0 Simple disulfide: " SG CYS A 14 " - " SG CYS A 14 " distance=0.10 Simple disulfide: " SG CYS A 140 " - " SG CYS A 140 " distance=0.08 Simple disulfide: " SG CYS A 144 " - " SG CYS A 144 " distance=0.54 Simple disulfide: " SG CYS A 147 " - " SG CYS A 147 " distance=0.18 Custom bonds: Sorry: More than one atom selected: "chain A and resname CYS and resid 140 and name SG" Number of selected atoms: 2 my ligands are attached to the cysteines, so i suspect some trouble here but can't see it - shouldn't be a problem, right? if i set disulfide_distance_cutoff= 1.0 or less, phenix drives the system into swap. any pointers, appreciated. -bryan

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effect of solvent fraction on density modification/solvent flattening for a membrane protein
by Pascal EGEA 08 Jun '08

08 Jun '08

Dear All, This is a question about the effect of solvent fraction estimation on the quality of the initial phases. I am trying to solve the structure of a membrane protein at moderate resolution 3.5A from a MAD data set (peak, inflection and high energies). I have one copy of my complex which gives me a solvent fraction of 0.7 without considering the contribution of the detergent. With a related molecule I found a Phaser-MR solution but it does not refine although it is right. I am using Phenix with the phases obtained from molecular replacement and combining them with the MAD signal to locate the seleniums. A visual inspection of the anomalous fourier difference map shows 6 sites out of the 7 expected at 4sigma contouring. If I let Phenix decide by itself it goes on its own with two copies in the ASU and considers a solvent fraction of 0.50; then it finds 7 sites (and not 14 ? why is that?) (the seventh is weak but we expect this for this region of the complex). now if I force Phenix to take ncs_copies=1 and solvent fraction=0.7 then it only find 6 sites. Wether it is 2 "freely chosen" molecules/ASU and 0.5 of solvent or 1 "forced" molecule/ASU and 0.7 of solvent, the 6 first sites are identical (although occupancies are quite higher in the first case) Should I take into account the detergent and lower somewhat my solvent fraction (in the 0.6 range maybe) with the fixed one copy ASU estimation or just trust Solve/Resolve when it runs the density modification part. Does it really affect the quality of the phasing? Between these two extremes I am surprised to see that the quality of the resolve map are quite similar apparently showing clear new structural features. Thanks in advance for your comments, Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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OS X source install relocatable?
by Ben Eisenbraun 06 Jun '08

06 Jun '08

Howdy, I'm doing an install from source on Mac OS X from the latest Phenix source packages. We install everything on an NFS mount so we can share it out to the workstations, so it's a little different than most OS X installs I suspect. Anyway, the installer was failing like this: (from the top level source directory) ./install --prefix=/programs/i386-mac/phenix/1.3-rc2 Which was getting me: configuring python compiling python csh: /programs/source/phenix/1.3-rc2/osx86/phenix-installer-1.3/bin/check_lib: No match. installation of python failed problem building main python library Looking at bin/install-from-source, it was failing on line 482: set py_lib = `$PHENIX_TAR/bin/check_lib $PHENIX_BUILD/base/Python.Framework/Versions/Current/lib/python*/config python` The reason for the failure is that the python framework installs with a lower case 'f': /programs/i386-mac/phenix/1.3-rc2/phenix-1.3-rc2/build/mac-intel-osx/base/Python.framework/ On a default HFS+ volume, which is case insensitive, this works just fine, but it fails when you try to install on a case-sensitive volume. Editing bin/install-from-source and :%s/Python.Framework/Python.framework/g seems to have fixed the build problem. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

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constraining alpha-helical geometry in phenix
by Pascal EGEA 05 Jun '08

05 Jun '08

Dear All, I am currently refining a structure at moderate resolution (~3.4A) which is mainly composed of alpha-helices . Is there a way to constrain the backbone geometry of the alpha helical regions in the model used for refinement. Many Thanks, Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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