- phenixbb - phenix-online.org

Hydrogen occupancies
by Florian Sauer 01 Dec '10

01 Dec '10

Dear all, I'm currently refining a small protein against 0.96A data using phenix.refine (1.6-486) from the GUI. Refinement without hydrogens yielded Rwork/free of 12.4/14.2. I then added H-atoms with phenix.reduce and switched to individual refinement of hydrogens which dropped the R-factors to 11.3/13.4. After this refinement the occupancies of some hydrogens dropped to 0 which makes me a little concerned. See e.g.: ATOM 752 H LYS A 45 -7.443 2.613 9.537 1.00 4.73 H ATOM 753 HA LYS A 45 -9.707 1.128 9.401 0.55 2.42 H ATOM 754 HB2 LYS A 45 -8.476 2.797 7.435 1.00 10.58 H ATOM 755 HB3 LYS A 45 -9.795 1.948 7.166 0.95 8.70 H ATOM 756 HG2 LYS A 45 -10.840 3.210 8.889 0.00 33.83 H ATOM 757 HG3 LYS A 45 -9.604 4.206 8.775 0.00 33.83 H ATOM 758 HD2 LYS A 45 -11.227 3.615 6.563 0.00 62.10 H ATOM 759 HD3 LYS A 45 -11.508 4.867 7.507 0.00 62.10 H ATOM 760 HE2 LYS A 45 -9.229 5.527 6.985 1.00 83.62 H ATOM 761 HE3 LYS A 45 -9.348 4.488 5.786 0.00 83.86 H ATOM 762 HZ1 LYS A 45 -10.909 5.758 4.853 1.00 99.63 H ATOM 763 HZ2 LYS A 45 -11.131 6.534 6.042 0.35100.44 H ATOM 764 HZ3 LYS A 45 -9.917 6.715 5.257 0.39100.08 H I would like to ask whether it is possible in phenix to group the occupancies to keep them at the same value as the rest of the residue but still refine xyz and isotropic adp of the individual hydrogens? Thank you in advance for your answers, Florian

2 1

wander wall interaction
by subhash bihani 01 Dec '10

01 Dec '10

hi all I am working on a enzyme-ligand complex structure. For some analysis I need to remove wander wall interactions between protein and ligand. How can I do that in Phenix? Something similar to igroup statement in CNS? Thanks in adwance -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

4 3

phaser and threads
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ] i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... oh, hmmm... i seem to have just got this at the packing function : |python: malloc.c:4591: _int_malloc: Assertion `(unsigned long)(size) >= (unsigned long)(nb)' failed. -Bryan

2 3

building from source : svn_checkout
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-596 from source using --no-gui --no-apps --openmp ] README-DEV mentions ./bin/svn_checkout ... i cannot find this (but i do find bundle_update and recompile). any pointers appreciated. -Bryan

2 1

Refinement of a complex with a symmetric inhibitor lying on the axis of symmetry
by Ina Lindemann 01 Dec '10

01 Dec '10

Hi, I try to refine a crystal structure of a protein - inhibitor complex. The protein is a homodimer and the two molecules have a crystallographic symmetry. The space group is P6122. The symmetric inhibitor binds symmetrically to the protein so that I refine the half of it. The core of the inhibitor is a five-membered ring with a nitrogen lying directly on the axis of symmetry. I achieved to refine this by setting the occupancy to 1.0. And now, here is my problem: Two C atoms of this ring system are bound across the symmetry axis - how could I include this in the refinement? Is there any possibility to generate restraints to the other part of the inhibitor (of the symmetry equivalent)?? Thanks for your help in advance, Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

2 1

autosol : unmerged data with input_phase_file
by Bryan Lepore 30 Nov '10

30 Nov '10

dev-595 i gather that autosol will not take unmerged data when the input_phase_file originates from merged data. e.g. in "method #2 for MRSAD". -Bryan

2 2

dev-590 compile from source : -lGLU, -lGL
by Bryan Lepore 30 Nov '10

30 Nov '10

[ dev-590 ] [ gcc 4.4.4 ] [ GNU/Linux 32-bit ] [ Ubuntu 10.10-ish ] * OpenGL/GLUT is of unstable nature* got an error compiling from source (see after sig). i tried using --openmp first, then --openmp --nogui in the same build directory and the error occurs both times. just trying this out, not critical - was interested to know if there's an easy workaround anyone might think of (besides touching GL/GLUT - shudder ). -Bryan /usr/bin/ld: cannot find -lGLU /usr/bin/ld: cannot find -lGL collect2: ld returned 1 exit status scons: *** [lib/gltbx_fonts_ext.so] Error 1

2 5

sculptor : "Wrong alignment format:"
by Bryan Lepore 29 Nov '10

29 Nov '10

(starting a new thread?) trouble with alignment format. tried this : fubar.fas : Sorry: Unknown file(s): fubar.fas fubar.fasta : Sorry: Wrong alignment format: fubar.fasta i compared to one that worked yesterday and its not obvious : first sequence is the target, the pdb sequence is in there (somewhere), i changed a ">sp" to ">gi".... if anyone knows what i'm missing here,... -Bryan

3 13

International Conference on Structural Genomics May 10-14, 2011, Toronto -- registration now open
by Tom Terwilliger 29 Nov '10

29 Nov '10

Dear Colleagues, We are pleased to announce that registration is now open for the International Conference on Structural Genomics 2011, which will be held in Toronto, Canada on May 10-14, 2011. This meeting is the 6th in this series of biennial meetings of the International Structural Genomics Organization. The meeting is designed to serve as a forum to discuss the most recent developments in structural genomics, structural/chemical biology, and their impact on research in biology, medicine and disease. A substantial number of short talks will be selected from submitted poster abstracts. Also, a limited number of student travel fellowships will be available for travel to this meeting. Please see http://www.icsg2011.org for further details. We hope to see you there! Best regards, Cheryl Arrowsmith ICSG 2011 Organizer Ted Baker Stephen Burley Dino Moras Joel Sussman Shigeyuki Yokoyama Tom Terwilliger ISGO Executive Committee

1 0

occupancy refinement
by Dalibor Milic 25 Nov '10

25 Nov '10

Dear all! How to refine occupancies of mutually dependent structural fragments found in alternate conformations, but not consecutive in a sequence? E.g. I want to refine occupancies of two alternate conformations of residues 30 and 451 (see below the corresponding parts of a PDB file). Because of the nature of the structural disorder, an occupancy for altLoc A should be strictly the same in both fragments - the same is valid for altLoc B. Of course, the sum of occupancies for altLoc A and B should add up to 1. Thanks for your suggestions, Dalibor Milic ... ATOM 376 N AGLU A 30 23.241 86.975 31.961 0.52 17.13 N ATOM 377 N BGLU A 30 18.971 88.677 32.817 0.48 9.05 N ATOM 378 CA AGLU A 30 23.240 85.507 31.907 0.52 18.89 C ATOM 379 CA BGLU A 30 19.108 87.234 32.991 0.48 10.00 C ATOM 380 CB AGLU A 30 21.848 84.946 32.256 0.52 18.78 C ATOM 381 CB BGLU A 30 17.727 86.562 33.046 0.48 11.01 C ATOM 382 CG AGLU A 30 21.247 85.562 33.524 0.52 26.38 C ATOM 383 CG BGLU A 30 16.935 87.037 34.275 0.48 19.26 C ATOM 384 CD AGLU A 30 20.264 84.659 34.277 0.52 33.36 C ATOM 385 CD BGLU A 30 15.694 86.223 34.542 0.48 26.60 C ATOM 386 OE1AGLU A 30 19.437 83.968 33.620 0.52 31.85 O ATOM 387 OE1BGLU A 30 15.401 85.288 33.762 0.48 33.05 O ATOM 388 OE2AGLU A 30 20.310 84.678 35.535 0.52 29.12 O ATOM 389 OE2BGLU A 30 15.007 86.527 35.538 0.48 30.95 O ATOM 390 C AGLU A 30 23.750 84.946 30.575 0.52 18.22 C ATOM 391 C BGLU A 30 19.976 86.652 31.877 0.48 10.17 C ATOM 392 O AGLU A 30 24.319 83.853 30.534 0.52 19.40 O ATOM 393 O BGLU A 30 20.621 85.606 32.059 0.48 10.67 O ... ATOM 4627 N AALA A 451 31.047 82.837 22.335 0.52 18.30 N ATOM 4628 N BALA A 451 29.107 84.432 26.354 0.48 9.81 N ATOM 4629 CA AALA A 451 31.958 83.502 23.284 0.52 18.73 C ATOM 4630 CA BALA A 451 29.655 85.424 27.274 0.48 9.73 C ATOM 4631 CB AALA A 451 32.880 84.486 22.541 0.52 20.38 C ATOM 4632 CB BALA A 451 30.469 86.474 26.478 0.48 11.60 C ATOM 4633 C AALA A 451 31.176 84.206 24.406 0.52 18.79 C ATOM 4634 C BALA A 451 28.556 86.128 28.089 0.48 6.84 C ATOM 4635 O AALA A 451 30.019 84.593 24.197 0.52 18.25 O ATOM 4636 O BALA A 451 27.441 86.357 27.604 0.48 6.81 O ... -- Dalibor Milic, Dr. Sc. Laboratory of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia phone: +385 1 460 6377 fax: +385 1 460 6341 e-mail: dmilic(a)chem.pmf.hr

3 8