- Chimera-users - RBVI Mailing Lists

Announcement: Release of DOCK 6.6
by Scott Brozell 05 Jan '13

05 Jan '13

We are pleased to announce the release of DOCK 6.6. DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: Grid-based footprint scoring and SASA-based scoring. The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids. Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues. The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket. In addition, a symmetry corrected RMSD (Hungarian matching) method was added to facilitate pose reproduction studies. For full information on what is new in DOCK 6.6, please visit: http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.6.txt Sincerely, The DOCK Team Please visit us at the DOCK Web site. http://dock.compbio.ucsf.edu

1 0

3DConnexion Space Navigator dead-zone
by Gökhan Tolun 03 Jan '13

03 Jan '13

Hi, Is it possible to set a dead-zone for the 3DConnexion Space Navigator in Chimera? I tried doing this using its OSX driver, but I cannot find such an option in its control panel. Thanks. Gökhan

2 1

Circular DNA minimization
by Damien Larivière 03 Jan '13

03 Jan '13

Dear all, I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing. The first phase, the Steepest Descent Steps, works fine. However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen. If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected. I'm not versed in the art of minimization. Do you know the reason of this behavior? Thanks for your help, Damien ps: I'm working on Windows 7 with a core i5

2 2

GLYCAM force fields and Chimera
by john Kerk 28 Dec '12

28 Dec '12

Dear Users I want to assign the partial charges of a glucose molecule using chimera-1.7 but I can not find this force field in Add charge suite although the GLYCAM force field files are existing under amber12. can I get help wishing merry Christmas , John

3 2

a PyMol file into Chimera
by Anindito Sen 21 Dec '12

21 Dec '12

Dear All, Questions of the following type/s may have been answered many times before but will be of help if you can reply (again). I have a PyMol file with file extension 'pse' . I want to Visualize it Chimera. Is there any trick to do that ? Best Andy Dr. Anindito Sen (Ph.D) >Department of Cell Biology & Anatomy >Graduate School of Medicine >University of Tokyo >Tel & fax: +81-3-5841-3339

2 1

More on initial energy value from Chimera
by Thomas Sturgill 20 Dec '12

20 Dec '12

Elaine has explained that the initial energy is a total energy and not a free energy. Understood. I want to verify that a negative energy is "better" than a positive energy, and a more negative energy is "better" still. This is what I assume now, but I had an angst that the energy value is somehow based on absolute value, so the "best" minimized energy is zero. Humor my question, because I have to be 100% certain. No need to go into caveats about the ability of Chimera minimization to make models worse, and how difficult the energy parameter is to interpret. Tom. Thomas W. Sturgill, M.D.-Ph.D. Biozentrum, University of Basel Department of Biochemistry/Hall Lab Klingelbergstrasse 70 CH4056 Basel, Switzerland TEL: (+41 61) 267 2172 FAX: (+41 61 267 2149 Visiting Professor U. of Virginia, Pharmacology Charlottesville, VA 22908 USA FAX: (434) 924-5207

2 1

Display at low definition
by Damien Larivière 20 Dec '12

20 Dec '12

Dear all, I have a basic question: In the image below, on the left, the definition of the atoms is quite good, they are perfect spheres. On the right, they are not anymore. I probably activated something in Chimera, but I'm not able to remember. May you tell me what to do to get a good definition again? Many thanks for your help, Damien

3 3

RNA structure creation plugin
by Eric Pettersen 19 Dec '12

19 Dec '12

Hi All, Dr. Fabrice Jossinet from the University of Strasbourg recently released Assemble2, a Chimera plugin for designing RNA structures in 2D and then generating the corresponding 3D structure. If you're an RNA person, maybe you'd like to try it out and offer feedback. Here's the Assemble2 web site: http://bioinformatics.org/assemble/index.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

Adjust bond angle doesn't seem to work
by oxi 19 Dec '12

19 Dec '12

Hi, I'm new to Chimera Using 1.7 candidate build 37955 When I select two adjacent bonds and adjust their relative angle in Tools->Build Structure->Adjust bond angles, nothing seems to actually change in the graphic view I tried selecting the 3 atoms involved afterwards and measure the angle, and it still reports the original angle, so I don't think it's a graphic glitch but the angle isn't actually being changed. Is this a bug or am I doing it wrong? Thanks

2 3

rotation axis display
by Hernando J Sosa 19 Dec '12

19 Dec '12

Hi, Is there a way to display an axis line? I would like to display the rotation and translation axis as given in the reply log after a fit in map operation. Thanks Hernando

2 2