January 2012 - Chimera-users - RBVI Mailing Lists

inertia axis
by Luca Pellegrini 23 Jan '12

23 Jan '12

Hello, Can you please explain how the inertia axis is calculated in: Tools -> Structural analysis -> Structure Measurements -> Define Axes when one uses the 'Selected atoms' and 'Mass weighting' option? Formally one can define three principal axes of inertia for an object, but only one axis seems to be calculated. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

2 1

save / restore camera angles
by Greenberg, Charles 22 Jan '12

22 Jan '12

I'd like to be able to manipulate things at various angles and be able to return back to a fixed camera view for when I want to save an image. I want to take a series of images with things colored differently, but they won't look quite the same if I have to manually try to move the camera each images. Does that make sense? Thanks. --Charles

2 1

matchmaker
by David Stokes 20 Jan '12

20 Jan '12

Is there a way to align two models based on a subset of residues selected from each model (or even just a subset of residues from the reference molecule). I haven't found it and this would really be helpful. Thanks, David -- David L. Stokes Skirball Institute, NYU Medical Center tel: 212-263-1580 http://saturn.med.nyu.edu/~stokes ---- New York Structural Biology Center tel: 212-939-0660 x9116 http://nysbc.org/ fax: 646-219-0300

2 2

Chimera output into Collada .dae file format
by Evan Kantrowitz 20 Jan '12

20 Jan '12

Hi, The new iBooks Author system uses the collada .dae for its 3D widget. Chimera does not seem to output this format, is that correct? Does anyone know the best way to convert one of the available save scene formats to a collada .dae file. Thanks Evan R. Kantrowitz, Ph.D Boston College

2 1

Is it possible to change the protonation state of only one residue (histidine) of a protein ....
by Sergio Garay 19 Jan '12

19 Jan '12

Hi all I'd like to know if it is possible to change the protonatation state of only one particular residue (histidine) in my protein.. I've been trying to do it using addh tool but with no success, I think it can only work with the protein as a whole, isn' it ? Please, any suggestion is welcomed Sergio -- Sergio Garay Dr. en Ciencias Biológicas Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221

2 1

Distance label
by Damien Larivière 19 Jan '12

19 Jan '12

Dear all, I often use the distance tool in order to display the distance between two atoms. It is possible to set several parameters to render the distance (line, stick, color, display the Angstrom symbol or not,...). I would like to increase the size of the label indicating the distance in Angstrom, and eventually to move the label somewhere else in the viewport. Is it possible to do that? Thanks Damien

3 3

DNA Ribbon
by Yoshus Kumka 19 Jan '12

19 Jan '12

Hello, Does anyone know how to assign ribbon attributes to DNA... So I created a stretch of DNA in Spartan and converted the file to pdb which does not contain any attributes such as helical information to automatically have chimera show backbone as a ribbon... I would like to display the DNA backbone as a ribbon and show the bases... But I don't know how to assign the backbone atoms a ribbon property... Please help Thanks

2 1

Minimizing RNA, no MMTK name for H3"
by Tom Goddard 18 Jan '12

18 Jan '12

I'm trying to minimize a few RNA nucleotides using Chimera (Tools / Structure Editing / Minimize Structure) but I get the error message No MMTK name for atom H3" in standard residue C. Chimera adds hydrogens and creates this H3" atom on the 3' terminus (O3' atom) of the RNA. Is there some trick to terminate the 3' end of the RNA so MMTK minimization will work? Here's an example of the problem open 2d1b del ~ :39.B min spec #0 nogui true Thanks! Tom

2 3

Using local PDB file for homology modelling
by Steven Bottomley 18 Jan '12

18 Jan '12

Hi Is there any way to use a pdb structure file stored locally for homology modelling using the Chimera interface to Modeller? Presently the only option seems to be an automatic association from the pdb database. I simply want to use my own structure file as a template and not the one in the pdb database. Thanks for your help.

2 3

morph and 2dlabels
by Brunner,Matthias 17 Jan '12

17 Jan '12

Hi, I have generated a movie in which a morph "loop" between volume A and B is running while the volume is rotating...this works fine. Is there a convenient way to fade in a 2D label whenever the volume B endpoint is reached during morphing (at exactly this frame and maybe a few adjacent ones to make it smoother)? Even better would be if it were possible to label both endpoints (as "volume A" and "volume B"). In effect, this should result in a 2dlabels fade-in/out loop that is synchronous with the morph loop. I would greatly appreciate your help! Best regards -- Matthias Brunner <matthias.brunner(a)imba.oeaw.ac.at> PhD student, Marlovits Lab -Research Institute of Molecular Pathology (IMP) -Inst of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3, A-1030 Vienna, Austria Phone: +43 1 79044 4791

2 2