- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] quick angles question
by Tom Goddard 15 Aug '08

15 Aug '08

Hi Jeff, Here is a Python script to report the angles made by bonds attached selected atoms. Just select the atoms, then open the script. Output will be printed to the reply log. Tested in Chimera 1.2548 but should work in much older versions. Tom Jeff Triffo wrote: > hi Tom, > > if I have a Chimera marker file full of interconnected markers, is > there a quick/easy way to report all the angles formed in the > meshwork? (screenshot attached) > > I figure the easiest way is to cycle through the markers and survey > the angles it makes with each attached marker, but I don't know how to > do that (but it sounds like something that is probably straighforward > in python) > > thanks for any input there, > > -Jeff > # ----------------------------------------------------------------------------- # Report all angles made by bonds originating from selected atoms. # from chimera import selection, angle atoms = selection.currentAtoms() print '%d atoms selected' % len(atoms) c = 0 for a in atoms: bonds = a.bonds for b1 in bonds: for b2 in bonds: if b1 < b2: a1 = b1.otherAtom(a) a2 = b2.otherAtom(a) t = angle(a1.coord(), a.coord(), a2.coord()) print ('Angle %s %s %s = %.3f degrees' % (a1.oslIdent(), a.oslIdent(), a2.oslIdent(), t)) c += 1 print '%d angles reported' % c import Accelerators.standard_accelerators as sa sa.show_reply_log()

1 0

Re: [Chimera-users] midas/6155 (Chimera error)
by Eric Pettersen 14 Aug '08

14 Aug '08

On Aug 14, 2008, at 1:23 PM, Christine Deillon wrote: > Hi Eric, > > I try to save a movie of a collagen molecule (cylinder shape) > just moving around its major axis (along the molecule) for about > 15 secondes, then I would like to play the movie in the microsoft > power point program > is it possible to do that with chimera? > > Christine Hi Christine, Yes, absolutely you can do that. There is a Chimera tutorial that covers movie-making in good detail here: Movie Making in Chimera The "Spin Movie" section of the tutorial is almost exactly what you are asking for. Issues with embedding movies into PowerPoint are at the very end of the Movie Recorder documentation page: problems in PowerPoint --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

1 0

version 1.2540 stability
by James Fethiere 14 Aug '08

14 Aug '08

Hi, I just upgraded my May version with the last version of Chimera for PC and am having stability problems. Every now an then (every 10' or so), chimera freezes and the cursor flickers for a couple of seconds; then all goes back to normal. Sometimes, it just crashes completely. Is this last version more demanding on memory? Thanks James

2 3

Re: [Chimera-users] calculation of volume
by Elaine Meng 14 Aug '08

14 Aug '08

Hi Navnit, Sorry, I don't know of a way to calculate the van der Waals volume in Chimera. You can see the VDW volume, of course, by simply displaying the atoms in the sphere representation, but that does not give the volume value. In theory, you could get values closer to the VDW volume by calculating molecular surface with smaller and smaller probe radius. In practice, this tends to increase the number of surface calculation failures, and currently the smallest allowed probe radius value is 0.5 angstroms. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 14, 2008, at 7:01 AM, Navnit Kumar Mishra wrote: > Hi Elaine; > > Thank you for so detailed description. I am interested in measuring > the compactness of the complex during the simulation, I think the > calculation of the ratio of molecular volume to van der waals volume > provides the compactness. I have tried the procedure as you > suggested to calculate the molecular volume, the value in replylog > file is in two digits precision, for these calculation can I get the > value in four digits precision. I am using latest chimera version > 1.2540. I can calculate the total van der waals volume using the van > der Waals radii for each atom excluding the hydrogen atoms. Is there > a way in chimera to calcualte the van der waals volume. I would be > thankful to you for any suggestions. > > with regards, > navnit

3 3

Color zone with transparency
by Tom Goddard 14 Aug '08

14 Aug '08

Daniel Wilson wrote: > Hi Tom, > > ... > > The other thing I noticed is that you lose transparency on a whole volume when you color zone one region of it? or am I making something wrong? Is it not possible to have a single volume with two different colours and transparent? > > Thanks for you advice and kind offer, > regards > Daniel > Hi Daniel, When I make a transparent surface for a volume by pressing the volume dialog color button and making opacity 0.5 and then use color zone to color part of the surface (using a PDB model), the transparent part far from the zone remains transparent. Also works if select the volume surface and use the Actions / Surface / Transparency menu then color zone. What are the exact steps you use when it fails to preserve transparency? Tom

1 1

Two transparent models
by Tom Goddard 14 Aug '08

14 Aug '08

On Aug 11, 2008, at 12:15 PM, Daniel Wilson wrote: > Dear Elaine, > > I realise that there have already been requests about fixing the bug > in Chimera for displaying two transparent maps at the same time, so I > guess I am just asking whether this is likely to be fixed anytime > soon? We are desperate to use this function for a figure for a paper :) > > THanks, > Daniel > > Dr. Daniel N. Wilson > > Gene Center Munich > Department of Chemistry and Biochemistry > Ludwig-Maximilians-Universität München > Feodor-Lynen-Str. 25 > 81377 Munich, Germany Hi Daniel, The incorrect transparency in Chimera when 2 or more models are transparent is very difficult to fix and will not be fixed any time soon. The trouble is that Chimera draws each model separately and it is not possible to correctly handle transparency without intermixing the drawing of parts of models (in depth order). If you use Chimera image saving in the POVray raytracing mode it will correctly show multiple transparent models. The trouble is that this takes a long time to render and adjusting the levels of transparency many times to get the right appearance may be tedious. It would be possible to make a script that combines the currently displayed map surfaces into a single model and hides all the original models so that multimodel transparency would appear correct on-screen. But the combined model would not update when you changed the transparency, color, ... settings of the separate maps. It would require rerunning the script that makes the single model. This would be tedious to use. But if you think it worth trying I can write the script and send it to you. It would not work for transparent molecular models (ribbons and atoms), just surfaces. Tom

1 1

Hydrogens in proteins
by Walter Novak 13 Aug '08

13 Aug '08

Hi group, So I am struggling with hydrogens in proteins. I have neutron data which shows H-atom positions. Well, Deuterons, but here are the issues. If I open a pdb in Chimera with old school hydrogen names like HG1, how can I get it to write out the new ones (like HG11) without explicitly adding the hydrogens in Chimera? I don't want the atom positions to change. Also, I notice Chimera doesn't seem to handle deuterons optimally. Writing out the pdb moved the atom name column to the left one space and changed the atom type in the last column back to H. The problem is caused by Coot, which we use to perform real space refinement of atom positions, but to quote George Sheldrick, "I think that we will have to 'remediate' Coot (and the whole of CCP4 for good measure). I advise all SHELXL users NEVER to deposit hydrogen atoms, it saves lots of hassle." Unfortunately, the point of my project is to see the hydrogens!!!! Thanks for any help you can offer, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

2 2

opening CASTp results
by Walter Novak 13 Aug '08

13 Aug '08

Hi all, How can I open my own CASTp results easily? The fetch command works great, but I need to submit some modified structures, and I don't see CASTp under file type in the open window. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

3 4

calculation of volume
by Navnit Kumar Mishra 13 Aug '08

13 Aug '08

Hello all; I am trying to compute the molecular volume of a complex. Chimera first computes solvent-excluded surface area using MSMS. I see it does not compute the surface area of ligand. I am wondering if I can add the extra parameters or atom types for my ligand in some file. I would like to calculate the molecular volume from amber trajectory. Can some one suggest me how to automate the computation of surface area and molecular volume for each snapshot. If you know, please point out the article which describes the procedure for the volume calculation. with regards, Navnit

2 1

representing 70s ribosome in ribbon
by Bong-Gyoon Han 12 Aug '08

12 Aug '08

Hi, I am tring to show the full 70S ribosome structure (PDB id: 1GIX and 1GIY) in ribbon representation with EM experimental density together. These PDB data consist of backbone atoms only (single alpha carbon for each a.a and single phosphate for each nucleotide). Ribbon option does not generate any ribbon (due to the incomplete information in the PDB?). Is there any way to show this molecule in ribbon format? I assume that backbone atoms must be enough to generate ribbons. BGHan

2 1