- Chimera-users - RBVI Mailing Lists

model panel: add/edit note
by Dougherty, Matthew T 03 Aug '10

03 Aug '10

Is there a command to be able to modify notes on the model panel? If not, it would a useful addition when creating a command file to load in & color datasets.

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Small molecules and antechamber
by Jon Rumbley 02 Aug '10

02 Aug '10

I have several small organic molecules constructed in ChemDraw and converted in Chem3D to .mol2 files. I can open them in Chimera but cannot seem to add charges to. I was simply using the add charge menu commands and AM1-BCC and assuming the structures would be read as nonstandard but antechamber reports an error with residue ****. The error log has no real indication of what the trouble might be. Are there additional steps I must take before assigning charges? The structures already have hydrogens added. An example .mol2 file is below: @<TRIPOS>MOLECULE **** 44 45 1 0 0 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C -2.8306 2.5311 -0.9622 C.2 1 **** 0.0000 2 C -2.8728 1.1718 -1.0363 C.2 1 **** 0.0000 3 C -4.0552 0.3840 -0.9622 C.1 1 **** 0.0000 4 C -1.6082 0.4134 -1.1450 C.2 1 **** 0.0000 5 N -5.0052 -0.2769 -0.8917 N.1 1 **** 0.0000 6 O -1.8883 -0.9222 -1.2800 O.3 1 **** 0.0000 7 O -0.4722 0.8459 -1.1451 O.2 1 **** 0.0000 8 C -0.8034 -1.8901 -1.1282 C.3 1 **** 0.0000 9 C -0.3965 -1.8485 0.3585 C.2 1 **** 0.0000 10 C -1.4383 -3.2075 -1.5077 C.3 1 **** 0.0000 11 N 0.6925 -2.6041 0.6991 N.am 1 **** 0.0000 12 O -1.0062 -1.1536 1.1745 O.2 1 **** 0.0000 13 C 1.2426 -2.6055 2.0833 C.3 1 **** 0.0000 14 C 2.4273 -3.5343 2.1380 C.ar 1 **** 0.0000 15 C -3.9592 3.4353 -0.8741 C.ar 1 **** 0.0000 16 C -3.7802 4.6664 -0.1923 C.ar 1 **** 0.0000 17 C -4.8234 5.5702 -0.0757 C.ar 1 **** 0.0000 18 C -6.0611 5.2454 -0.6673 C.ar 1 **** 0.0000 19 C -6.2633 4.0447 -1.3692 C.ar 1 **** 0.0000 20 C -5.2063 3.1490 -1.4690 C.ar 1 **** 0.0000 21 O -7.0408 6.1768 -0.5154 O.3 1 **** 0.0000 22 C 3.5525 -3.2801 1.3388 C.ar 1 **** 0.0000 23 C 4.6333 -4.1642 1.3545 C.ar 1 **** 0.0000 24 C 4.6017 -5.2952 2.1768 C.ar 1 **** 0.0000 25 C 3.4888 -5.5395 2.9865 C.ar 1 **** 0.0000 26 C 2.3994 -4.6635 2.9668 C.ar 1 **** 0.0000 27 H -1.8332 3.0176 -0.9495 H 1 **** 0.0000 28 H 0.0351 -1.5845 -1.7993 H 1 **** 0.0000 29 H -0.6942 -4.0150 -1.5686 H 1 **** 0.0000 30 H -1.9272 -3.1457 -2.4932 H 1 **** 0.0000 31 H -2.2150 -3.5214 -0.7935 H 1 **** 0.0000 32 H 1.1669 -3.2048 0.0167 H 1 **** 0.0000 33 H 1.5395 -1.5662 2.3712 H 1 **** 0.0000 34 H 0.4439 -2.9024 2.8058 H 1 **** 0.0000 35 H -2.8085 4.9012 0.2576 H 1 **** 0.0000 36 H -4.7042 6.5169 0.4530 H 1 **** 0.0000 37 H -7.2285 3.8279 -1.8322 H 1 **** 0.0000 38 H -5.3406 2.2282 -2.0442 H 1 **** 0.0000 39 H -7.9024 5.8992 -0.9622 H 1 **** 0.0000 40 H 3.5844 -2.3950 0.7014 H 1 **** 0.0000 41 H 5.5045 -3.9710 0.7250 H 1 **** 0.0000 42 H 5.4465 -5.9867 2.1870 H 1 **** 0.0000 43 H 3.4659 -6.4183 3.6333 H 1 **** 0.0000 44 H 1.5299 -4.8643 3.5946 H 1 **** 0.0000 @<TRIPOS>BOND 1 1 2 2 2 1 15 1 3 1 27 1 4 2 3 1 5 2 4 1 6 3 5 3 7 4 6 1 8 4 7 2 9 6 8 1 10 8 9 1 11 8 10 1 12 8 28 1 13 9 11 1 14 9 12 2 15 10 29 1 16 10 30 1 17 10 31 1 18 11 13 1 19 11 32 1 20 13 14 1 21 13 33 1 22 13 34 1 23 14 22 2 24 14 26 1 25 15 16 2 26 15 20 1 27 16 17 1 28 16 35 1 29 17 18 2 30 17 36 1 31 18 19 1 32 18 21 1 33 19 20 2 34 19 37 1 35 20 38 1 36 21 39 1 37 22 23 1 38 22 40 1 39 23 24 2 40 23 41 1 41 24 25 1 42 24 42 1 43 25 26 2 44 25 43 1 45 26 44 1 Thanks for any help you can provide. Dr. Jon N. Rumbley Assistant Professor Dept. of Pharmacy Practice and Pharmaceutical Sciences University of Minnesota-Duluth 127 LSci 1110 Kirby Dr. Duluth, MN 55812 Phone: 218-726-6047 email: jrumbley(a)d.umn.edu

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model panel: color patch
by Dougherty, Matthew T 31 Jul '10

31 Jul '10

using a command or python file, how do I set the color patch on the model panel?

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Fwd: Visualizing inertia axes as arrows
by Eric Pettersen 31 Jul '10

31 Jul '10

Hi Miguel, Thanks for the corrections! I just fired that one off without testing it. I thought there might be an error or two. I'm glad you find it useful after fixing it. --Eric Begin forwarded message: > From: Miguel Ortiz Lombardía <miguel.ortiz-lombardia(a)afmb.univ-mrs.fr> > Date: July 31, 2010 1:39:33 AM PDT > To: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Visualizing inertia axes as arrows > > Hi Eric, > > Thanks for this useful script! > > I think I found two errors though: >> >> from chimera.selection import currentAtoms, numpyArrayFromAtoms > > should be: > > from chimera.selection import currentAtoms > from chimera import numpyArrayFromAtoms > > and: > >> for val, vec in zip(vals, vecs): >> bildString += ".arrow %g %g %g %g %g %g .1 .2 .9\n" % ( >> centroid[0], centroid[1], centroid[2], >> centroid[0] + val[0] * vec[0], >> centroid[1] + val[1] * vec[1], >> centroid[2] + val[2] * vec[2]) > > has to be: > > for val, vec in zip(vals, vecs): > bildString += ".arrow %g %g %g %g %g %g .5 1. .9\n" % (centroid[0], > centroid[1], centroid[2], centroid[0] + val * scale * vec[0], > centroid[1] + val * scale * vec[1], centroid[2] + val * scale * > vec[2]) > > (you can ignore the scale thing, that's simply a 50/max(vals) > correction > so the longest axis is 50 A) > > Best, > > > -- > Miguel > > Architecture et Fonction des Macromolécules Biologiques (UMR6098) > CNRS, Universités d'Aix-Marseille I & II > Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France > Tel: +33(0) 491 82 55 93 > Fax: +33(0) 491 26 67 20 > e-mail: miguel.ortiz-lombardia(a)afmb.univ-mrs.fr > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. >

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Visualizing inertia axes as arrows
by Jozef Lewandowski 30 Jul '10

30 Jul '10

Hi everybody, Lately, I have been using "measure inertia" command a lot. For my purposes I needed to visualize the inertia axes as arrows instead of the default ellipsoid. I used the vectors from the reply log to write BILD files defining the arrows for the inertia axes. Is there an easy way to script just that? Or differently, is there an easy way to visualize as arrows inertia axes for peptide planes in a protein? Any tips would be appreciated. Thanks, Józef

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Re: [Chimera-users] about transformation matrix
by Tom Goddard 28 Jul '10

28 Jul '10

Hi Julio, I guess you are using the fitnogui.py script. http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/fitnogui.py The parameters are right near the top -- ijk_step_size_min is the one you're interested in. The initial contour level is set as described in the documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum… The "volume" command can set the contour level: volume #0 level 27.6 Tom > Hi Tom, > > Thanks again. Editing the line of code would be perfect for us, since we are calling Chimera from our program with the "nogui" option. Could you point me the place where I need to change that 0.01? > > What happens with the contour level when I'm calling Chimera in that way (nogui)? Can I similarly set it somewhere in the code? Or with an option in the command line? > > Best, > Julio > > > > Hi Julio, > > The details of the fitting algorithm are given in the User's Guide. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.ht… > > You should definitely read that if you want the best understanding. But > the brief answers to your questions are that the convergence criteria > looks for optimization steps of less than 0.01 grid index to decide > convergence. The user interface does not allow you to change the 0.01 > grid index criteria -- it could be done by editing a line of Python. > The default settings do mask using the contour level of the fit map as > an outer boundary. So that level is important. > > Tom > > >

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Camera parameters
by Tom Goddard 28 Jul '10

28 Jul '10

Hi Matt, The Chimera camera always points along the negative z-axis. The positions of the models are moved/rotated to get different view-points. Do you mean you want camera location (x,y,z) and horizontal angular field of view to the edges of the window (for perspective projection)? I know how to get at these using Python code, but I'm not sure if any Chimera commands report those values. Also I don't know if that info makes its way into X3D or VRML exported from Chimera. Greg Couch would know these answers. He is at SIGGRAPH this week. A quite gruesome way to get the parameters is to find them in the Chimera session file. grep formattedPositions mysession.py formattedPositions = {'p2': (0.3954088241213373, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.628906249999993), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((13.338430482851305, 2.7738552720503122, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (29.312384727061698, 10.919780805124898, 8.628906249999993), False), 'p1': (1.0, 18.749999499320985, (14.059999585151672, 7.399999618530273, 8.62890625), (36.02048479676247, -18.762672296762467), 8.62890625, {(0, 0): ((-1.913954659058722, -0.7459259145443079, 6.309792459458727), (0.3889244976446376, 0.8937166155966246, 0.22362545950400858, 33.757570197325826))}, {(0, 0, 'Volume'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (14.059999585151669, 7.399999618530277, 8.628906249999993), False)} This is pretty messy and the values depend on which Chimera version saved the file. The values are defined by Python code chimera/share/Midas/__init__.py in the _savePosition() routine: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping ) If you want a Python script to simply dump the camera positions for all savepos positions I can provide that. Tom > Hi Tom, > > I am creating a workaround for my graphics problem. What I have done in the past is to create a VRML file from Chimera export, extract the openGL camera parameters using a text editor, start up Amira, using TCL I would recreate the same camera view within Amira. At this point I could splice animation clips made by Chimera& Amira using Final Cut Pro. > > It has been a while since I have done this. I am now looking at the exported VRML files and they are lacking the camera info. > > Is there a command I can use to get the camera parameters for the savepos keyframes? > > thanks, Matt > >

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coordinate transformation
by Dougherty, Matthew T 28 Jul '10

28 Jul '10

I was trying to locate details on maxtrix, coordinate transformations & scenegraph, relative to camera transformations.

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about transformation matrix
by Kovacs, Julio A 28 Jul '10

28 Jul '10

Hi, I am doing fitting of two maps and am getting different values of the transformation parameters: the ones given in the window where I specify the options (these seem to be correct), and those given by using the command "matrixget" --- these give a very large translation vector, and moreover, I don't see any relation between that vector and the correct translation. Also, could you tell me what is the order used in Chimera: rotation, then translation? or translation, then rotation? Thank you very much. Julio Kovacs

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Problem
by Reza Heidari 27 Jul '10

27 Jul '10

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