- Chimera-users - RBVI Mailing Lists

MultiScale.color_surfaces_to_match_atoms() and MultiScale mesh resolution ???
by Darrell Hurt 20 Aug '08

20 Aug '08

Hi there, I¹m trying to use the command MultiScale.color_surfaces_to_match_atoms(). I want to point out a mutation on the surface of a virus. I can color the atoms correctly, but I can¹t figure out how to apply that color to the MultiScale low-resolution surface. Any hints on how to use this command? Also, how can I increase the mesh resolution on MultiScale surfaces for input for 3D printing? Thanks! Darrell -- NIH Researchers: check out our new web site <http://inside.niaid.nih.gov/topic/IT/bioinformatics/Pages/default.aspx> Darrell Hurt, Ph.D. Section Head, Biocomputing Research Consulting Bioinformatics and Scientific IT Program (BSIP) NIAID Office of Technology Information Systems (OTIS) National Institutes of Health, DHHS Contractor, Lockheed Martin 4 Memorial Drive, Room 424 Bethesda, MD 20892-0485 Mobile: (301) 758-3559 Fax: (301) 402-0366 NIAID Intranet: http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Re: [Chimera-users] Distance and Angles
by Thomas Goddard 19 Aug '08

19 Aug '08

Hi Andy, To show a distance between atoms select the two atoms and use menu entry Tools / Structure Measurements / Distances and press the Create button. You can show distances for multiple pairs of atoms. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… Not sure what you mean by the angle between two density map surfaces. The surfaces intersect in many places making different angles. You could place 3 markers with Volume tracer and measure the angle made by those 3 markers using the Angles/Torsions tab of the Structure Measurement dialog. Tom Anindito Sen wrote: > Hi Tom > > Probably this question is already answered before- > > How do I show multiple distances between different amino acids of two > molecules from two different parts of the density map. > > Also do can I determine the angle between two surfaces? > > Thanks > Andy > > Dr. Anindito Sen (Ph.D) > Research Associate , Dept. of Biochemistry and Molecular Genetics > University of Virginia > Box 800733 Charlottesville, VA 22908

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saving maps generated with molmap - origin?
by Grigore Pintilie 19 Aug '08

19 Aug '08

Hello, I'm wondering why when I generate a density map from a pdb structure (using the molmap command) and then save it, once I reopen it it seems to have shifted with respect to the structure. I'm noticing that before saving it, the generated map has a certain origin (shown in the Coordinates pane in the Volume Viewer), and then when I reopen it the origin appears as 0 0 0. If I copy the origin shown initially and then paste it into the origin of the opened file, this shifts the map to the correct position, but why isn't the right origin saved with the file? I'm using alpha version 1 build 2509 2008/05/01, platform win32 Many thanks, Greg

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How to Create Isopotential Contours, not Surfaces, with Chimera
by Charles Letner, Ph.D. 19 Aug '08

19 Aug '08

Hello all, I have a map of electrostatic potentials. Using volume viewer I am able to display the surfaces at any potential value I would like (as well as multiple values by having multiple bars in the volume viewer histogram). Now, I would like to be able to take a slice through that potential surface and see a line associated with a given value of the potential in that slice - call that the contour. I would like to have multiple potential contours, each with a different constant value in that contour (-10 for one contour, -20 for the next, -30 for the third, and so on- call these the iso-potential contours). This would allow the contours of potential to be seen in a single plane. Seems like I am so close using planes but that just isn't working. Am I approaching this right and if so any hints would be appreciated? If I am off base with the approach, I sure would appreciate a nudge in the right direction? Cheers, Chuck

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Flipping between alternate conformations (depiction/movie)
by David Chenoweth 19 Aug '08

19 Aug '08

Dear Chimera team, Is there a movie command that can easily depict the interconversion between two alternate conformations in a nucleic acid or protein residue (designated conformation a and b) within a pdb file. I am really trying to illustrate with a movie how the phosphates flip between two well defined states in an ultra-high resolution DNA crystal structure using a chimera movie. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen(a)caltech.edu **********************************************

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Question about Measure Volume and Area
by Patrick Redmill 18 Aug '08

18 Aug '08

Hi all, I am using the the calculate "Area and Volume" option in Chimera to estimate the SASA and excluded volumes of a family of fullerene materials. I need to calculate the area and volume using two different probe sizes (1.4 and 2.0, to be specific). For most of my particles, you see that the volume and area are relatively insensitive to a change in probe size (which I would expect). For one particle, however, I find the results to be quite different and unintuitive. For instance: 1.4: Area: 1174 Volume: 3534 2.0: Area: 1692 Volume: 2493 My (perhaps wrong??) assumption is that the area calculator uses a Connolly algorithm. If that is the case, I can't understand why a larger probe would give a larger area (smaller probes samples more surface). Also, why would a larger probe give a larger volume? Again, I thought the volume calculator used a Voronoi algorithm, which, to me seems independent of probe size. Any idea what may be wrong about my understanding? I've attached a .pdb of the molecule in question if you'd like to take a gander. Thanks in advance! ~Patrick

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stereo
by Matthew Dougherty 16 Aug '08

16 Aug '08

I have been using chimera/macAqua with sequential stereo with no problems on a CRT. I am running into problems using the depth-q stereo projector because of the way their frame buffer works. Their left and right is inverted relative to the CRT. On other packages I activate a left/right image swap to get around this. Is there something I can do to achieve this on Chimera? Matt National Center for Macromolecular Imaging

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Fwd: Question about Measure Volume and Area
by Elaine Meng 15 Aug '08

15 Aug '08

Begin forwarded message: > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: August 15, 2008 12:11:33 PM PDT > To: Patrick Redmill <patrickredmill(a)gmail.com> > Cc: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Question about Measure Volume and Area > > Me again, I just wanted to quickly reiterate that if you want > analytical values, just look in the Reply Log after first showing/ > creating the surface. That will report the analytical values, and > not just the totals but also the values for each component > (disconnected blob, so outer surface and inner surface are two > components), and also both SAS and SES areas even though only the > SES is actually displayed in Chimera. > > So for molecular surfaces, there isn't really any reason to use > Measure Volume and Area or Measure and Color Blobs. Those tools are > mainly needed for other, nonmolecular surfaces. I didn't present > this clearly in the previous messages, sorry. > Best > Elaine

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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()

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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

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