- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] 3D-glassen
by Dan Gurnon 16 Oct '09

16 Oct '09

Thomas, I've been using the Quadro fx 380 for a couple weeks now, and I would say that the results are marginally better than with the fx 4500. There is still some occasional flickering, and for some reason, the card has trouble resetting to the normal windows aero after I close chimera with the view set to sequential stereo. I also have occasional issues when using stereoplayer or Pymol, so it looks like Nvidia still has to work out some driver issues with their 3Dvision. On Fri, Oct 2, 2009 at 4:23 PM, Thomas Classen < Thomas.Classen(a)uni-duesseldorf.de> wrote: > Thank you for your help. > > > > > > > > --------------------------------- > > Thomas Classen, M. Sc. Biochemie > > Thomas.Classen(a)uni-duesseldorf.de > > > ------------------------------ > > *Von:* doublehelix00(a)gmail.com [mailto:doublehelix00@gmail.com] *Im > Auftrag von *Dan Gurnon > *Gesendet:* Freitag, 2. Oktober 2009 16:28 > *An:* Thomas Classen > *Cc:* chimera-users(a)cgl.ucsf.edu > *Betreff:* Re: [Chimera-users] 3D-glassen > > > > Tom, > I use the 3D vision system with Chimera. Note that in order for the > 3Dvision to work you'll either need a 100Hz or better CRT or a 3D-ready > 120Hz LCD from Samsung or Viewsonic. It won't work with standard LCDs. > You'll also need to be running Vista or Windows 7. > http://www.nvidia.com/object/3D_Vision_Requirements.html > > You're also going to want a Quadro card, not the GTX285 geforce card you > have listed below. The Geforce cards can't do sequential stereo in windowed > mode, and I'm not sure if Chimera would even allow sequential stereo even in > full screen mode with a geforce (but I haven't tested it with a geforce > card). > > In my experience, the sequential stereo with the Nvidia hardware has been > just "ok"...its nice when it works, but it hasn't always worked. I really > think my issue has been my hardware...I have a Quadro FX 4500, which is an > older (albeit expensive!) card with an onboard DIN-connector. I just found > out that its not supported by the 3D vision drivers, so thats hopefully why > I'm having occasional display problems. Here's a list of compatible quadro > cards: > > http://www.nvidia.com/object/quadro_pro_graphics_boards.html > > The nice thing about Nvidia's 3D vision is that you don't need to buy one > of the very expensive Quadro cards with stereo output through an onboard > DIN-connector (the fx 3000 series and up). In fact, I just ordered a Quadro > Fx 380 for about $125, which I hope will solve the issues I'm having with > the fx 4500. It should be here next week- I'll let you know how it goes. > > > Dan > > On Fri, Oct 2, 2009 at 4:12 AM, Thomas Classen < > Thomas.Classen(a)uni-duesseldorf.de> wrote: > > Dear colleaques; > > > > I want to use 3D-glasses of nVidia for the sequential stereo view in > chimera. Are there any experiences with that system in combination with > chimera? > > Or are there some problems with that kind of technology known? > > > > Wanted hardware > > - nVidia GF 3D Vision 3D-Glasses > > -nVidia graphicboard; GTX285 Series min. 1024MB > > > > Additional hardware: > > - Intel 2 Duo Quad Prozessor; Q9650; boxed > > - 8GB DDR2 RAM PC1066 > > > > > > Thanks for your help from germany > > Tom > > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > -- > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > > p: 765-658-6279 > e: danielgurnon(a)depauw.edu > -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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questions about volume tracer
by Jean-Francois Menetret 16 Oct '09

16 Oct '09

I have a few questions about *volume tracer*: Is it possible to add marker(s) in an existing marker set ? Is it possible to change the marker note of an existing markers ?

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Re: [Chimera-users] Hydrodynamic radius
by Tom Goddard 14 Oct '09

14 Oct '09

Hi Sudheer, I don't know if the theoretical hydrodynamic radius Rhyd defined on the wikipedia page http://en.wikipedia.org/wiki/Hydrodynamic_radius is a good approximation to the Stokes' radius. The Stokes' radius depends on both shape and hydration details. I've added a request for this calculation in Chimera to our feature request page (item 220). http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests This is much more specialized than typical Chimera features and I would not expect it to be implemented any time soon. If you wished to implement it I could probably show you how to get out of Chimera a list of grid points within a displayed contour level that would be the input to the calculation. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Hydrodynamic radius From: Sudheer To: goddard(a)cgl.ucsf.edu Date: 10/14/09 2:03 PM > Hi Tom, > > Im interested in the optical properties of a protein. Yes, "the > hydrodynamic radius for a uniform solid bounded by a contour surface > of your map would be useful". Yes, Stocks radius. Actually I'm running > Dynamic light Scattering experiment to find the variation in the size > distribution of a protein with change in Temperature. (I mean im > trying to find at what temperature the protein forms monomer and > dimer...!) I already have Cryo-EM map of the dimer and so just thought > of comparing the Hydrodynamic radius between the cryo-map and the DLS > result. > > I hope you got my interest in finding the Hydrodynamic radius of my > protein. > > Thank you very much for your help, > Sudheer. > > > Date: Wed, 14 Oct 2009 13:54:03 -0700 > > From: goddard > > To: Sudheer > > CC: chimera-users(a)cgl.ucsf.edu > > Subject: Re: [Chimera-users] Hydrodynamic radius > > > > Hi Sudheer, > > > > Chimera isn't able to compute hydrodynamic radius of maps or > > molecules. Are you primarily interested in diffusion properties or > > optical properties of your structure? Do you think the hydrodynamic > > radius for a uniform solid bounded by a contour surface of your map > > would be useful? Do you mean Stokes' radius or the R_H defined on the > > wikipedia page? > > > > http://en.wikipedia.org/wiki/Hydrodynamic_radius > > > > The latter looks like a pretty simple calculation. > > > > Tom > > > > -------- Original Message -------- > > Subject: [Chimera-users] Hydrodynamic radius > > From: Sudheer > > To: chimera users > > Date: 10/14/09 1:05 PM > > > Hi, > > > > > > Can I measure the Hydrodynamic radius a Cryo-EM density map using > Chimera? > > > > > > Thank you, > > > Sudheer Molugu. > > > > ------------------------------------------------------------------------

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Hydrodynamic radius
by skmolugu＠miners.utep.edu 14 Oct '09

14 Oct '09

Hi, Can I measure the Hydrodynamic radius a Cryo-EM density map using Chimera? Thank you, Sudheer Molugu.

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Running Chimera on Ubuntu
by Claudio Saracini 12 Oct '09

12 Oct '09

Hello, I installed Chimera on my MacBook Pro with Unix OS (Ubuntu). When I try to run the program from the bash I get: Bash: Chimera: Command not found I'm a newbie of Linux. I guess I forgot to do something after having installed Chimera. I would appreciate your help. Claudio *************************************************** Claudio Saracini Kenneth D. Karlin Research Group Department of Chemistry The Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 E-Mail: claudio.saracini(a)jhu.edu Group Website: http://www.jhu.edu/~chem/karlin/ ****************************************************

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Protein secondary structure
by Beale, John 08 Oct '09

08 Oct '09

I realize that this is probably simple, but I haven't been able to work this problem out. Is there a way to read a single pdb file into Chimera and then have the program show me what amino acid sequences of the protein are alpha helices, what are beta sheets, and what are 3,10 helices, etc? Thanks! John John M. Beale, Ph,D, Associate Professor of Medicinal Chemistry St. Louis College of Pharmacy 4588 Parkview Place St. Louis, Missouri 63110 (314)-446-8461 Cell: (314)-315-0409 FAX (314) 446-8460 jbeale(a)stlcop.edu

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Pseudobonds
by David Chenoweth 08 Oct '09

08 Oct '09

Hi, I am trying to delete/hide a single pseudobond in a group of pseudobonds. Can anyone tell me how to do this, or to specify a set of new pseudobonds which doesn't include the one I would like to remove. I tried to do this in the pseudobond panel but didn't get anywhere. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno(a)mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------

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Re: [Chimera-users] Displaying Surface For Selected Residues
by Eric Pettersen 07 Oct '09

07 Oct '09

On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote: > Thanks Eric, but just to follow up on the surf sel command, > > It displays the surface for the selected residues, > > does it assign solvent-excluded and solvent-accessible surface areas > per atom and residue to attributes named areaSES and areaSAS to the > selected residues or to the whole protein?. > > after I do "surf sel" I have select:/areaSAS > 50 , looks like it > selects for the whole protein. Shouldn't it show only for the > selected surface region. > Hi Thiru, Surfaces are computed for the entirety of the molecule (that the surface covers), not just the residues you display the surface on. So therefore other residues also got areaSAS/SES attributes. To get what you want I think you need: sel :/areaSAS > 50 & @/surfaceDisplay --Eric > Thanks > > -Thiru > > --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Subject: Re: Displaying Surface For Selected Residues > To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> > Date: Wednesday, October 7, 2009, 5:14 PM > > Yes, most commands work on everything if you don't specify what to > work on. For instance "color red" colors everything red whereas > "color red sel" colors the selection red. > > --Eric > > On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote: > >> Worked fine, Thanks, Eric >> >> -Thiru >> >> --- On Wed, 10/7/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >> >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> Subject: Re: Displaying Surface For Selected Residues >> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >> Date: Wednesday, October 7, 2009, 5:04 PM >> >> "surface sel" >> >> --Eric >> >> On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote: >> >>> Hi Eric, >>> >>> I have a protein with a few residues selected, and I wanted to >>> show surface only on the selected residues, when I go to Actions - >>> Surface -Show , it shows surface only for the selected residues, >>> but when I use the command surface on the command line it shows >>> the surface for the entire protein. Is there a command line >>> option to show surface only for the selected residues on the >>> protein. >>> >>> Thanks >>> >>> Thiru >>> >>> --- On Thu, 10/1/09, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: >>> >>> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >>> Subject: Re: [Chimera-users] Solvent Accessible Surface Area >>> To: "Thiruvarangan Ramaraj" <thiruvaranganr(a)yahoo.com> >>> Cc: "UCSF Chimera Mailing List" <chimera-users(a)cgl.ucsf.edu> >>> Date: Thursday, October 1, 2009, 3:38 PM >>> >>> Oops, spotted a bug in the script. This line: >>> >>> out = open(os.path.expanduser("~/out", "w")) >>> >>> should be: >>> >>> out = open(os.path.expanduser("~/out"), "w") >>> >>> --Eric >>> >>> >>> >> >> > >

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Re: [Chimera-users] Chimera pov-tracing question
by Tom Goddard 07 Oct '09

07 Oct '09

Hi Maya, Your mesh is transparent in the povray image (zoom in on the image and look at the mesh lines) but I guess is much less transparent than in the Chimera window. I ran some test images with the current Chimera 1.4 daily build which also showed the povray mesh looked much different (darker, thicker and less transparent) than in the Chimera window. While we have improved the match between povray images and what you see in the Chimera window it is still very bad. Dozens of messages on the chimera-users mailing list relate to the poor quality of Chimera Povray images. http://www.google.com/search?hl=en&q=povray+site%3Awww.cgl.ucsf.edu%2Fpiper… As suggested in the following message, with these poor quality povray results a better presentation can almost always be obtained by not using povray: http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-June/004030.html Attached are 5 test images showing some of the problems. 1mwm chain A, molmap 6 angstroms. test.png - povray transparent mesh 0.24, appears very dark test2.png - povray transparent mesh 0.04, black specks all over the mesh test4.png - povray transparent surface 0.24, ugly multilayer mosaic test5.png - no povray, transparent surf 0.24, glossy lighting, silhouette edges test6.png - no povray, same as test5 but mesh. Tom -------- Original Message -------- Subject: Chimera pov-tracing question From: maya shcushan To: 'Thomas Goddard' Date: 10/7/09 9:59 AM > > Dear Dr Goddard, > > > > You previously assisted me with other problems with Chimera, so now I > am asking your help again. > > I have a density map and a structure mapped on it. I showed the map as > transparent mesh, and tried to pov-ray the image. However, the picture > came up with the map not transparent (attached). Do you have any idea > how to resolve this issue, making the map transparent in the image as > it is in the main window > > > > Thanks, > > Best, > > *Maya Schushan* > > Department of Biochemistry > > George S. Wise Faculty of Life Sciences > Tel Aviv University >

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