- Chimera-users - RBVI Mailing Lists

command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by sabuj pattanayek 26 Jan '06

26 Jan '06

Hi, I'm trying to make a movie using a cmd file. I want to show and hide (same as clicking the checkbox for shown in the model panel) models from the cmd file since the system becomes too slow to do it manually while the movie is recording and timing frames is even more difficult. I also want to decrease and increase the isosurface threshold level in the volume viewer from the cmd file. Is it possible to do these without using the mouse while a movie is recording? Thanks, Sabuj Pattanayek

4 4

Fwd: command line for showing and hiding (same as clicking shown checkbox in model panel?) and volume viewer options in a cmd file?
by Elaine Meng 25 Jan '06

25 Jan '06

> From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2006 10:42:40 AM PST > To: sabuj pattanayek <sabuj.pattanayek(a)vanderbilt.edu> > Subject: Re: [Chimera-users] command line for showing and hiding > (same as clicking shown checkbox in model panel?) and volume viewer > options in a cmd file? > > Hi Sabuj, > I failed to read Tom's mail first, oops. Just wanted to mention, > however, that I am pretty sure you want the command "modeldisplay" > and not "display": the latter turns all the atoms on, whereas > "modeldisplay" leaves the atom and ribbon display bits as they are > and is equivalent to the Show/Hide stuff in the Model Panel. > Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

1 0

Re: [Chimera-users] distance not shown
by Mingfeng Yang 24 Jan '06

24 Jan '06

Eric Pettersen wrote: > Hi Mingfeng, > ATI has come out with a new driver version for your card: > 8.21.7. Could you try that version and see if things start working? > Let me know. Thanks! > > --Eric > Hi, Eric, I just updated the driver to 8.21.7, and it can't work out. :( Meanwhile, I tried the radeon driver included in Xorg, and the distance can be displayed. So, yes, it's the driver's fault. Mingfeng > On Jan 11, 2006, at 6:09 AM, Mingfeng Yang wrote: > >> Hi, Eric, >> >> I am using ATI FireGL 8800 graphics card with driver fglrx-8.20.8. >> The 2D label does work. Labeling an atom or residue showed nothing. >> Change font size and style didn't solve the problem. >> I remember this feature works perfectly in the previous versions >> (probably before build 1.6???) on this same machine. >> >> Regards, >> Mingfeng >> >> >> Eric Pettersen wrote: >>> Hi Mingfeng, >>> You are the second person to report this behavior -- the other >>> person was also on Linux. Can you tell me what graphics cards you >>> have and what driver version? Do regular atom labels show up? Do >>> 2D labels work (Tools->Utilities->2D Labels)? Can you check your >>> Background preferences and make sure the default font size is > 0 >>> and try changing the font style to see if that makes any difference? >>> >>> --Eric >>> >>> Eric Pettersen >>> >>> UCSF Computer Graphics Lab >>> >>> pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu> >>> >>> http://www.cgl.ucsf.edu >>> >>> >>> >>> On Jan 10, 2006, at 2:56 PM, Mingfeng Yang wrote: >>> >>>> >>>> I am using Chimera build 1.2186 on Gentoo linux. Strangely, when >>>> the distance between two atoms is shown by the command "distance", >>>> the number is no longer displayed along the yellow dashed line. >>>> Did the developers removed this function? Or is it a bug? >>>> >>>> Regards, >>>> Mingfeng >>>> >>>> >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> > >

2 1

Question
by Jin Chai 23 Jan '06

23 Jan '06

Dear Sr/Ms, I wonder if chimera molecular modeling system can be used beyond molecular level. we try to use chimera to create 3D images on mouse colon crossection images(dataset) we collected from SKYSCAN Micro-CT 1076 . Do you think it will work? Looking forward to your opinion. Thanks in advance, Jin --------------------------------- Yahoo! Photos Showcase holiday pictures in hardcover Photo Books. You design it and well bind it!

2 1

CIF file format?
by Jason Sharpe 17 Jan '06

17 Jan '06

Hi, how do I open mmCIF (.cif) files in Chimera. This is the standard format of structure files supplied by the Cambridge Structural Database. thanks, Jason Sharpe University of Toronto

2 1

Saving a multiscale model in VRML
by R. Andrew Byrd 17 Jan '06

17 Jan '06

Greetings, Our publications group has a new device that they call a 3D printer. It can make solid models from a data file. They have made models from pdb files as ball-and-stick, and I saw one surface rendered model. They tell me that the input is in VRML. So, I am wondering how to make a VRML file from a session in Chimera where Multiscale Model tool is used to make a surface rendering of a complex model...several proteins. My model is not as complex as the virus examples for multiscale models, but the ability to make different resolution surfaces is a powerful aid. I would like to try and 'print' a 3D model of this surface rendered complex. Any help in out to output the VRML file for the printer?> Thanks Andy -- R. Andrew Byrd, Chief Structural Biophysics Laboratory National Cancer Institute V 301-846-1407 F 301-846-6231 -------------------------------------------------

3 2

Slow framerates (on a nice laptop)
by Charlie Moad 17 Jan '06

17 Jan '06

So in general I get really good performance with chimera, but for some reason I get really bad frame rates with more recent releases on windows with my laptop. It has a really nice card, GeForce 6200TC Go. It is even on a pcix16 bus. I am guessing that since it is a newer chipset, chimera is using shaders of some kind? The molecule looks visually smoother/better than when in linux. In any case, it seems something is getting enabled that really bogs it down, and I would like to be able to disable it. Sony Vaio FS500 Chimera 1.2184 Thanks, Charlie

2 1

distance not shown
by Mingfeng Yang 10 Jan '06

10 Jan '06

I am using Chimera build 1.2186 on Gentoo linux. Strangely, when the distance between two atoms is shown by the command "distance", the number is no longer displayed along the yellow dashed line. Did the developers removed this function? Or is it a bug? Regards, Mingfeng

2 1

yet another binary plugin question
by Charlie Moad 06 Jan '06

06 Jan '06

So I have been able to create a working binary plugin for windows/linux 1.2184 and osx.4 1.2186. My problem now is osx.3 1.2184. I can compile the plugin, but it crashes chimera with a TCLfree call to a null pointer. I used the chimera-1.2183-linux-headers.tar.gz download. The 1.2186-osx headers didn't work either. 1.2186 won't launch for 10.3 either. The python module is matplotlib. It uses Numeric, freetype, tcl/tk, and libpng. I provide the only missing dep, libpng, and compile against the rest which are provided in chimera. Any help on what approach I should be using? Thanks, Charlie

2 7

Help or feature request
by Mingfeng Yang 22 Dec '05

22 Dec '05

It's a very common problem to calculate the twist angle between to beta-strands or two alpha-helix. So I am wondering if Chimera can fit a group of atoms into a straight line, and give the angle of two fitted line. If chimera does do this, hopefully somebody can tell me how to do this. If not, it would be worthwhile to add this function in. Thank you very much! Happy holiday! Mingfeng

2 1