- Chimera-users - RBVI Mailing Lists

problem in displaying pdb file
by venkataraman kabaleeswaran 30 Jan '06

30 Jan '06

I am having a problem in displaying the pdb file, chimera didnot display the whole molecule , around 100 residues is missing in the display, but other programs like pymol displaying without any problems. what is wrong? thanks vk Kabaleeswaran Venkataraman Arise, Awake and stop not until goal is Reached - Swami Vivekanand __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Fwd: control the movie play speed
by Eric Pettersen 27 Jan '06

27 Jan '06

Forgot to cc this to the list for the good of future generations. :-) --Eric Begin forwarded message: > From: Eric Pettersen <pett(a)cgl.ucsf.edu> > Date: January 27, 2006 1:42:37 PM PST > To: Mingfeng Yang <mfyang(a)gmail.com> > Subject: Re: [Chimera-users] control the movie play speed > > Hi Mingfeng, > You can use the main interface's playback slider to change the > rate that frames are played back. With the slider to the far right > there is no delay between frames, with it to the far left there is > a one-second delay between frames. This interacts with recording > just like you would expect -- extra frames get recorded during the > delay which produces a movie with the same apparent playback speed > as with a non-recorded playback. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > pett(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu > > On Jan 27, 2006, at 12:59 PM, Mingfeng Yang wrote: > >> Hi, >> >> I am using chimera to record the movie of a MD trajectory into a mpeg >> format vedio. How can I set the interval between neighboring >> snapshots? >> It seems the playback option in the MD movie dialog can't do >> that. Thanks! >> >> Mingfeng >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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control the movie play speed
by Mingfeng Yang 27 Jan '06

27 Jan '06

Hi, I am using chimera to record the movie of a MD trajectory into a mpeg format vedio. How can I set the interval between neighboring snapshots? It seems the playback option in the MD movie dialog can't do that. Thanks! Mingfeng

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Background transparency
by Alon Ben-David 27 Jan '06

27 Jan '06

Hi My name is Alon and I am a graduate student at the Technion, Israel institute of technology. My question is how can I create a transparent background to pictures I am generating with Chimera. I read at the site that not all hardware's permit a transparent background, but I don't know how can I check if my hardware do. Thank you in advance and best regards Alon

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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

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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

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Re: [Chimera-users] distance not shown
by Mingfeng Yang 25 Jan '06

25 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 >>> >> > >

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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!

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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

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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 -------------------------------------------------

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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

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distance not shown
by Mingfeng Yang 11 Jan '06

11 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

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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

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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

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Save image from Chimera
by Juhan Kim/CIRES 22 Dec '05

22 Dec '05

Hello, Does anybody know how to save the image from the chimera? I'm using PC version of Chimera and whenever I'm trying to save the image using the menu file>save image, I always fail to save the image and only get the following "reply log" ----reply log----- Opening "file.pdb" Done opening "file.pdb" Unable to save image: (0, 'Error') Unable to save image: encoder error -2 when writing image file Unable to save image: encoder error -2 when writing image file Unable to save image: (0, 'Error') If anybody knows how to solve this please let me know. Thank you. Juhan UCB, Boulder

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how to not include CONECT, RIBBON, HELIX, SHEET keywords in a pdb when saving from the pdb file dialog
by Sabuj Pattanayek 19 Dec '05

19 Dec '05

Hi, I was wondering how it might be possible to not include the CONECT, RIBBON, HELIX, or SHEET keywords in a pdb when saving from the save pdb file dialog? It can be done using "pdbrun nouser cat | grep -v HELIX | grep -v SHEET" ...etc but I can't save the pdb model relative to another model on the screen using that command. Thanks, Sabuj Pattanayek

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Fit Models
by Bernard Heymann 14 Dec '05

14 Dec '05

I'm interested in using the "Fit Models in Maps" feature in Chimera. However, the version I installed (release 1.2184) under Mac OSX 10.4 does not have this in the Tools/Volume Data menu as described in the documentation. Can anyone tell me if this is intentional or can I get this feature? Bernard Heymann, Research Fellow Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH Bethesda MD 20892 Tel. 301-451-8241, Fax. 301-480-7629

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new version available
by Eric Pettersen 14 Dec '05

14 Dec '05

Hi all, We've put out a new version (1.2180) which we believe fixes the problems that some people were having on XP platforms. We're hoping that those of you that were having problems will try out the new version at your earliest convenience and let us know how it works. Thanks! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 12 Dec '05

12 Dec '05

Greetings, I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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Concerns regarding secondary structure
by rquiroga＠immf.uncor.edu 09 Dec '05

09 Dec '05

I have some concerns with Chimera's secondary structure detection/depiction. I am using Modeller to predict some 3D structures. I open my predicted structure in pdb file in Chimera along with the original structure I based my prediction on, and find that my predicted structure lacks two beta sheets that the model protein has, though the AA that compose the B-sheet are identical for the two proteins when I compare sequences with Matchmaker. I tried opening my predicted structure in MolMol and it detects the B-sheet, though I hugely prefer Chimera, so if you could solve this problem for me I would be very greatful. Thanks in advance, and regards Rodrigo Quiroga

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Re: [Chimera-users] Moving selected atoms
by Thomas Goddard 08 Dec '05

08 Dec '05

I improved the mouse mode for moving selected atoms so if no atoms are selected it moves everything like the normal rotation and translation mouse modes -- all active models are moved. The new code is http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar For installation instructions see my previous chimera-users message. http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-December/000609.html The new behaviour makes it easy to move some atoms, then rotate the view, then move the atoms again. After moving the atoms you can clear the selection using ctrl-click on the background of the graphics window, then rotate everything to the new view point, then press the left arrow key (undo selection) to revert to the previous selection, and continue moving the atoms. Tom

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Moving selected atoms
by Thomas Goddard 08 Dec '05

08 Dec '05

I wrote a Chimera extension that allows moving just selected atoms with the mouse. This is for modifying molecular structures. Here is the code http://www.cgl.ucsf.edu/home/goddard/temp/moveselection.tar that adds mouse modes to move selected atoms. The archive contains a directory called MoveSelection. Put it in your Chimera distribution in chimera/share or on Mac in Chimera.app/Contents/Resources/share Then when you start Chimera use menu entry Favorites / Preferences, and choose category "Mouse" from the preferences dialog. This shows the mouse modes table with the available modes along the top line. The last two are for shifting and rotating selected atoms. Reassign mouse buttons (say buttons 1 and 2) to these modes and you can move selected atoms. There is no undo. I'll have to make this easier to use and put it into Chimera. Tom

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Re: [Chimera-users] chimera for linux ppc
by Geoffrey H Wathen 08 Dec '05

08 Dec '05

I've used YellowDog in the past, and I think it is a good dist. I wouldn't mind seeing a PPC Linux version of Chimera, either. Geoff. On Dec 7, 2005, at 10:50 AM, A. Zelter wrote: >> I think Conrad is saying that on the x86 architecture they can >> compile for RedHat and it will run on most distributions of x86 >> Linux. He's asking if there's a similar situation on PPC Linux, >> and which distribution of PPC Linux would provide the best >> prospects for such coverage. It seems to me that this is to >> minimize the occurrence of someone saying "I see you have the >> binaries for XYZ PPC Linux, but they don't run on my distribution >> of ABC PPC Linux. Could you please compile it for ABC PPC Linux?" > > Ahhh thanks. I knew I didn't get something. Well, I'm no expert on > that kind of thing, but Fedora Core 4 has a ppc version. I think > this is a little more modern than Red Hat Linux 7.1 - it runs > kernel 2.6.11. However, RedHat did make a PPC version of their 7.1 > distro (Red Hat Linux 7.1 for pSeries). I suppose that would be > equivalent. Another good bet might be yellowdog linux. The latest > version is 4.0.1, and it uses kernel 2.6.10. Yellowdog is based on > redhat but built specifically for Macs. This is probably what I > would try using. > Alex > >

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Missing tools
by Luke Kontogiannis 07 Dec '05

07 Dec '05

I had installed the current production release chimera-1.2184-linux.exe. Just now I downloaded and installed the latest snapshot release chimera-1.2186-linux.exe and this version has the multiscale tool under Tools -> Higher-order structure Luke

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chimera for linux ppc
by Alex Zelter 07 Dec '05

07 Dec '05

Hi, I was wondering if it would be possible for the developers to compile a binary version of chimer for use on linux ppc architecture seeing as it is not possible for a user to compile for themselves due to the proprietary solvent-accessible molecular surfacing library. I know this is not a common architecture, but some people do use it. Thanks in advance, Alex Zelter

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