- Chimera-users - RBVI Mailing Lists

cavity cropped view
by Randy Heiland 15 Feb '07

15 Feb '07

What options exist in Chimera for letting me show only that portion of a protein that is "near" another smaller molecule? Specifically, I have a ligand in a cavity of a large protein and would like to eliminate the "clutter" of the protein away from the cavity of interest. Thanks, Randy

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making movies with MorphMap, exporting povray scenes, FitMapInMap
by Gatsogiannis, Christos 14 Feb '07

14 Feb '07

Dear Chimera users and developers, recently I used the new morph map tool and it worked very nice in my case. I encountered a problem while exporting the animation in any movie-format within Morphmap, I just get empty or very small files, which cannot be displayed in any media-player. I decided then to use the chimera-movie recorder utility to record the morphing animation and this worked fine (I´ve tested this with mpeg-2 format). At the moment I´m using the chimera-version 1.2309 in a SUSE LINUX 9.2 environment. Is this a version problem or a bug? Furthermore, I´ve exported some scenes in the povray format and I´ve noticed that the final images are of lower quality in comparison with images made some months ago with older chimera versions. I haven´t changed the povray-version, the rendering settings and the settings for the visualisation of my data in chimera (brightness etc...). The colors are too pale, I could send you some example-images if needed. I´ve tried also the Fit Map in Map tool recently and it worked perfectly (you sent this tool to a group-colleague some months ago). I´m wondering why you didn´t put this tool on the experimental site yet....and one more last question...after using Fit Map in Map, is there any possibility to save the "fitted" map with it´s new orientation? Thanks, Christos Christos Gatsogiannis Institute of Zoology Johannes Gutenberg University 55099 Mainz, Germany Tel: +49(0)6131-39-23091 email: gatsogia(a)uni-mainz.de

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Request for Chimera on CD
by Tom Goddard 13 Feb '07

13 Feb '07

Hi Zia, Our Chimera software can be downloaded from the web http://www.cgl.ucsf.edu/chimera/download.html We have never distributed it by CD. Perhaps we can do it. Our program needs about 512 Mbytes of computer memory. What operating system do you need it for? Windows? Linux? Mac OS X? Because almost all molecular structure and sequence data used in research is obtained from the web I suspect our software will be of limited use to you without internet access. Tom zia muhammad wrote: > Respected Dear Dr. > > I am teaching Bioinformatics at International Islamic University > Islamabad, Pakistan. I am teaching molecula Docking and Protein > Structure prediction, CHIMERA or HMMs methodology. I hvae done all > theoratical work but could not perform any practical due to lack of > softwares. I will thankful to you if you kindly provide me some basic > softwares in this respect. After basic knowledge and establishing > proper labs we will purchase relatd softwares but on initial basis we > need your help. I also could not download different softwares so can > you kindly send me on CD. > Your kind attention will be highly acknowledged. > > Please reply. > > Regards > > Zia > > > ******************************** > *Muhammad Zia* > *Room # 7, Hostel # 2* > *Quaid-i-Azam University,* > *Islamabad. Pakistan* > *45320* > *********************************ue

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display two volumes alternatively
by Montserrat Samso 13 Feb '07

13 Feb '07

Hi, I am trying to compare two cryoEM density maps of the same protein, the only difference between them is a conformational change. Is there a way to switch directly from one volume to the other without having to display both of them together in between? Thanks, Montserrat ------------------------------------------------------- Montserrat Samso, Ph.D. Assistant Professor Department of Anesthesia Research Brigham and Women's Hospital Harvard Medical School 75 Francis St. Boston, MA 02115 Tel: 617 7328107 Fax: 617 7326927 E-mail: msamso(a)zeus.bwh.harvard.edu -------------------------------------------------------- CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s). The information contained in this message may be private and confidential, and may also be subject to the work product doctrine. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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programmatic representation
by Randy Heiland 12 Feb '07

12 Feb '07

I'd like to be able to set the representation (wire, stick, bs, cpk) of a model programmatically, in this case, from a plugin. I was trying the following, but the newly displayed model would always be displayed in wire: self.model = ReadSDF.readSDF(tmpfile.name) chimera.openModels.add(self.model) #Midas.represent('stick', self.model) Midas.represent('cpk', self.model) Suggestions? thanks, Randy

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Re: [Chimera-users] opacity for stick representation in chimera
by Elaine Meng 12 Feb '07

12 Feb '07

Hi Jerome, First make a transparent color and then use it on the atoms/bonds - there are a handful of routes. You can make the transparent color using the Color Editor (under Tools... Utilities; click the Opacity to get a slider for that, then adjust the red/green/blue/opacity sliders as desired). This color can be used on atoms/bonds, ribbons, whatever (depending on the current target setting under Actions.. Color) by choosing "Actions... Color... from editor" or it can be used in coloring commands using the color name "fromeditor" Color Editor description: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/colortool.html Alternatively, you can make the transparent color with the command "colordef" and give it whatever name you want. The new color name can then be used in coloring commands. Color definitions are saved in sessions. Or, if you don't want to save sessions, just make a command file with all of your favorite color definitions and read it in whenever you want those colors defined. "colordef" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/colordef.html I hope this makes sense - feel free to write back if it doesn't! Best, E ----- 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 On Feb 11, 2007, at 5:14 PM, Jerome Nilmeier wrote: > Hi Elaine: > > I was wondering: can you adjust the opacity of the stick > representation in chimera? > > best, J

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xforms, cpk scale
by Randy Heiland 08 Feb '07

08 Feb '07

Is there a command to scale sphere of a CPK rep? Is there a command to save the current viewing transformation to a file and then read it back/apply it at a later time? Thanks, Randy

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Drawing Artifacts
by Albion Baucom 08 Feb '07

08 Feb '07

Using the latest stable current production release of Chimera, 1.2304, I have begun to experience some drawing problems that I never had in previous versions. Specifically I frequently get a thin wireframe rendering of my protein structure when I draw the structure as a ribbon with a volume open at the same time. This wire frame persists even when I turn the display of the molecule off in the model panel, and it also does not rotate or translate if the protein is selected as the only active object. In effect it leaves behind a ghost image. Curiously this representation alternates from a light gray/white color to black when I open dialog boxes. The artifact toggles on and off with the volume in some instances. My processing and graphics hardware have not changed recently, nor has operating system (Linux). I do not experience this behavior with my last version of Chimera, 1.2199; it never renders this artifact. I have a nVidia Geforce 6800GT graphics card with the nVidia Linux drivers 1.0-9746. My X11 server is version 6.8.2. Here is a screen image of this phenomenon http://msg.ucsf.edu:8100/~baucom/images/chimera_image.jpg I have rotate the model slightly to show that the thin wireframe stays behind. It is not a separate object in the model panel. Thanks Albion

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Morph Map
by Tom Goddard 07 Feb '07

07 Feb '07

I've added a Chimera extension called Morph Map http://www.cgl.ucsf.edu/chimera/experimental/morph_map/morphmap.html to the experimental features web page: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html It interpolates between two volume data sets and makes animations. The original version of this tool was written by Wei Zhang in Pawel Penczek's lab. Tom

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Re: [Chimera-users] Map Orientation for Symmetry Plug-in
by Tom Goddard 07 Feb '07

07 Feb '07

Hi Albion, Ok, I made the "fit map in map" tool print out a point on the rotation axis. The new code for use with Chimera 1.2318 is here: https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmap231… The zip file contains a directory FitMap that you put in your Chimera distribution under chimera/share or on Mac Chimera.app/Contents/Resources/share For more installation details see http://www.cgl.ucsf.edu/chimera/experimental/install.html This FitMap directory replaces your existing one. After restarting Chimera you can fit a helically symmetric map in a rotated copy of itself then get the axis point (shown in Favorites / Reply Log) and adjust the map origin (volume dialog Features / Origin and Scale) to put the axis point at (0,0,0). I described this in more detail in my previous message: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-February/001313.html The output of the axis point will be included in the next Chimera snapshot due out in one to three weeks. The matrix you sent me had no rotation, just a translation by 52 along z. You will need to rotate the map copy before fitting to get a meaningful rotation axis point. In fact I suspect the accuracy will be increased for rotations near 180 degrees rather than small rotations (e.g. 30 degrees). Tom Albion Baucom wrote: > Thanks Tom. > > OK, here is my rotation matrix after following your instructions > > 0.99944468 -0.03326699 0.00190528 -0.09024247 > 0.03326443 0.99944566 0.00136109 0.10539160 > -0.00194951 -0.00129696 0.99999726 52.82194789 > > Sorry, I forgot how to compute the rotation axis vector from this > matrix ... its been awhile since I had to do that manually ... its > pretty simple if I remember right. > > Any code to automate this would be greatly appreciated. > > Thanks again! > > Albion

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