Hi Chinmaya, I think the idea of making a 3-dimensional density map where "confidence" values correspond to intensity isn't going to make a useful visualization. If by confidence you mean how accurately the point is placed then maybe you should display each point as a sphere with the sphere radius proportional to "confidence". Chimera is for displaying atomic models where standard atom radii are used, but there are some quirky ways to change the radii to those specified in a file. One is to use the Chimera defattr command. Another approach is to rewrite your CSV file into a Chimera marker file which describes spheres with specific positions, radii and colors. All of these will require you to do some programming. Since you are trying to use a molecular visualization program for data that isn't much like a molecule you can't avoid that. We probably won't be able to do this programming for you -- too many actual molecule problems to solve! Tom
Dear Elaine,
First of all sorry for writing only a step at a time earlier.
well this is what exactly I want to do. I want to display the points as spread out gaussians of density and not simply dots or spheres. I expect to show the confidence values with different intensity/transparency. no I do not want to display anything else other than rotate, translate and making a movie out of them. Can you suggest me something?
Well what exactly is the image is of a stick man being imaged with different postures as apart of the project. So I have to open the stack of such images perform these viewpoint operations and make a movie out of it. Right now the imput of image is in .xyz format so it opens the spheres. But I also want to inlude the confidence values as described above. From a set of these images I want to make a movie.
Regards, Yours Sincerely, Chinmaya Joshi
On Mon, Jun 13, 2011 at 9:44 AM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Dear Chinmaya, Please describe the whole picture of what you want to do:
How do you expect to display the points? (spread out into Gaussians of density, or as dots or spheres? something else?)
How do you expect to show the confidence values (with colors? or making the spheres different sizes? something else?)
Are there other things you wanted to do with the display besides rotate, translate, make a movie?
It is impossible to answer well when you only ask about one step at a time. Sometimes a good way to do one step is not compatible with the next step.
Thanks Elaine
On Jun 13, 2011, at 7:06 AM, chinmaya joshi wrote:
> > Dear Elaine, > > > Thanks a lot for the molmap command. > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > Regards, > Chinmaya > On Mon, Jun 13, 2011 at 10:05 AM, chinmaya joshi <jchinu2014@gmail.com <mailto:jchinu2014@gmail.com>> wrote: > Hello Elaine, > > Can you please help in how to map this data (confidence map) in the following attachment. > It has a fourth dimension which is the confidence. > You can open the attachment with notepad. > > Regards, > Chinmaya > > > > On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi <jchinu2014@gmail.com <mailto:jchinu2014@gmail.com>> wrote: > Dear Elaine, > > > Thanks a lot for the molmap command. > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > Regards, > Chinmaya > On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > Hi Chinmaya, > Forget the script, just use the Chimera "molmap" command. That python script may have been written before we had the command. Now that you already figured out an input format and opened it in Chimera, you only need to show the command line (from Favorites menu in Chimera) and enter one "molmap" command, something like > > molmap #0 15 > > where the first number is the model number of the points and the second number is a resolution, related to Gaussian width. You may wish to use a different resolution, and there are other options, see > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> > > I would have mentioned "molmap" earlier if you had said you wanted to make a map from your points. > Elaine > > On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: > > > Hey Elaine, > > > > Thanks for the mail. > > > > Just open the file in notepad and save it as .xyz (dont need to do that I am attaching the file here now) > > Then I have just opened this .xyz file in chimera and chimera loads the desired image(attached: open with notepad or any text editor)(I have also attached the output image of chimera) > > > > Now my question is that > > How do I use the script calle xyzmap.py on the following link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > for opening the above file from the command line. > > what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py code with? > > > > Regards, > > Chinmaya > > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > > Hi Chinmaya, > > The way to see if Chimera opens your file is to either > > (A) look at the list of file types in the link I sent in the previous message, or > > (B) start Chimera, and try using File... Open in the menu. > > > > However, no: Chimera does not read a ".csv" file. You never said what your file is supposed to contain, but from the name and contents of the file it appears to be x,y,z coordinates of a bunch of dots. If you just want to display this as a bunch of dots or spheres in Chimera, you could convert this file (write a script to do it in any language you like) to the simple "BILD" text format described here: > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html> > > > > Then the "BILD" file (name it something.bild) can be opened in Chimera to display the dots or spheres. > > > > As I mentioned earlier I do not know python, and I don't recommend it in this case. Using python would require some knowledge of Chimera code. Instead use a Chimera command script. > > > > Just start Chimera, open the BILD file, show the Chimera command line (choose from the Favorites menu), try typing in commands. Figure out the movement commands you want, then put the commands and movie-recording commands in text file to make the Chimera script. Command "roll" does rotation, "move" does translation, "scale" does scaling, "movie" does the movie stuff. The script might be as simple as: > > > > movie record > > roll y 1 360; wait > > wait 10 > > movie stop > > movie encode mformat mov output /MyPath/mymovie.mov > > > > ... but you would need to look at the command documentation to see what options you want. There are links to that documentation and to example Chimera command scripts in my previous message. > > Elaine > > > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > > > Hello Elaine, > > > > > > Thanks a lot for your mail. I am working on the points you have suggested. However I am a bit confused whether my input files will work in chimera or not? > > > Herewith I am attaching a sample example of the dataset which I will be taking as the input, perform some viewpoint operation on it and then make a movie. > > > Can you please let me know whether this can be done in chimera or not? > > > If yes, can it be done in a python script file? > > > > > > Regards, > > > Chinmaya Joshi > > > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > > > Hi Chinmaya, > > > Before you start scripting, the first thing to consider is whether Chimera can do what you want. Have you tried doing what you want to show in the movie, but while using Chimera interactively? From your description, I am concerned that Chimera may not read your input format. The input types are generally 3D data files, not images. The one exception is that an image stack can be used as a "volume data" input format. Here is information on what formats Chimera can read: > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> > > > > > > If you think Chimera can do what you want, here is information on making movies, > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html> > > > > > > ...including commands for rotation and translation, etc. > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> > > > > > > ...and example scripts > > > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples> > > > > > > ...however, these examples are Chimera command scripts, not python scripts. I think python scripts would be more difficult to make than Chimera command scripts, and you would only start working with python if (A) Chimera can do what you want or nearly so, but (B) there are no Chimera commands for those things. After you figure out what you want to do by using Chimera interactively, then figure out the commands for those actions, then put them into a script. The last step would be to add movie recording commands to that script. > > > > > > I don't know python, so I can't say any more about using that approach. > > > > > > I hope this helps, > > > Elaine > > > ----- > > > Elaine C. Meng, Ph.D. > > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > > Department of Pharmaceutical Chemistry > > > University of California, San Francisco > > > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > > > Hello, > > > > I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. > > > > > > > > Can someone please let me know how it can be done. > > > > > > > > I am new to python. > > > > > > > > Can anyone tell me any good links for these? > > > > > > > > The documentation on chimera ucsf is a bit confusing. > > > > Thanks. > > > > Chinmaya > > > > > > > > > <pointcloud.csv>_______________________________________________ > > > Chimera-users mailing list > > > Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > <trial5.xyz><image_stickman2.png>_______________________________________________ > > Chimera-users mailing list > > Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > <confidencecloud4.csv>_______________________________________________ > Chimera-users mailing list > Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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