[Chimera-users] showing points and confidence values

Tue Jun 14 16:03:27 PDT 2011

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 at 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 at 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 at 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 at 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 at 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 at 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>_______________________________________________
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> > > > Chimera-users at cgl.ucsf.edu
> > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> > >
> > >
> > >
> <trial5.xyz><image_stickman2.png>_______________________________________________
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> >
> >
> >
> >
> > <confidencecloud4.csv>_______________________________________________
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>
>
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