[Chimera-users] help

chinmaya joshi jchinu2014 at gmail.com
Mon Jun 13 07:06:03 PDT 2011


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