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Hi Chinmaya,<br>
<br>
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!<br>
<br>
Tom<br>
<br>
<blockquote
cite="mid:BANLkTinYS4TErLxq0gSgp8aCePCW0dtC-Q@mail.gmail.com"
type="cite">Dear Elaine,<br>
<br>
First of all sorry for writing only a step at a time earlier.<br>
<br>
well this is what exactly I want to do.<br>
I want to display the points as spread out gaussians of density
and not simply dots or spheres.<br>
I expect to show the confidence values with different
intensity/transparency.<br>
no I do not want to display anything else other than rotate,
translate and making a movie out of them.<br>
Can you suggest me something?<br>
<br>
Well what exactly is the image is of a stick man being imaged with
different postures as apart of the project.<br>
So I have to open the stack of such images perform these viewpoint
operations and make a movie out of it.<br>
Right now the imput of image is in .xyz format so it opens the
spheres.<br>
But I also want to inlude the confidence values as described
above.<br>
From a set of these images I want to make a movie.<br>
<br>
Regards,<br>
Yours Sincerely,<br>
Chinmaya Joshi<br>
<br>
<div class="gmail_quote">On Mon, Jun 13, 2011 at 9:44 AM, Elaine
Meng <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Dear Chinmaya,<br>
Please describe the whole picture of what you want to do:<br>
<br>
How do you expect to display the points? (spread out into
Gaussians of density, or as dots or spheres? something else?)<br>
<br>
How do you expect to show the confidence values (with colors?
or making the spheres different sizes? something else?)<br>
<br>
Are there other things you wanted to do with the display
besides rotate, translate, make a movie?<br>
<br>
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.<br>
<br>
Thanks<br>
Elaine<br>
<br>
On Jun 13, 2011, at 7:06 AM, chinmaya joshi wrote:<br>
<br>
><br>
> Dear Elaine,<br>
><br>
><br>
> Thanks a lot for the molmap command.<br>
><br>
> I want to map the x,y,z co-ordinates and the intensity of
each pixel.<br>
><br>
> Regards,<br>
> Chinmaya<br>
> On Mon, Jun 13, 2011 at 10:05 AM, chinmaya joshi <<a
moz-do-not-send="true" href="mailto:jchinu2014@gmail.com">jchinu2014@gmail.com</a>>
wrote:<br>
> Hello Elaine,<br>
><br>
> Can you please help in how to map this data (confidence
map) in the following attachment.<br>
> It has a fourth dimension which is the confidence.<br>
> You can open the attachment with notepad.<br>
><br>
> Regards,<br>
> Chinmaya<br>
><br>
><br>
><br>
> On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi <<a
moz-do-not-send="true" href="mailto:jchinu2014@gmail.com">jchinu2014@gmail.com</a>>
wrote:<br>
> Dear Elaine,<br>
><br>
><br>
> Thanks a lot for the molmap command.<br>
><br>
> I want to map the x,y,z co-ordinates and the intensity of
each pixel.<br>
><br>
> Regards,<br>
> Chinmaya<br>
> On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng <<a
moz-do-not-send="true" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>>
wrote:<br>
> Hi Chinmaya,<br>
> 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<br>
><br>
> molmap #0 15<br>
><br>
> 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<br>
> <<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html"
target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a>><br>
><br>
> I would have mentioned "molmap" earlier if you had said
you wanted to make a map from your points.<br>
> Elaine<br>
><br>
> On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote:<br>
><br>
> > Hey Elaine,<br>
> ><br>
> > Thanks for the mail.<br>
> ><br>
> > Just open the file in notepad and save it as .xyz
(dont need to do that I am attaching the file here now)<br>
> > 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)<br>
> ><br>
> > Now my question is that<br>
> > How do I use the script calle xyzmap.py on the
following link <a moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts"
target="_blank">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><br>
> > for opening the above file from the command line.<br>
> > what should I replace the 'xyz_path' and the
'xyz_list' in the xyzmap.py code with?<br>
> ><br>
> > Regards,<br>
> > Chinmaya<br>
> > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng <<a
moz-do-not-send="true" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>>
wrote:<br>
> > Hi Chinmaya,<br>
> > The way to see if Chimera opens your file is to
either<br>
> > (A) look at the list of file types in the link I
sent in the previous message, or<br>
> > (B) start Chimera, and try using File... Open in the
menu.<br>
> ><br>
> > 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:<br>
> > <<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html"
target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html</a>><br>
> ><br>
> > Then the "BILD" file (name it something.bild) can be
opened in Chimera to display the dots or spheres.<br>
> ><br>
> > 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.<br>
> ><br>
> > 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:<br>
> ><br>
> > movie record<br>
> > roll y 1 360; wait<br>
> > wait 10<br>
> > movie stop<br>
> > movie encode mformat mov output /MyPath/mymovie.mov<br>
> ><br>
> > ... 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.<br>
> > Elaine<br>
> ><br>
> > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote:<br>
> ><br>
> > > Hello Elaine,<br>
> > ><br>
> > > 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?<br>
> > > 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.<br>
> > > Can you please let me know whether this can be
done in chimera or not?<br>
> > > If yes, can it be done in a python script file?<br>
> > ><br>
> > > Regards,<br>
> > > Chinmaya Joshi<br>
> > ><br>
> > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng
<<a moz-do-not-send="true" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>>
wrote:<br>
> > > Hi Chinmaya,<br>
> > > 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:<br>
> > > <<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html"
target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html</a>><br>
> > ><br>
> > > If you think Chimera can do what you want, here
is information on making movies,<br>
> > > <<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html"
target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html</a>><br>
> > ><br>
> > > ...including commands for rotation and
translation, etc.<br>
> > > <<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands"
target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands</a>><br>
> > ><br>
> > > ...and example scripts<br>
> > > <<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples"
target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples</a>><br>
> > ><br>
> > > ...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.<br>
> > ><br>
> > > I don't know python, so I can't say any more
about using that approach.<br>
> > ><br>
> > > I hope this helps,<br>
> > > Elaine<br>
> > > -----<br>
> > > Elaine C. Meng, Ph.D.<br>
> > > UCSF Computer Graphics Lab (Chimera team) and
Babbitt Lab<br>
> > > Department of Pharmaceutical Chemistry<br>
> > > University of California, San Francisco<br>
> > ><br>
> > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi
wrote:<br>
> > ><br>
> > > > Hello,<br>
> > > > 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.<br>
> > > ><br>
> > > > Can someone please let me know how it can
be done.<br>
> > > ><br>
> > > > I am new to python.<br>
> > > ><br>
> > > > Can anyone tell me any good links for
these?<br>
> > > ><br>
> > > > The documentation on chimera ucsf is a bit
confusing.<br>
> > > > Thanks.<br>
> > > > Chinmaya<br>
> > ><br>
> > ><br>
> > >
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