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Hi Veysel,<br>
<br>
Ok, I put a script xyzsdmap.py on the Chimera scripts web page that
reads x,y,z and sigma x, sigma y, sigma z values (6 column text file)
and makes the volume data set from Gaussians using those parameters.
If you also have different amplitudes for the points that could be
handled by reading another column and modifying the "weights" array in
the script.<br>
<br>
<a class="moz-txt-link-freetext" href="http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a>
<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] loading atomic coordinates without drawing
or calculating bonds<br>
From: Veysel Berk<br>
To: Tom Goddard <br>
Date: 8/5/09 1:31 PM<br>
<blockquote type="cite">Dear Tom,
<br>
<br>
It looks like a great idea. I will try both options today and let's see
of it works for me.
<br>
<br>
Thanks very much for your advise.
<br>
<br>
would it be possible to implement to define three more column on the
xyz file for standard deviations of Gaussians in each dimensions to
calculate the volume data in future releases of the script? Is it
technically doable? My localization data have x, y, z and sigx, sigy,
sigz.
<br>
<br>
Bests,
<br>
<br>
Veysel Berk
<br>
Department of Molecular & Cell Biology
<br>
University of California, Berkeley
<br>
<br>
<br>
On Aug 5, 2009, at 10:34 AM, Tom Goddard <a class="moz-txt-link-rfc2396E" href="mailto:goddard@cgl.ucsf.edu"><goddard@cgl.ucsf.edu></a>
wrote:
<br>
<br>
<blockquote type="cite">Hi Veysel,
<br>
<br>
You will have a rough time trying to open 1 million atoms in Chimera
because it is very memory inefficient, taking about 2 Kbytes per atom.
So 1 million atoms will take about 2 Gbytes and this is unlikely to
work with 32-bit versions of the program. Only the 64-bit linux
version is likely to handle it.
<br>
<br>
You are probably better off making a volume data set from your million
points. There is a Python Chimera script called xyzmap.py you can use
to do this.
<br>
<br>
<a class="moz-txt-link-freetext" href="http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a>
<br>
<br>
Each point is treated as a Gaussian of specified width. After making
the map you can save it with the volume dialog File / Save Map As...
menu entry or the volume command.
<br>
<br>
Tom
<br>
<br>
-------- Original Message --------
<br>
Subject: [Chimera-users] loading atomic coordinates without drawing
or calculating bonds
<br>
From: Veysel Berk
<br>
To: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
<br>
Date: 8/5/09 2:52 AM
<br>
<blockquote type="cite"><br>
Hello,
<br>
<br>
I am trying to load a large atomic coordinates file in xyz format.
<br>
The atomic coordinates are meaningless to crystallography in terms
<br>
of distances of atoms and as a result, while chimera try to load
<br>
the coordinate and calculate the bonding between atoms, it crashes
<br>
or suspends for ever. The data is from single molecule
<br>
localization experiments where I want to use chimera to visualize
<br>
this 3D data by treating each localization as an atom. I am trying
<br>
to load about a million atoms.
<br>
<br>
Is it possible to turn off automatic bonding calculations and only
<br>
show atoms without bonds to prevent crashing? or does anyone know
<br>
any simple method or software to convert atomic coordinates into
<br>
voxel map which I can use in volume visualizer module of chimera
<br>
without worrying about bond calculations?
<br>
<br>
Thanks in advance,
<br>
<br>
Bests,
<br>
<br>
Veysel Berk
<br>
<br>
<br>
</blockquote>
<br>
</blockquote>
</blockquote>
<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] loading atomic coordinates without drawing
or calculating bonds<br>
From: Tom Goddard<br>
To: Veysel Berk<br>
Date: 8/5/09 10:34 AM<br>
<blockquote cite="mid:4A79C2BB.3010604@cgl.ucsf.edu" type="cite">
<pre wrap="">Hi Veysel,
You will have a rough time trying to open 1 million atoms in Chimera
because it is very memory inefficient, taking about 2 Kbytes per atom.
So 1 million atoms will take about 2 Gbytes and this is unlikely to work
with 32-bit versions of the program. Only the 64-bit linux version is
likely to handle it.
You are probably better off making a volume data set from your million
points. There is a Python Chimera script called xyzmap.py you can use
to do this.
<a class="moz-txt-link-freetext" href="http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a>
Each point is treated as a Gaussian of specified width. After making
the map you can save it with the volume dialog File / Save Map As...
menu entry or the volume command.
Tom
-------- Original Message --------
Subject: [Chimera-users] loading atomic coordinates without drawing or
calculating bonds
From: Veysel Berk
To: <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
Date: 8/5/09 2:52 AM
</pre>
<blockquote type="cite">
<pre wrap=""> Hello,
I am trying to load a large atomic coordinates file in xyz format.
The atomic coordinates are meaningless to crystallography in terms
of distances of atoms and as a result, while chimera try to load
the coordinate and calculate the bonding between atoms, it crashes
or suspends for ever. The data is from single molecule
localization experiments where I want to use chimera to visualize
this 3D data by treating each localization as an atom. I am trying
to load about a million atoms.
Is it possible to turn off automatic bonding calculations and only
show atoms without bonds to prevent crashing? or does anyone know
any simple method or software to convert atomic coordinates into
voxel map which I can use in volume visualizer module of chimera
without worrying about bond calculations?
Thanks in advance,
Bests,
Veysel Berk
</pre>
</blockquote>
<pre wrap=""><!----></pre>
</blockquote>
<br>
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