[Chimera-users] Using marker files to place oriented density maps inside a tomogram

Tom Goddard goddard at sonic.net
Wed Nov 14 13:47:11 PST 2012


Hi Daniel,

   You can use a Chimera marker file but that only knows how to place 
spheres.  If you wanted to make use of the "map" and "matrix" attributes 
you added to the markers then that would require some extra Python 
script.  That could be done -- it is just a different format of input 
from the script I sent you.

   If you can't display hundreds of copies of the map due to slow 
graphics then it doesn't matter how you input the data.  Having hundreds 
of copies of the same map open doesn't load the map data more than 
once.  So you shouldn't run out of memory.  But the surface for each map 
might have a million triangles and it does make a separate surface copy 
for each copy you place in your tomogram.  Of course you won't see the 
detail in a tiny map put into a tomogram so the solution would be to 
display a very coarse image of the map that is being placed many times 
in the tomogram.   I've worked recently on making Chimera display 
multiple copies of identical objects without making copies of the 
surface in memory -- just reuse the same surface.  But it is not in 
Chimera yet.  And your graphics speed will still become unusable if you 
try to display too many copies with too much detail.  So the main need 
is to show an appropriate low level of detail for all or most of your 
hundreds of copies.

     Tom


-------- Original Message --------
Subject: Re: [Chimera-users] Using marker files to place oriented 
density maps inside a tomogram
From: Daniel Castano Diez
To: Tom Goddard
Date: 11/14/12 1:28 PM
> Hi Tom,
>
> thanks for the answer. Actually I already wrote some scripts for 
> placing each different copy of the density map as an individual model, 
> but this is not practical for placing hundreds of copies (as it's the 
> case with tomograms).  I will try your python script.
>
>
> I was under the impression that a .cmm markerfile was a better 
> approach, as I though that one could define a marker with more 
> attributes as in the example:
>
> <marker id="1" x="-6.1267" y="17.44" z="-3.1338" radius="0.35217"/>
>
> I mean, something like:
>
> <marker id="1" x="-6.1267" y="17.44" z="-3.1338"  map ="my_map.em"  
> matrix = "my_matrix.txt" />
>
> or similar with quaternions or euler angles... but I guess that was 
> wrong? That'll be a pitty,  as I am interfacing Chimera with the 
> subtomogram averaging package Dynamo and the most stable way seemes to 
> be having Dynamo converting its "table" files (lists of positions and 
> angles) into .cmm files that could then be directly fed into Chimera.
>
> Thanks!
>
> Daniel
>
>
>
>
>> Hi Daniel,
>>
>>   Take a look at the placem.py script which can place copies of maps 
>> or molecules at specified positions.
>>
>>     http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts
>>
>> It specifies the rotation as a quaternion which is close to a 
>> rotation axis and angle description.  I could show you how to adapt 
>> it to use Euler angles or a 3x3 rotation matrix if you like.
>>
>>     Tom
>>
>>
>>
>>> Hi,
>>>
>>> I'd like to use a Chimera marker file to place multiple copies of a 
>>> density map in different spatial positions inside a tomogram. My 
>>> input is thus a single map file a set of 3d locations, each attached 
>>> to an euler triplet (or a rotation matrix)
>>>
>>> With the documentation I could find
>>>
>>> http://www.cgl.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html 
>>> it is explained how to place spheres without orientation in a 
>>> volume, but I was not able to figure out how to place a density map 
>>> at those locations, and also how to impart a different orientation 
>>> to the density map located at each position.
>>>
>>> My question is: where could I find a description of the marker file 
>>> syntax that describes this functionality?
>>>
>>> thanks,
>>> Daniel
>>>
>>>
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>>>
>>
>>
>
>
>
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