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

Tom Goddard goddard at sonic.net
Thu Nov 15 10:56:12 PST 2012

Hi Daniel,

   I see.  You'd like to control the contour level, color, surface/mesh 
style, step size... of all the copies as if they were one model instead 
of 100 different models, each a copy of the same map.  For making 
hundreds of copies of an atomic model, the multiscale dialog in Chimera 
does this using a single model.  But that doesn't currently work with 
maps.  One disadvantage of having a single model for all the copies of a 
map is that the maps will all have to have the same color, same step 
size, same contour level because all those properties are stored with 
the model. Maybe that restriction is fine for your use.  I would like to 
make that possible by allowing Chimera to place identical copies of any 
type of model by just specifying the list of positioning matrices.  The 
model would just remember the list of matrices for the different placements.

   For now using a hundred different models of the same map is 
workable.  You can't adjust all of them at the same time with the volume 
dialog.  But you can adjust one to figure out the contour level you like 
and then use one volume command to set the level for all the copies, for 
example, "volume #1-100 level 1.24 color yellow step 2".

   Another approach is to make a single map by adding your hundred 
placed copies on a single grid (e.g. the tomogram grid).  Then you open 
that one map and all the copies appear.  The drawback is that you may 
want finer grid spacing on the individual copies then you have with the 
tomogram, and that would make the map to large and slow to work with 
(and mostly empty).  If you are interested in trying this approach 
though you can use a command like "vop add #1-100 onGrid #0" to produce 
such a map after placing the hundred separate models with your current 
script.  Then save that new map and use it in the future instead of the 
100 copies.


-------- 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: 11/15/12 7:12 AM
> Hi Tom,
> thanks for the helpful explanation. The extension that you mention 
> you've been working on  seems interesting. I guess that will allow the 
> user to change the isosurface level in one single model to change it 
> in all the models simultaneously, am I right? This would solve another 
> problem I'm having with my scripts, as they fed each copy of the map 
> into Chimera as a different model. So, I'm looking forwards to trying 
> it when it becomes available.
> best,
> Daniel
>> 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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