[Chimera-users] Small molecule dimensions

[Tom Goddard]

Another idea is use the "measure inertia" command

     
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia

which prints the principal axes of inertia of the molecule and their 
lengths in the Reply Log.

     Tom


-------- Original Message --------
Subject: Re: [Chimera-users] Small molecule dimensions
From: Eric Pettersen <pett at cgl.ucsf.edu>
To: le monk <le_monk at hotmail.com>
Date: 4/21/10 11:37 AM
> On Apr 21, 2010, at 11:20 AM, le monk wrote:
>
>> Thank you Eric - this is really helpful. But as these are minimum x y 
>> z lengths then the reported dimensions will be different if the 
>> molecules coordinates were transformed.
>
> The function used in the script (coord()) uses untransformed 
> coordinates.  xformcoord() would use transformed coordinates.
>
>> Can this script be modified to give the minimum dimensions of the 
>> molecule (not just the x y z dimensions)?
>
> What would be the algorithm for computing that?
>
>> For example, can a box be drawn around the Van der Waal radii whose 
>> volume was the minimum possible for that molecule, and report the 
>> lengths of each of its dimensions?
>
> Again, how?
>
> You can get a rough estimate by using the Axes tool to draw an axis 
> along the principal axis of the molecule, with the axis radius equal 
> to the average atom-atom distance from the axis.  The axes information 
> can be saved to a file.
>
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
>
> --Eric
>
>> This would be really nice to directly compare the size of small 
>> molecules.
>>
>> Many thanks
>>
>>
>> ------------------------------------------------------------------------
>> CC: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
>> From: pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>
>> To: le_monk at hotmail.com <mailto:le_monk at hotmail.com>
>> Subject: Re: [Chimera-users] Small molecule dimensions
>> Date: Sun, 18 Apr 2010 07:52:31 -0700
>>
>> Yes, something like this:
>>
>> from chimera import openModels, Molecule
>> for m in openModels.list(modelTypes=[Molecule]):
>> print m.name
>> atoms = m.atoms
>> for dim in range(3):
>> atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim], 
>> a2.coord().data()[dim]))
>> print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - 
>> atoms[0].radius)
>> print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data()[dim] - 
>> atoms[-1].radius)
>>
>> Put the above in a file ending in ".py" and open it in Chimera and it 
>> will print the min/max xyz values accounting for radius in the Reply Log.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>> On Apr 16, 2010, at 10:46 AM, le monk wrote:
>>
>>     Hello,
>>
>>     I have a few pdb files of small molecules that I would like to
>>     know the dimensions of. Is it possible to use Chimera the measure
>>     the minimum x y z lengths - taking into account Van der Waals
>>     radii? Or perhaps you could suggest other software for this?
>>
>>     Many thanks
>>
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