[Chimera-users] Radius of Gyration questions

George Tzotzos gtzotzos at me.com
Fri Apr 7 11:16:43 PDT 2017


Hi Elaine,

The reason I asked is because I’ve measured the radius of gyration of a particular ligand during the course of an MD trajectory using AmberTools. Comparing the mean radius of gyration of the ligand during the trajectory with the corresponding value generated by the Chimera script, the difference is by a factor of 4. AmberTools radius of gyration is also in angstrom.

Have a good day

George

> On 7 Apr 2017, at 19:58, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi George,
> Units would be the same as your atomic structure coordinates, so yes, angstroms if you are just using “regular” PDB files.  I’m not sure why you would expect different units.
> Best,
> Elaine
> 
>> On Apr 7, 2017, at 10:48 AM, George Tzotzos <gtzotzos at me.com> wrote:
>> 
>> Thank you Eric,
>> 
>> The problem was exactly what you identified. I assume the units are in Angstrom
>> 
>> George
>> 
>>> On 7 Apr 2017, at 01:46, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>> 
>>> Hi George,
>>> 	First, that script measures the radius of gyration for all the atoms in a model, not just ligands atoms or some subset of the model’s atoms.  So, my best guess is that the model that’s from your MD simulation has a lot solvent atoms that Chimera isn’t displaying by default.  So you should check that there are the same number of atoms in both models.  One way to do that is with the command:
>>> 
>>> sel #0  (number of selected atoms [all of model 0] shown in the status line)
>>> sel #1  (same thing for model 1).
>>> 
>>> 	If the difference in the models is the solvent you would want to use the command “delete solvent” before running the gyration script.
>>> 
>>> —Eric
>>> 
>>> 
>>> 	Eric Pettersen
>>> 	UCSF Computer Graphics Lab
>>> 
>>> 
>>>> On Apr 6, 2017, at 12:35 PM, George Tzotzos <gtzotzos at me.com> wrote:
>>>> 
>>>> Taking a reference PDBID 3n7h, I’ve generated for an MD simulation topology and restart files.
>>>> 
>>>> I’ve loaded on Chimera 3n7h and then the starting frame of the MD simulation. 
>>>> Used the MatchMaker and found perfect superposition of the protein backbone and two ligands (3n7h is #0 and the ligands #0:129.A and #0.132.B
>>>> 
>>>> I run the radius of gyration script (see attached). I found that the radii of gyration for the ligands in the two models are completely different.
>>>> 
>>>> #0 center of mass: 12.6543 10.4356 15.4086, radius of gyration: 21.182
>>>> #1 center of mass: 42.7381 42.5171 42.6163, radius of gyration: 37.390
>>>> 
>>>> I don’t follow why this is so. Any explanation would be most welcome.
>>>> 
>>>> A second question regards the units of the radii of gyration. Are they Angstrom or nm?
>>>> 
>>>> Thank you in advance
>>>> 
>>>> George
>>>> 
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>> 
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