[Chimera-users] viewing same size atoms within multiple molecules

Elaine Meng meng at cgl.ucsf.edu
Mon Jun 10 09:21:57 PDT 2019

My answer pertains to showing different molecules at the same time, but not if you are opening them one by one, as the view is automatically scaled in Chimera and big molecules will be shown smaller so that they fit in the window.

Once I realized you were the same person who asked about voxel coordinates, I think that may be what you meant.  In that case, don’t understand why you are using Chimera at all; might as well just use the PDB files defining the atomic structures directly.


> On Jun 10, 2019, at 9:13 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Andrew,
> Well, there are a couple of things going on:
> (1) perspective (closer things are bigger)
> (2) different radii for different atom types, when shown in “sphere” style (full VDW radius) or “ball” (scaled VDW radius)
> You can turn off perspective with command: set projection orthographic
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#projection>
> There are several ways to change VDW radii, including command “vdwdefine”… see the bottom section of this page:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>
> For example, to make all carbon atoms have radius 1.5, command: vdwdefine 1.5 C
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Jun 10, 2019, at 7:46 AM, Andrew Garven <garvena at mcmaster.ca> wrote:
>> Hi,
>> I am trying to implement a script so that each individual atom in each molecule I view on chimera is the same size (ie each carbon atom i view, regardless of the size of the molecule views a the same size). I realize this must be a function of the scale factor which changes the size of the molecules to appropriate viewing size. Is there a way to properly scale each molecule so that they have a standard atom viewing size.
>> I would appreciate any help in this regard. 
>> Andrew 

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