[Chimera-users] measure the vertical distance between aromatic planes

Repic Matej matej.repic at epfl.ch
Wed Aug 19 16:00:51 PDT 2015

Hi Bing Wang,

As I understand your question, you should actually be measuring the
distance between a plane and a centroid rather than another plane. The
planes in chimera, while shown as finite disks, are actually infinite
internally and thus only perfectly parallel planes will have a non-zero

On the other hand, if you are measuring the distance between plane p1 and
a centroid c2 lying on plane p2, you specify that chimera should measure
the shortest distance between a plane p1 and a defined point on plane p2.
This distance is measured along the perfectly "vertical" (e.g.
perpendicular to the plane p1) line from the plane p1 to the centroid c2.


Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
BCH 4108
CH - 1015 Lausanne


On 8/17/15, 20:12, "chimera-users-bounces at cgl.ucsf.edu on behalf of Elaine
Meng" <chimera-users-bounces at cgl.ucsf.edu on behalf of meng at cgl.ucsf.edu>

>Hi Bing Wang,
>It depends what you mean by ³vertical².  You can get the closest distance
>of two planes (considering them as infinite) by selecting both their rows
>in the axes/planes/centroid tables, or with  the distance command, for
>distance p1 p2
>However, there is no simple way to get the distance only along a specific
>I hope this helps,
>Elaine C. Meng, Ph.D.
>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>Department of Pharmaceutical Chemistry
>University of California, San Francisco
>> On Aug 13, 2015, at 7:54 PM, Wang, Bing <bingwang at ou.edu> wrote:
>> Hi Chimera,
>> Is there a way to measure the vertical distance of two planes in the
>>structure? I do know how to measure the angle between two planes or one
>>line and one plane by the Axes/Planes/Centroids in Chimera. I don't need
>>the distance of two centroid of two planes. I do need the vertical
>>distance of two planes. Could you please show me in detail?
>> Thanks a lot!
>> Bing Wang
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu

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