[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
distance.

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.

Best,
Matej



------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
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>
wrote:

>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
>example:
>
>distance p1 p2
>
>However, there is no simple way to get the distance only along a specific
>direction.
>I hope this helps,
>Elaine
>----------
>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
>
>
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