if there are two planes which are not parallel to each other, we may have to define a center of each plane, then get the vertical distance1 between center1 and plane2 and the second vertical distance2 between center2 and plain1. if they are not parallel, distance 1 is not equal to distance2. if follow this idea (i am not sure it is correct or not), I just figure out how to measure it by Chimera. I am also curious how to measure it by PYMOL.
I should tell more about my aim to get this kind of parameters. I want to get this answers because we want to know how overlap the orbital of ligand with some metals in protein. this can help us to undersdand how the ligand interact with metal (e.g. nitric oxide can bind with Fe with liner or bent mode), in furthur we can know the reactivity for each of different of interaction (e.g. the liner mode of NO is more electrophilic and more reactive with thiols). Anyway~~~
Thanks!
Bing
________________________________________
From: Ronald E Stenkamp [[log in to unmask]]
Sent: Friday, August 14, 2015 10:47 AM
To: Wang, Bing
Subject: Re: [ccp4bb] Pymol question: measure the angle between a line and a plane
Hi.
I'm confused by your question. I don't know what you mean by "vertical". If the planes are parallel, I assume "vertical" means along the line perpendicular to them. If you have two planes that are not parallel to one another, how do you define "vertical"? I think most structure analysis programs, especially those found in the small molecule crystallography programs, determine the distance between the centers of the planes.
I'm not familiar with the most current small molecule crystallography programs, but older programs had the ability to calculate the equation of a plane through several atoms. They could also do that for several planes and calculate the distances and dihedral angles between them.
Ron
On Fri, 14 Aug 2015, Wang, Bing wrote:
> I really appreciated your help! It works perfectly!!!
>
> Can i ask another question? Sorry to keep bother you! Is it possible to measure the vertical distance between two planes by PSICO? I really like this powerful tool. Not the distance between two pseudoatoms in the center of two planes. I want to get the vertical distance of the two planes in space.
>
> Thank you very much!
>
> Bing Wang
> ________________________________________
> From: Thomas Holder [[log in to unmask]]
> Sent: Thursday, August 13, 2015 5:18 PM
> To: Wang, Bing
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Pymol question: measure the angle between a line and a plane
>
> Hi Bing,
>
> here's your PyMOL + PSICO solution:
>
> ring_sele = '...' # selection expression of ring atoms
> line_sele = '...' # selection expression of two atoms
>
> import math
> import chempy.cpv
> import psico.orientation
>
> ring_normal = psico.orientation.plane_orientation(ring_sele, guide=0)[1]
> line_direction = psico.orientation.cafit_orientation(line_sele, guide=0)[1]
> angle = chempy.cpv.get_angle(ring_normal, line_direction)
>
> print 'angle: ', math.degrees(angle), 'degrees'
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On 13 Aug 2015, at 15:12, Wang, Bing <[log in to unmask]> wrote:
>
>> Hi Heroes,
>>
>> Does anybody know how to measure the angle between a line (e.g. a line between two atoms) and a plane (e. g. a plane from aromatic ring) in PYMOL. I do know how to use PISCO to measure the angle between two planes. I am not sure whether I can still use PISCO in this case, or I do need another plugin, or some any other methods. Please show me the details.
>>
>> Thank you very much!
>>
>> Bing Wang
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
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