Dear Bing,

Here a few remarks from my side: 
Most graphics programs have options to click on two atoms to get a distance and to click on three atoms to get an angle. The only problem is that you need atoms where you can click on. One way is to calculate the coordinates of the start and end points of the vectors you want to display and generate dummy atoms for these positions and insert these with a text editor in your pdb file. Using LINK records, or using the make link option, you can create "bonds" between these "atoms" to display the vectors. You can also click on the dummy atoms to get the distances, angles etc. you need. 

Another, more fundamental point is that the resolution normally obtained in protein crystal structures, is not sufficient to decide on the basis of experimental data whether a bond is single or double. Also the refinement programs use parameter files with contain assumptions whether a bond is single or double and you get back the distance which was specified in your parameter file. What I do in these cases is generate parameter files for both possibilities, say with a single and with double bond and do parallel refinements with both options. Afterwards I compare the results in a graphics program and especially check things like: are the atoms in the center of the electron density or at the edge? Does positive and/or negative difference density appear, gets the molecule distorted during refinement? Especially in cases of sp2/sp3 hybridisation and planar/non planar molecules it is often possible to find out which possibility fits best with the data.

Good luck!
Herman

-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Wang, Bing
Gesendet: Freitag, 14. August 2015 14:59
An: [log in to unmask]
Betreff: Re: [ccp4bb] Pymol question: measure the angle between a line and a plane

I am sorry to post this off-topic pymol question here.  Thank everyone here for the replies!

The question I give is a "simple" or boring question of the standard trigonometry. However these questions are necessary to be answered for bio-inorganic application (e.g. single bond or double bond, from possible electron distribution to possible reaction mechanism, or you want to know the possible drug insertion  between two Trps) when you have very high resolution protein structures or you have a high resolution of small molecule.

The problem is, it is hard to precisely measure these parameters from the standard trigonometry in a 3D space within a display software because it is relate to the many vectors in a 3D space. The hardest part is to display these vectors and measure either the angle or distance among them. I don't think most people know how to do this kind of job and how to access these parameters easily, visibly.

Later, concluded email will be posed for the methods you guys listed here when I have a little bit free time, especially I am still waiting some important relies from PSICO.

Thanks!

Bing
________________________________________
From: Adrian Goldman [[log in to unmask]]
Sent: Friday, August 14, 2015 5:15 AM
To: Wang, Bing
Subject: Re: [ccp4bb] Pymol question: measure the angle between a line and a plane

Bing,

        I don't wish to sound unsympathetic, but these are part of standard trigonometry.

                                                Adrian Goldman


Adrian Goldman, Ph. D.
Division of Biochemistry,
Biological and Environmental Sciences,
P. O. Box 56, Viikinkaari 5
FIN-00014 University of Helsinki
Finland
Tel:            +358 29 41589087
email:  [log in to unmask]

School of Biomedical Sciences
Faculty of Biological Sciences,
University of Leeds
Leeds
West Yorkshire
LS2 9JT
United Kingdom
Tel:            +44 113 343 8537
email:  [log in to unmask]