RE: [PyMOL] selecting residues around

[Warren D. <wa...@de...>]

Jason

Ah, I found the problem:

Sticks represent bonds, not atoms.  Normally, in order to see a bond, *BOTH*
atoms involved have to have either sticks or lines shown.  That's why you
weren't seeing anything until increasing the radius of the selection sphere,
which included the first bond atom and thus the first complete bond.

The solution is simple:

If you want to see half bonds, then "set half_bonds, on" and now you'll pick
up the rest of those missing atoms.

However, what I tend to do instead is:

show sticks, byres A// within 4 of C//
indicate A// within 4 of C//

since that way you see complete residues, with the proximal atoms being
selected...

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020
  

> -----Original Message-----
> From: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> Jason Thomas Maynes
> Sent: Friday, July 09, 2004 4:50 PM
> To: pym...@li...
> Subject: [PyMOL] selecting residues around
> 
> Hello:
> 
> I am trying to highlight residues that are within 4A of a 
> chain (but in a different chain):
> 
> I have tried:
> show sticks, c. c around 4 & c. a
> show sticks, c. a within 4 of c. c
> 
> Both show some residues within 4A but not all.  For example, 
> I can measure a distance of 3.3 A between 2 atoms in the 
> chains but these do not show up with the commands issued 
> above.  Interesting if I increase the distance cutoff to 4.1A 
> they do show up.  And some interactions that are >3.3A apart 
> do show up with the 4A cutoff.  Am I missing something?  This 
> is kind of scary since I cannot rely on the display to 
> consistently show me all residues within 4A.
> 
> Cheers,
> JTM
> 
> "We can be sure that if a detailed understanding of the 
> molecular basis of chemo-therapeutic activity were to be 
> obtained, the advance of medicine would be greatly accelerated."
> 
> Linus Pauling, Nobel Laureate 1954
> 
> "...everything that living things do can be understood in 
> terms of the jigglings and wigglings of atoms."
> 
> Richard Feynman, Nobel Laureate 1965
> 
> *************************
> Jason Thomas Maynes
> PhD/MD Program
> Department of Biochemistry
> Faculty of Medicine
> University of Alberta
> ja...@bi...
> *************************
> 
> 
> 
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