Re: [PyMOL] Finding distances along molecular tunnels

2012-04-03 Thread Thomas Holder 
Hi Sajeewa,

> [...]
> If I follow wizard --> measurements --> distance it asks for atoms to
> click on, but as the tunnels are empty space when I click on the
> starting points of the tunnels nothing is recognized.
> What would be the most accurate way of measuring the above two distances?

The tunnel is not really empty space, it's actually composed of 
pseudo-atoms and it's just a matter of visual representation. Hiding the 
surface and showing lines should be sufficient.

hide surface
show lines

Now try to use the measurement wizard.

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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[PyMOL] Finding distances along molecular tunnels

2012-04-02 Thread Sajeewa Pemasinghe 
Hello everyone,

I have 2 molecular tunnels inside one protein corresponding to two starting
points, created by the CAVER plugin. The two tunnels join to form one
common tunnel.

I want to measure

1) The distance between the two starting points of the tunnels

2) The distance from each starting point to the junction

If I follow wizard --> measurements --> distance it asks for atoms to click
on, but as the tunnels are empty space when I click on the starting points
of the tunnels nothing is recognized.
What would be the most accurate way of measuring the above two distances?

Thank you

Sajeewa Dewage
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