To add my two cents, I am not at all a fun of stereo for routine use,
but I appreciate it if I have to look at a long ligand bent 90 deg in
the middle to bury in my protein, and all that at 3.0-3.5 A
resolution ... So, I must have both types of brain damage that Jan
refers to. No surprises here I guess.
A.
On Mar 23, 2011, at 3:16, Phoebe Rice wrote:
My 2 cents worth on the stereo-dependent:
1) They have carpal tunnel syndrome that makes it painful to keep
the molecule in motion while rebuilding it (NOTE: enough constant
mouse-wiggling and you will get carpal tunnel problems if you don't
have them yet!)
2) They work on big, low-resolution structures where you need to see
a bigger-picture view. I've had people tell me that can fit 3-3.5A
maps just fine without stereo, but having viewed their work, I beg
to differ.
Phoebe
---- Original message ----
Date: Tue, 1 Mar 2011 22:30:54 +0000
From: CCP4 bulletin board <[email protected]> (on behalf of Jan
Löwe <[email protected]>)
Subject: Re: [ccp4bb] while on the subject of stereo
To: [email protected]
Ah! The question of to stereo or not to stereo! There has to be a
scientific reason why this question is more popular than asking for
what
Linux distro is more fashionable this spring or why an Rmerge of
0.90 in
the outermost shell is good for you and your structure.
I am offering my two (conflicting) theories (and apologies that both
seem to imply some problem):
A) people who do use stereo have a problem with their brain because
they
cannot produce three dimensional vision from depth cues alone.
B) people who do not use stereo have a problem with their brain
because
they cannot see properly in three dimensions and rely on depth cues
alone.
I personally prefer people with A) when I am their passenger in a car
since they do not need to rotate by 90° to see how far the braking
lights of the car in front are away :-)
jan
On 01/03/2011 21:35, Jim Pflugrath wrote:
I will offer my view.
I hate stereo glasses and hate stereo in general.
One should be able to see 3D from the depth-cueing and by keeping
the view
in motion. For fitting, I like to flip the view by 90 degrees. I
know I am
going to move in displayX and displayY, but never in displayZ. I
then
rotate the view around the vertical axis so thatn the old displayZ
becomes
displayX.
Furthermore, I don't waste too much time fitting. I know the
software can
fit the map better than me, so I let it do its job. I only need
to get the
coordinates within the radius of convergence of the refinement
program. I
also know that 9 times out of 10, the displayed electron density
is probably
suspect, so I believe in stereochemistry more than I believe in
the map.
The main trick is to realize that as a human being, you really are
not that
good at fitting the map or that it is unnecessary to waste your
time since
the software is really so much better than you. Refinement is
quick enough
that you can try various hypotheses as in: "If I move this here,
then
refinement will do the trick" and "Well, that didn't work, so I
will move
that over there and see if refinement will do the trick."
As for stereo figures, you should be able to convey what you want
to say
from a good figure with depth-cueing, shadows, etc. Don't ever
use stereo
glasses in a public seminar. Maybe my opinion will change with
better
stereo technology.
OK, I know quite a lot of people will disagree with me. :)
Jim
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf
Of David
Roberts
Sent: Tuesday, March 01, 2011 10:29 AM
To: [email protected]
Subject: [ccp4bb] while on the subject of stereo
Hi again,
I'd like to ask a question about the pedagogy of stereo. That is,
using
stereo with students in the classroom.
Do you all find that, after setting up these elaborate stereo
devices,
students really use the stereo or do they tend not to?
I am a huge fan of stereo - and frankly here we have quite a few
options for
doing stereo - from the active Nvidia systems that people have
recently been
discussing to passive zalmans. ...
As I mentioned, I like stereo a lot, but really projecting on a
nice bright
lcd monitor also has it's advantages, and with the ease of moving
things
using the mouse (or whatever device you use), the overall need for
stereo
seems to be decreasing. I don't know - I just wonder what peoples
views are
out there for the actual "need" for stereo. It's incredibly cool
- and I
think is a very powerful way to show things - but I'm wondering if
we focus
too much on it because it's cool and not because it's pedagogically
necessary.
Just wondering, no worries. Thanks
Dave
P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
