Re: [COOT] Zalman Coot

[Bernhard Lohkamp]

You can use the command:

(set-hardware-stereo-angle-factor -1)

to invert the image too. I shall make some buttons for this (and the
Zalman stereo too).
Additionally I am thinking of querying the window position and size to
automatically set this.
Not sure when I'll get to this though (other issues more burning
currently)...

B

 ;; These should be even numbers to keep the stereo
 ;; the right way around
 (set-graphics-window-position 0 0)
 (set-graphics-window-size 1680 1050)
 
 In general, if the image is inverted, just move the window up or 
 down 1
 pixel.
 
 
 
 On Thu, August 6, 2009 8:04 am, James Partridge wrote:
  Has anyone noticed that the 3D image in coot is inverted?  Things 
 that are
  in the front on
  the mono image are switched to the back in the Zalman mode image.
  PyMOL has an option to flip the polarization of the image.  Is 
 there a
  similar command for
  coot?  Or is there a monitor setting that anyone has figured out?
 
  Thanks
  James
 
 
 
 
 William G. Scott
 
 Contact info:
 http://chemistry.ucsc.edu/~wgscott/
 

Re: [COOT] Zalman Coot

[William G. Scott]

Dear Jürgen:

I've been using the DVI cable provided and full resolution (I had to  
set this manually in display preferences).  I assume what works with  
my mini and my airbook would also work with a macbook pro.  I haven't  
tried the VGA option, but assume that would work too.


One thing I discovered is it doesn't work if you have display  
mirroring on.  If that is the case, turn it off in display  
preferences, and hopefully it will then work.


If not, try tilting the screen up or down a little bit (or move your  
head relative to the screen).


I went through a bit of frustration but it was all due to user error  
on my part.


Is the DVI cable just dead?

Did you issue the command in coot to start the stereo specific to  
Zalman mode?


Try the latest PyMOL too.  You have to rename it MacPyMOLZalman.app  
first.  Then open it, and if it isn't already in stereo, just hit the  
stereo menu item.


Depending on the positioning of the window, and number of pixels, you  
can have the image reversed, so check to see if that is happening, as  
it ruins the 3D effect.


Good luck.  Hope it is working for you soon.

Bill


On Aug 5, 2009, at 11:46 AM, Jürgen Bosch wrote:


Hi Bill,

I have received my two Zalmans yesterday and I wanted to try them  
out today. I don't seem to have the right settings I assume as I get  
a double vision image e.g. a loop that is supposed to be in the back  
in 3d splits up and you can see two lines (that's as Calpha). I have  
played with the resolution of the monitor to decrease it to 768x1024  
but the two lines still persist.
I'm using the latest  15 MacBookPro via MiniDisplayport to VGA as  
the DVI does not seem to work with the cable provided by Zalman I  
assume.


My coot is
0.6-pre-1 rev 2037

I turned of spaces and enabled mirroring to keep it simple but I'm  
not quite happy right now. I have not yet tried Pymol as my version  
does not support the Zalman monitors.


Any suggestions what I can try to get rid of the double lines ?

Thanks,

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.me.com/bosch_lab/

Re: [COOT] Zalman Coot

[Paul Emsley]

Coot will only work with Zalman with revision 2134+

Paul.


William Scott wrote:

I should add that I can only confirm that it works post revision 2134

The latest in fink is 2172.  I'll make a new intel stand-alone if that 
helps.



On Aug 5, 2009, at 11:46 AM, Jürgen Bosch wrote:


My coot is
0.6-pre-1 rev 2037