[COOT] regularize zone fits to density?

[Francis E Reyes]

Hi all

With the regularize zone button, does it fit it to the density and  
idealizes the residue or just the latter?

Thanks

FR



-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [COOT] regularize zone fits to density?

[Schubert, Carsten [PRDUS]]

Probably just the latter (guess on my part) If you need tighter geometry
you can decrease the matrix weight under Extensions->Refine->Set Matrix
for the real space refinement. The default (60, in 0.6pre) is suitable
for good density, set it lower for marginal density. That way you still
get good geometry and a decent density fit. 

Cheers,

Carsten

> -Original Message-
> From: Mailing list for users of COOT Crystallographic Software
> [mailto:c...@jiscmail.ac.uk] On Behalf Of Francis E Reyes
> Sent: Wednesday, August 05, 2009 9:05 AM
> To: COOT@JISCMAIL.AC.UK
> Subject: [COOT] regularize zone fits to density?
> 
> Hi all
> 
> With the regularize zone button, does it fit it to the density and
> idealizes the residue or just the latter?
> Thanks
> 
> FR
> 
> 
> 
> -
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> 
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
> 
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

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

[William Scott]

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

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