[sharp-discuss] xtalview/coot setup

[Clemens Vonrhein]

Dear Sid,

the command xtalview-setup is for XtalView configuration on the SERVER
(not the client - which is the machine you are running your
firefox/mozilla/xyz browser on). The only reason for the
xtalview-setup command is to tell the server where the skeletonisation
program is (for looking at electron density maps with a skeleton). But
the skeletons in XtalView aren't that nice (I think). The once in Coot
are better and the ones in O (via G. Kleywegt's MAPMAN program) are
the best (I think).

You're getting an error when looking at maps with XtalView probably
because that Xtalview skeletonisation program doesn't work on your
machine. Solution:

  - go to your main SHARP Control panel
  - enter the Preferences page
  - disable the skeleton options in the viewer section

Anyway, coming back to your setup for the client/browser for coot: in
$BDG_home/bin/helpers.local you need to set a variable CootSetup to
point to a sh-script, e.g.

  CootSetup=/where/ever/coot_setup.sh

This sh-script it points to can contain anything you want, as long as
after 'sourcing' it the command 'coot' is in the PATH and is
working. E.g. with the latest 0.3.3 release of coot it could contain
a single line like

  PATH=/public/xtal/Coot/Linux-bubbles/bin:$PATH

When you then select to view maps with Coot from the SHARP/autoSHARP
interface, your browser might ask the very first time what to do with
it. You need to give it the path to

  $BDG_home/bin/helpers.x-coot

(obviously with $BDG_home substituted by the correct value of your
installation directory).

Hope that helps ...

Cheers

Clemens

On Fri, Jul 06, 2007 at 01:55:45PM +0100, Sudharsan Sridharan wrote:
> Dear all,
> 
> I've installed sharp/autosharp just yesterday and it works fine. But
> I've tried setting up for xtalview using xtalview-setup. during the
> setup the right directory where xtalview resides was picked up. After
> the jobs were finished, when I click on the Plot/Script buttons to
> display maps choosing xtalview I get "Internal server error". I did
> not get any error messages when I ran xtalview-setup. and I've tried
> typing in the xtalview directory manually when asked for the path. Do
> i need to setup anything else for this to work? and also how can I
> setup coot ?
> 
> I'd appreciate you help.
> 
> Thanks,
> Sid.
> 
> -- 
> Sudharsan Sridharan
> Dept. of Biochemistry
> Cambridge University
> 80 Tennis Court Road
> Cambridge CB2 1GA
> UK.
> Ph: +44-01223-766028 (Office)
> 
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> 

-- 

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