[cmview-users] problem in displaying triangle contact map instead of square

[M. F.]

Dear supporting team,


Do I need to elaborate on something? or no one has seen my email?
I read a little about MySQL and cannot understand why this error even appears?
Although, I don't 
understand what is the relation between having MySQL on your computer 
and having a triangle display instead of square display. If it needed MySQL in the calculation step, why 
didn't it need it before and now it needs it?


Best regards
Maryam

________________________________
 From: M. F. <mfaridun at yahoo.com>
To: "cmview-users at bioinformatics.org" <cmview-users at bioinformatics.org> 
Sent: Monday, June 17, 2013 3:07 PM
Subject: Re: [cmview-users] problem in displaying triangle contact map instead of square
 





Hi there,

In the tutorial after it loads the pdb it gets a triangle display while I get a square display. As it is mentioned in the manual, this is an 
experimental feature (?). So, I should add this line to the config file: USE_EXPERIMENTAL_FEATURES = true
I added the line right after the directories like this:
#Properties file for CMView 1.1

PYMOL_EXECUTABLE=../MacPyMOL.app/Contents/MacOS/MacPyMOL
DSSP_EXECUTABLE=../dssp-2.1.0/dssp
DALI_EXECUTABLE=/usr/bin/DaliLite
DEFAULT_DISTANCE_CUTOFF=8.0
DEFAULT_CONTACT_TYPE=Ca
USE_EXPERIMENTAL-FEATURES = TRUE

and this error  appeared:

Connecting to database...
Warning: MySQL connection file /Users/Maryam/.my.cnf doesn't exist. Will use default parameters for connection
No database found. Some functionality will not be available.

I guess this means a lot of work should be done, but I am not aware of 
the steps I should take to make this work. Is this related to having triangle instead of square display.

Thanks in advance,
Maryam




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