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

[Jose Duarte]

Hi Maryam

As Sheila said (and Henning before that), the screenshots with half the 
contact map (triangular one) are from an older version. Unfortunately 
the current version will always display both (symmetric) sides of the 
contact map.

The MySQL errors you saw when switching on the experimental features are 
not related to that problem at all. In any case I would suggest to 
switch off the experimental features because they haven't been fully tested.

Cheers

Jose



On 06/18/2013 12:32 PM, M. F. wrote:
>
> 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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>
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