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<div class="moz-cite-prefix">Hi Maryam<br>
<br>
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. <br>
<br>
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.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
<br>
On 06/18/2013 12:32 PM, M. F. wrote:<br>
</div>
<blockquote
cite="mid:1371551566.9658.YahooMailNeo@web140703.mail.bf1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:arial,
helvetica, sans-serif;font-size:12pt">
<div><span><br>
</span></div>
<div style="color: rgb(0, 0, 0); font-size: 16px; font-family:
arial, helvetica, sans-serif; background-color: transparent;
font-style: normal; ">Dear supporting team,<br>
<br>
</div>
<div style="color: rgb(0, 0, 0); font-size: 16px; font-family:
arial, helvetica, sans-serif; background-color: transparent;
font-style: normal; ">Do I need to elaborate on something? or
no one has seen my email?<br>
I read a little about MySQL and cannot understand why this
error even appears?<br>
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?<br>
<br>
<br>
Best regards</div>
<div style="color: rgb(0, 0, 0); font-size: 16px; font-family:
arial, helvetica, sans-serif; background-color: transparent;
font-style: normal; ">Maryam</div>
<div style="font-size: 12pt; font-family: arial, helvetica,
sans-serif; ">
<div style="font-size: 12pt; font-family: 'times new roman',
'new york', times, serif; ">
<div dir="ltr">
<hr size="1"> <font size="2" face="Arial"> <b><span
style="font-weight:bold;">From:</span></b> M. F.
<a class="moz-txt-link-rfc2396E" href="mailto:mfaridun@yahoo.com"><mfaridun@yahoo.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-rfc2396E" href="mailto:cmview-users@bioinformatics.org">"cmview-users@bioinformatics.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:cmview-users@bioinformatics.org"><cmview-users@bioinformatics.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Monday, June 17, 2013 3:07 PM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [cmview-users] problem in displaying triangle
contact map instead of square<br>
</font> </div>
<div class="y_msg_container"><br>
<div id="yiv9319928577">
<div>
<div style="color: rgb(0, 0, 0); background-color:
rgb(255, 255, 255); font-size: 14pt; font-family:
'times new roman', 'new york', times, serif; "><br>
<div style="font-size: 14pt; font-family: 'times new
roman', 'new york', times, serif; ">
<div style="font-size: 12pt; font-family: 'times
new roman', 'new york', times, serif; ">
<div class="yiv9319928577y_msg_container">
<div id="yiv9319928577">
<div>
<div style="color: rgb(0, 0, 0);
background-color: rgb(255, 255, 255);
font-size: 14pt; font-family: 'times new
roman', 'new york', times, serif; ">
<div><br>
Hi there,</div>
<div style="color: rgb(0, 0, 0);
font-size: 18.6667px;
background-color: transparent;
font-style: normal; font-family:
'times new roman', 'new york', times,
serif; "><br>
</div>
<div style="color: rgb(0, 0, 0);
font-size: 18.6667px;
background-color: transparent;
font-style: normal; font-family:
'times new roman', 'new york', times,
serif; ">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: <i><code>USE_EXPERIMENTAL_FEATURES
= true<br>
</code></i>I added the line right
after the directories like this:<br>
#Properties file for CMView 1.1<br>
<br>
PYMOL_EXECUTABLE=../MacPyMOL.app/Contents/MacOS/MacPyMOL<br>
DSSP_EXECUTABLE=../dssp-2.1.0/dssp<br>
DALI_EXECUTABLE=/usr/bin/DaliLite<br>
DEFAULT_DISTANCE_CUTOFF=8.0<br>
DEFAULT_CONTACT_TYPE=Ca<br>
USE_EXPERIMENTAL-FEATURES = TRUE<br>
<br>
and this error appeared:</div>
<div style="color: rgb(0, 0, 0);
font-size: 18.6667px;
background-color: transparent;
font-style: italic; font-family:
monospace; "><br>
Connecting to database...<br>
Warning: MySQL connection file
/Users/Maryam/.my.cnf doesn't exist.
Will use default parameters for
connection<br>
No database found. Some functionality
will not be available.<br>
<br>
<span style="font-family: arial,
helvetica, sans-serif; "><span><font
size="3"><span><span>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.</span></span><br>
<br>
Thanks in advance,<br>
Maryam<br>
</font></span></span><br>
</div>
</div>
</div>
</div>
<br>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
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<br>
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