<html><body><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. <mfaridun@yahoo.com><br> <b><span style="font-weight: bold;">To:</span></b> "cmview-users@bioinformatics.org" <cmview-users@bioinformatics.org> <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>_______________________________________________<br>cmview-users mailing list<br><a ymailto="mailto:cmview-users@bioinformatics.org" href="mailto:cmview-users@bioinformatics.org">cmview-users@bioinformatics.org</a><br><a href="http://www.bioinformatics.org/mailman/listinfo/cmview-users" target="_blank">http://www.bioinformatics.org/mailman/listinfo/cmview-users</a><br><br><br></div> </div> </div> </div></body></html>