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Hi all<br>
<br>
First of all thanks a lot Inken for the detailed error reports, that
was very helpful indeed.<br>
<br>
I think I've now found what was wrong. There were a few problems in
the dali runner code. I've fixed this already in the svn code
repository and I will upload a new version to the web as soon as I
can, I will let you know.<br>
<br>
Cheers<br>
<br>
Jose<br>
<br>
<br>
On 08/15/2011 12:09 PM, Inken Wohlers wrote:
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cite="mid:1405341174.5871.1313402957303.JavaMail.root@zembox03.zaas.igi.nl"
type="cite">
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Hi Michael and hi CMview developers!
Here the answers to the questions below.
The operating system on which I am running CMview is Fedora 14.
I figured out now that in some cases the DaliLite alignment does work. For example, I can align 1c52A and 1gdvA if I load them from online pdb. Aligning 1c52A with 1c52A or 1gdvA with 1gdvA doesn't work though (maybe the problem is aligning identical proteins / pdbs with the same name?).
If I use my local pdb files by using "Load from PDB file", there is a slightly different error and I tried different pdb files but couldn't find any for which the Dali alignment works. The error message is always the same in these cases.
I attach my local copy of 1c52A and 1gdvA and the error messages. "out_err_1c52.txt" shows the errors for the case of loading the input files from online pdb, "out_err_1c52_local.txt" shows the errors for loading the input files from local pdb files.
Maybe from this you see an easy way of fixing it?
Thank you and best regards,
Inken
----- Original Message -----
From: "Michael Lappe" <a class="moz-txt-link-rfc2396E" href="mailto:drmlappe@googlemail.com"><drmlappe@googlemail.com></a>
To: "Inken Wohlers" <a class="moz-txt-link-abbreviated" href="mailto:Wohlers@cwi.nl">Wohlers@cwi.nl</a>>
Cc: <a class="moz-txt-link-abbreviated" href="mailto:cmview-devel@bioinformatics.org">cmview-devel@bioinformatics.org</a>
Sent: Friday, August 12, 2011 6:01:42 PM
Subject: Re: CMView DaliLite plugin
Dear Inken -
Thanks for the feedback! At the moment I can't reproduce the bug and so
I don't have a solution right away - hence I cc this to the
cmview-developers list
- maybe someone has got an idea or experienced something similar.
Maybe these questions will help us to nail the bug:
There were a couple of bugs which occurred only in one operating system
but not others - so which system are you running cmview on?
Is there any output on the console for errors?
Did you try running DaliLite on its own -
just to make sure the problem isn't there...
Thanks & best wishes! cheers .\\ichael
On Thu, Aug 11, 2011 at 7:13 PM, Inken Wohlers <a class="moz-txt-link-abbreviated" href="mailto:Wohlers@cwi.nl">Wohlers@cwi.nl</a>> wrote:
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Dear Dr. Michael Lappe,
Today I started using CMView, it is a very useful tool!
I have a problem though with displaying the DaliLite alignment. I hope you
can help me with this? I now use DaliLite version 2.4.5 (and set the
environment variable accordingly). Apparently the alignment is computed,
there is a file /tmp/cmviewDALI626802241258640/A-A.html containing the
alignment. But then nothing happens. When pointing on the window, there is
another icon instead of the arrow indicating that the program is working,
but for minutes nothing happens. There is also no error message, and it is
possible to continue using the window (which displays only the first contact
map). The other alignment functions are all working fine.
I also have DaliLite 3.3 available, but it doesn't seem to work. Should
this work? (Resultfiles are a bit different than in the older DaliLite
version).
Thank you for your help and time!
Best regards,
Inken Wohlers
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