[cmview-devel] CMView DaliLite plugin

Jose Duarte jose.duarte at psi.ch
Wed Aug 17 10:13:12 EDT 2011

I've now uploaded the bugged fix version as CMView-1.1.1


I've tested it with latest DaliLite (3.3) and all works well, please do 
let us know if it works as expected.



On 08/17/2011 10:19 AM, Jose Duarte wrote:
> Hi all
> First of all thanks a lot Inken for the detailed error reports, that 
> was very helpful indeed.
> 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.
> Cheers
> Jose
> On 08/15/2011 12:09 PM, Inken Wohlers wrote:
>> 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"<drmlappe at googlemail.com>
>> To: "Inken Wohlers"Wohlers at cwi.nl>
>> Cc:cmview-devel at bioinformatics.org
>> 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 WohlersWohlers at cwi.nl>  wrote:
>>> 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
>>> _______________________________________________
>>> cmview-devel mailing list
>>> cmview-devel at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/cmview-devel
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