[cmview-devel] CMView DaliLite plugin

[Jose Duarte]

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 Wohlers Wohlers 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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