[Chimera-users] Swapaa from Java Runtime.exec

[Eric Pettersen]

On Jun 10, 2008, at 10:25 AM, ProtEUS wrote:

> Hello again!
>
> I tried the way you explained me, but it doesn't seem to work.

I think I need more detail than "doesn't seem to work".  Did you get  
an error message?  Was the output wrong?  What specifically happened?

>  I also tried to use the script mode with simple commands, but i am  
> getting back error like:
>
> cannot execute 'gzip'...

That's just a warning that files compressed with 'compress' (i.e.  
ending in '.Z') won't be openable in Chimera because no gzip  
executable could be found.  You can ignore it assuming that none of  
the files you're using are compressed that way.

>
> and a series of other errors of python.

The text of the script you used and the contents of the error  
messages would be helpful.

--Eric

>
> Could you please help me with this situation?
>
> Thank you so much in advance...
>
> Andreas.
> ----- Original Message -----
> From: Eric Pettersen
> To: ProtEUS
> Cc: chimera-users at cgl.ucsf.edu
> Sent: Tuesday, June 10, 2008 1:31 AM
> Subject: Re: [Chimera-users] Swapaa from Java Runtime.exec
>
> If you run Chimera in nogui mode (i.e. with the command-line flag  
> "--nogui") with no script file argument then standard input would  
> be interpreted as Chimera commands.  Alternatively, you could  
> supply a script file (Chimera commands or Python) as an argument.   
> This is basically described here:
>
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#nogui
>
> You could use a series of commands like:
>
> open input.pdb
> swapaa TYR :15.a
> write output.pdb
>
> to do the swapaa.
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
>
> On Jun 9, 2008, at 1:14 PM, ProtEUS wrote:
>
>> Hello all!
>>
>> I am sorry if this is a dump question, but is it possible for  
>> swapaa to run fromJava server with Runtime.exec()?
>>
>> Thank you very much!!
>>
>> Andreas, Greece.
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>> Chimera-users at cgl.ucsf.edu
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>
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