[Chimera-users] 2D diagram and CDK-Depiction.jar

[David Ricardo Figueroa Blanco]

Hi Conrad.

Thank you for your quick reply, it works ! Additionally do you if it is possible to create a 2d interaction diagram with closest residues.

Best regards
David
________________________________
From: Conrad Huang <conrad at cgl.ucsf.edu>
Sent: Monday, April 6, 2020 12:02:09 PM
To: David Ricardo Figueroa Blanco <dr.figueroa10 at uniandes.edu.co>; chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] 2D diagram and CDK-Depiction.jar

Hi, David.

The CDK files were left behind when we upgraded our hardware.  They
should be back in place again.  Can you please try again and see if it
works?  Thanks.

Conrad

On 4/5/2020 7:00 PM, David Ricardo Figueroa Blanco wrote:
> Hi!
>
> I am trying to generate 2d diagrams with Dockview  from autodock vina
> outputs but I get this problem :
>
> Web Service: cdkdepiction converts either SMILES strings or MOL2 files
> into 2D structure diagrams in PNG format
> Opal service URL:
> http://webservices.rbvi.ucsf.edu/opal2/services/CDKDepictionService
> Opal job URL:
> http://webservices.rbvi.ucsf.edu/appCDKDepictionService1586137005272-807576004
> CDKDepictionService stderr
> -----
> Error: Unable to access jarfile /usr/local/cdk/CDK-Depiction.jar
> -----
> CDKDepictionService stdout
> -----
> [no output]
> -----
> Structure diagram generation failed; see Reply Log for more information
>
> Any suggestion or needed program to install?
>
> Thank you !
>
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