2D diagram and CDK-Depiction.jar
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/appCDKDepictionService1586137005272-8075760... 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 !
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/appCDKDepictionService1586137005272-8075760... 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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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@cgl.ucsf.edu> Sent: Monday, April 6, 2020 12:02:09 PM To: David Ricardo Figueroa Blanco <dr.figueroa10@uniandes.edu.co>; chimera-users@cgl.ucsf.edu <chimera-users@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/appCDKDepictionService1586137005272-8075760... 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 !
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi David, Sorry no, Chimera does not draw diagrams like those from Ligplot or Ligplot+: <https://www.ebi.ac.uk/thornton-srv/software/LigPlus/> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 6, 2020, at 10:21 AM, David Ricardo Figueroa Blanco <dr.figueroa10@uniandes.edu.co> wrote:
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
participants (3)
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Conrad Huang -
David Ricardo Figueroa Blanco -
Elaine Meng