Dear Conrad, Thanks for the prompt reply. I have a program available (called "chop") that is designed to be run from within UCSF midas. I have extensively used midas with chop in the past successfully and now that I have changed labs I would like to continue using chop with the Midas (or Chimera) graphical interface. The program's manual states that: "Although the midas program does lack a real scriptable language, it does provide a mechanism to interact with external program called the delegate utility. This mechanism is completely described in their manual but briefly, the delegate utility sets a name or prefix that when used at the beginning of a line will cause the remainder of the line to be sent to the delegate program. After the line is sent midas reads as its standard output a midas command that is generated by the delegate program, in this case "chop"." Therefore, the first command I was using was: delegate start chop chop –i 1aaq.pdb which starts the chop program and defines “chop” as the prefix for commands to be sent to delegate. Then a series of "chop" commands were input into midas. Unfortunately, it is not possible for me to re-write the chop program. If delegate was not carried over to Chimera and there is no other way to start chop from within Chimera, is there a way to access the Midas installer/source code in order to install and use it? Chop does not start Chimera by itself. Thanks a lot for your help. I am looking forward to hearing from you! Best wishes Zoe

Chimera is a completely different program than Midas but has retained some of the command language from Midas. The "delegate" command was not implemented because Chimera's Python interface provides a much richer environment for writing extensions. http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html provides some examples on extending Chimera using Python. (There is a ReadStdin tool, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/readstdin/readstdin..., which enables a single process to control Chimera via Midas commands, but it is intended for use by programs that start Chimera themselves.) Can you give a little more detail about what you'd like to do with Chimera? Thanks.

Conrad

On 10/24/11 8:16 AM, Zoe Cournia wrote:

...

Hello,

I am trying to use the "delegate" command from the Midas program in Chimera, but the error message I get is that "delegate is not yet implemented".

Is there an available "Extension Mechanism" in chimera?

If not, is it possible to get the source code for Midas in order to compile it and use it with delegate?

Thanks a lot for any help.

Best Zoe

-- ------------------------------- Dr. Zoe Cournia Investigator - Lecturer Level Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece zcournia@bioacademy.gr Office: +302106597195 Lab: +302106597568 Cell: +306944223123 -------------------------------

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------------------------------- Dr. Zoe Cournia Investigator - Lecturer Level Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece zcournia@bioacademy.gr Office: +302106597195 Cell: +306944223123 -------------------------------