zcournia at bioacademy.gr
Mon Oct 24 13:29:09 PDT 2011
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
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
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!
> 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.
> some examples on extending Chimera using Python. (There is a 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.
> On 10/24/11 8:16 AM, Zoe Cournia wrote:
>> 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
>> 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.
>> Dr. Zoe Cournia
>> Investigator - Lecturer Level
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27 Athens
>> zcournia at bioacademy.gr
>> Office: +302106597195
>> Lab: +302106597568
>> Cell: +306944223123
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
Dr. Zoe Cournia
Investigator - Lecturer Level
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27 Athens
zcournia at bioacademy.gr
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