I am evaluating Chimera as a tool for providing (pseudo-interactive) vis functionality from a web server and therefore would like to use it in a non-gui mode. I saw the earlier post/reply to this list (May 4) on this topic, and Eric indicated that one way to do this was to put all your cmds in a file then run "chimera --nogui <cmd-file>". Obviously this isn't ideal for my purposes. So, I'm wondering what the alternatives are? I'm a newbie to Chimera, but I've read how it was based on Midas, and so I decided to see how far I could get in reading in a pdb file and... I didn't get very far: (after install Chimera (Linux, beta 1 build 1951), plus dependent Python pkgs) %python
import chimera import Midas f=Midas.open('foo.pdb')
and I get an error about 'missing default material' and realize I'm doing the wrong thing anyway. Basic question: can I, from the Python interpreter, use Chimera/Midas to read in a pdb file and do basic Chimera functionality? For now, I don't even care if it assumes X is running and pops up windows. Thanks, Randy
Hi Randy,
I am evaluating Chimera as a tool for providing (pseudo-interactive) vis functionality from a web server and therefore would like to use it in a non-gui mode.
I'm not completely clear on what you mean by this. Exactly what type of functionality do you want to provide? Do you plan on using Chimera on the server-side, or client-side? There are several different [potential] solutions here, depending on what it is you want to do: (1) Chimera as a web-browser client A locally installed copy of Chimera can be used as a web browser 'helper application', responding to certain links clicked on in a web browser. These links contatin information about files to open, and commands or python code to execute in Chimera (Chimera runs in its own window -- not embedded in the browser). See http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata.htm... for more information. (2) The IDLE interpreter Currently, the only way to access Chimera's Python API in an interactive fashion is through the IDLE window (Tools->Programming->IDLE) from within Chimera. This, of course, requires having Chimera running in normal (i.e. not 'nogui') mode. If there is sufficient demand, we may include an 'interactive nogui' mode, that gives you access from the shell. (3) chimera --nogui As you already know, Chimera can be started with the '--nogui' flag, which doesn't bring up any graphics windows, and is used mainly for carrying out molecular calculations. Since there is no graphics window, it is not possible to do any visualization (including saving images). This sounds like an interesting problem - please let us know if any of these solutions are appropriate, or require further explanation. --Dan Greenblatt ---------------------------- Daniel Greenblatt UCSF Computer Graphics Lab dan@cgl.ucsf.edu
Thanks for the reply Dan. Yes, I was familiar with the 3 options you describe and none of them really do what I want, although, I guess, the 'interactive nogui' mode you hinted at would be closest. In short, I'd like server-side Chimera functionality; I don't want users to have to download/install Chimera. --Randy
-----Original Message----- From: Daniel Greenblatt [mailto:dan@cgl.ucsf.edu] Sent: Thursday, May 20, 2004 1:59 PM To: Randy Heiland Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] non-GUI use of Chimera
Hi Randy,
I am evaluating Chimera as a tool for providing (pseudo-interactive) vis functionality from a web server and therefore would like to use it in a non-gui mode.
I'm not completely clear on what you mean by this. Exactly what type of functionality do you want to provide? Do you plan on using Chimera on the server-side, or client-side?
There are several different [potential] solutions here, depending on what it is you want to do:
(1) Chimera as a web-browser client A locally installed copy of Chimera can be used as a web browser 'helper application', responding to certain links clicked on in a web browser. These links contatin information about files to open, and commands or python code to execute in Chimera (Chimera runs in its own window -- not embedded in the browser). See
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata .h
tml for more information.
(2) The IDLE interpreter Currently, the only way to access Chimera's Python API in an interactive fashion is through the IDLE window (Tools->Programming->IDLE) from within Chimera. This, of course, requires having Chimera running in normal (i.e. not 'nogui') mode. If there is sufficient demand, we may include an 'interactive nogui' mode, that gives you access from the shell.
(3) chimera --nogui As you already know, Chimera can be started with the '--nogui' flag, which doesn't bring up any graphics windows, and is used mainly for carrying out molecular calculations. Since there is no graphics window, it is not possible to do any visualization (including saving images).
This sounds like an interesting problem - please let us know if any of these solutions are appropriate, or require further explanation.
--Dan Greenblatt
---------------------------- Daniel Greenblatt UCSF Computer Graphics Lab dan@cgl.ucsf.edu
Do you need access to graphics, or just the data ? What are some intended scenarios ? It would take some work, but would certainly be possible to provide the kind of access you need from a shell. This is an idea we have considered before, and it is good to know that there is a demand for it. --Dan ---------------------------- Daniel Greenblatt UCSF Computer Graphics Lab dan@cgl.ucsf.edu On Thu, 20 May 2004, Randy Heiland wrote:
Date: Thu, 20 May 2004 14:21:56 -0500 From: Randy Heiland <heiland@indiana.edu> To: 'Daniel Greenblatt' <dan@cgl.ucsf.edu> Cc: chimera-users@cgl.ucsf.edu Subject: RE: [Chimera-users] non-GUI use of Chimera
Thanks for the reply Dan. Yes, I was familiar with the 3 options you describe and none of them really do what I want, although, I guess, the 'interactive nogui' mode you hinted at would be closest. In short, I'd like server-side Chimera functionality; I don't want users to have to download/install Chimera.
--Randy
-----Original Message----- From: Daniel Greenblatt [mailto:dan@cgl.ucsf.edu] Sent: Thursday, May 20, 2004 1:59 PM To: Randy Heiland Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] non-GUI use of Chimera
Hi Randy,
I am evaluating Chimera as a tool for providing (pseudo-interactive) vis functionality from a web server and therefore would like to use it in a non-gui mode.
I'm not completely clear on what you mean by this. Exactly what type of functionality do you want to provide? Do you plan on using Chimera on the server-side, or client-side?
There are several different [potential] solutions here, depending on what it is you want to do:
(1) Chimera as a web-browser client A locally installed copy of Chimera can be used as a web browser 'helper application', responding to certain links clicked on in a web browser. These links contatin information about files to open, and commands or python code to execute in Chimera (Chimera runs in its own window -- not embedded in the browser). See
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/webdata .h
tml for more information.
(2) The IDLE interpreter Currently, the only way to access Chimera's Python API in an interactive fashion is through the IDLE window (Tools->Programming->IDLE) from within Chimera. This, of course, requires having Chimera running in normal (i.e. not 'nogui') mode. If there is sufficient demand, we may include an 'interactive nogui' mode, that gives you access from the shell.
(3) chimera --nogui As you already know, Chimera can be started with the '--nogui' flag, which doesn't bring up any graphics windows, and is used mainly for carrying out molecular calculations. Since there is no graphics window, it is not possible to do any visualization (including saving images).
This sounds like an interesting problem - please let us know if any of these solutions are appropriate, or require further explanation.
--Dan Greenblatt
---------------------------- Daniel Greenblatt UCSF Computer Graphics Lab dan@cgl.ucsf.edu
participants (2)
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Daniel Greenblatt -
Randy Heiland