------- Start of forwarded message ------- Date: Fri, 4 Apr 2003 20:00:09 -0700 Subject: Re: [chimera-dev] Mailing list, etc.? Content-Type: text/plain; charset=US-ASCII; format=flowed From: Geoffrey H Wathen <wathen@physics.arizona.edu> To: Thomas Goddard <goddard@cgl.ucsf.edu> In-Reply-To: <200303191730.h2JHU1Kh779813@adenine.cgl.ucsf.edu> X-Filter-Version: 1.9 (cgl.ucsf.edu) Tom, I've downloaded the latest build of Chimera. It seems as stable as ever, but I do note that you chose to keep with the X server version, rather than going to Aqua. (I also noticed that the launcher now does give the error, informing you that you need to start the X server, if it isn't already running.) Any thoughts on a mailing list, yet? If you'd like to have someone volunteer to be a list moderator, I'd be happy to. (Also happy to help out any other way that I can...) Now to a comment. After some tinkering, I finally managed to output a new PDB file that contained models from several other PDB files. This, however, wasn't exactly an easy of intuitive thing to do. My first thought had been to use the 'Write PDB' command in the Model Panel. However, that button automatically greys itself out when more than one model is selected. I finally stumbled upon the command line command 'pdbrun cat > file'. So, I was able to do what I wanted, but I had to go through a rather backdoor method. Any chance that things like 'Write PDB' will be enabled when more than one model is selected? And what about a method of adding more atoms, other than just hydrogen? (I also know of 'backdoor' ways that I can do this, but I'd love to see Chimera become a more fully featured molecular modeler, and to that end, I'm quite happy to give all kinds of input.) In any event, thank you for all of your efforts. Geoff. On Wednesday, March 19, 2003, at 10:30 AM, Thomas Goddard wrote:
Hi Geoff,
We will be making a Chimera release in then next week or two possibly as early as this Friday. We have been testing an Aqua version of Chimera (no X server needed) but have encountered about a dozen problems with the Tk windowing toolkit on Aqua that Chimera uses. We are still considering whether to release an Aqua version or an X windows version.
If we decide to continue with an X windows Chimera on the Mac then I will look into how OpenOffice starts the X server if it is not yet started. I agree that the current Mac Chimera behaviour where no error is shown when you don't first start the X server is bad.
The tutorials on our web site describe our development version of Chimera that has not been released. We may have it up on the web because people at UCSF have access to that newer Chimera. I'll see if we can keep the current Chimera release manuals on the web. Your Chimera distribution came with the manuals and tutorials. If you go to the Chimera Help menu and select User's Guide the web browser will show the copy that came with your Chimera distribution which should be completely consistent (same menus, ...) with that version of Chimera.
We do not have a Chimera mailing list. This next release is the first official release (may still be a beta release on the Mac platform) and it makes sense to look into setting up a mailing list.
Tom
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