[wathen@physics.arizona.edu: Re: [chimera-dev] Mailing list, etc.?]
------- 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
------- End of forwarded message -------
Hi Geoff,
I have been using an Aqua version of Chimera for a few months. It has about 20 nuisance problems with the user interface that come from bugs in the Aqua Tk windowing interface. I plan on putting an Aqua version on the web with this list of bugs in the next week or two.
We just started mailing lists for Chimera users and Chimera developers. See the Feedback link at the Chimera home page.
http://www.cgl.ucsf.edu/chimera/docs/feedback.html
I'll let other Chimera developers address your questions about writing multiple models to a PDB file, and about adding atoms other than hydrogens.
Tom
On Monday, April 7, 2003, at 10:06 AM, Thomas Goddard wrote:
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.)
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?
I could enable 'write PDB' with multiple models selected. I guess my question is why do you want multiple PDB models in a single file? What will you do with that file? Knowing how you want to use the file will help me decide if simply enabling the button is the way to go or if some other interface is more appropriate. If I enabled it, the models would be separated by END records.
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.)
I'm currently working on smarter hydrogen addition (avoiding steric conflicts and maintaining hydrogen-bonding interactions). I should be done with that in time for our next release. I intend to work on some limited structure-building features after that. So a preliminary version might be available two releases from now. Even I'm not aware of backdoor ways to add non-hydrogen atoms! I guess the swapaa command _sort_ of does this, but it's not at all generic. Are you writing Python code to do this?
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
Currently, I'm exploring using Chimera to visualize chemical interactions. I know that this can be done using multiple pdb files, and the 'Save Session' command. (Indeed, this might be a better way to have Chimera handle it, as it seems that Chimera doesn't like finding hydrogen bonds between models in a single PDB file.) The one thing that is lacking in this approach is the ability to talk to other applications that can read PDB files, but, clearly, not the Chimera PY session files. As to the 'backdoor' method I'm using to add atoms, it's nothing so glamorous as programming in Python. Indeed, it's simply manually writing in the atom's code into the PDB file. By making it a separate model (using the END command), I can manipulate it separately from the rest of the PDB file, move it into the proper location, then write the PDB file out again. I can then edit the PDB file to remove the END command, and the atom is part of the overall structure. I am also working on a better way to do this by writing a program that will allow me to work within a better dimensional framework for placing the new atom, then will write out a PDB file. We'll see how it goes...
Geoff.
On Monday, April 7, 2003, at 04:36 PM, Eric Pettersen wrote:
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?
I could enable 'write PDB' with multiple models selected. I guess my question is why do you want multiple PDB models in a single file? What will you do with that file? Knowing how you want to use the file will help me decide if simply enabling the button is the way to go or if some other interface is more appropriate. If I enabled it, the models would be separated by END records.
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.)
I'm currently working on smarter hydrogen addition (avoiding steric conflicts and maintaining hydrogen-bonding interactions). I should be done with that in time for our next release. I intend to work on some limited structure-building features after that. So a preliminary version might be available two releases from now. Even I'm not aware of backdoor ways to add non-hydrogen atoms! I guess the swapaa command _sort_ of does this, but it's not at all generic. Are you writing Python code to do this?
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
On Tuesday, April 8, 2003, at 09:51 AM, Geoffrey H Wathen wrote:
Currently, I'm exploring using Chimera to visualize chemical interactions. I know that this can be done using multiple pdb files, and the 'Save Session' command. (Indeed, this might be a better way to have Chimera handle it, as it seems that Chimera doesn't like finding hydrogen bonds between models in a single PDB file.) The one thing that is lacking in this approach is the ability to talk to other applications that can read PDB files, but, clearly, not the Chimera PY session files.
Hi Geoff, I guess I'll enable 'write PDB' for multiple models and offer the option of writing to a single file or to multiple files distinguished by model number. FindHBond doesn't offer to find cross-sub-model hydrogen bonds since the only standard PDB files that have multiple models are ones containing different conformers of the same structure -- rather than heterogeneous models. I could allow cross-sub-model hydrogen bonds if you felt there was a real need even after the 'write PDB' change above.
As to the 'backdoor' method I'm using to add atoms, it's nothing so glamorous as programming in Python. Indeed, it's simply manually writing in the atom's code into the PDB file. By making it a separate model (using the END command), I can manipulate it separately from the rest of the PDB file, move it into the proper location, then write the PDB file out again. I can then edit the PDB file to remove the END command, and the atom is part of the overall structure. I am also working on a better way to do this by writing a program that will allow me to work within a better dimensional framework for placing the new atom, then will write out a PDB file. We'll see how it goes...
Never underestimate the ingenuity of frustrated users. :-) Obviously, the structure editing I'll be adding will be somewhat easier than this to use, but it's still a couple of releases down the line -- so keep using what works! I am impressed. :-)
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
participants (3)
-
Eric Pettersen -
Geoffrey H Wathen -
Thomas Goddard