As per Elaine's mail, great cover! As for the session issue, since the last production release I've completely redone session handling. There are no longer PDB files embedded in sessions. Instead, structures are built directly by the session. Also, attributes that are the same for all atoms (or residues/molecules) are recorded once instead of once per atom. As a result, sessions are smaller, use less memory when restoring, and restore faster. This new session code is in the 1.2224 snapshot release. If you try out 1.2224 and you still can't get a newly-saved session to restore (i.e. a session that was written using 1.2224), then let me know and I'll investigate to see if there are further bottlenecks I can eliminate. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On May 22, 2006, at 4:17 PM, Jonathan Hilmer wrote:
Notepad++ will do a great job of editing the .py files. I've found that this is an extremely convenient way to accomplish certain tasks, such as precise alignment of multiple clipping planes. However, you definitely have to know what you're looking for when digging through the files.
On a related issue, I have a question regarding the saved sessions. In some of the viral capsid models I've created a saved session is enormous (about 60 megabytes) and fails to compile either automatically when loading the .py session or manually using the python.exe included with Chimera. It seems to be a result of excessive explicit attribute assignments that I don't really care about (color etc) since they are easy enough to set once the model has loaded.
Does anyone have any suggestions or experience with this issue?
Jonathan
PS: Check out the most recent issue of Science. Although the editors chose the least visually impressive submission, non of the variations would have been possible without Chimera: great program.
Hello. My name is Anne Szklarski and I am a student at The College of New Jersey. I was wondering if there was a way that the python files could be modified in notepad. Does it require the Python software? The reason I ask is because I have been renaming certain atoms in the .ent files using notepad so that I may specifically select them in chimera. The only problem with my current method is that I have to start the rendering process from the beginning which is quite time consuming. So I was wondering if there was a way that I could alter the chimera file directly and not lose any of the colors, etc. that I have chosen. I appreciate any information on this matter.
Thank you, Anne Szklarski
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