On May 19, 2006, at 6:46 AM, szklars2@tcnj.edu wrote:
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
Dear Anne, The answer is yes, but it is awkward and many editors will choke on the long lines in most session files. I am thinking there must be a better way to accomplish what you want to do without editing the session. Perhaps you could give a little more detail on the context in which you are having trouble referring to specific atoms? I'm going to guess that we're talking about the command line (and let me know if I'm wrong). In the command line, you can color red atom CA of residue 14, chain A in model 0 with: color red #0:14.a@ca if you only have a single model open, then this will do: color red :14.a@ca If the difficulty is that you are having trouble remembering the syntax of atom specifiers (the ':14.a@ca' thing), you can use the 'alias' command to give it a more mnemonic name: alias ca14 :14.a@ca then henceforward the alias can be used in commands: color red ca14 Aliases are remembered in session files, so if you open your old session, create an alias, and save a new session, the new session will have the alias in it. If the trouble is that you have duplicate atom names in the same residue (some small molecules are like that), then you could refer to them by serial number (the first number after the ATOM or HETATM), like so: color red @/serialNumber=525 and you could again use an alias to make that more mnemonic. If I'm totally whiffing on guessing what the problem is, please fill me in! --Eric