Recommended folder names

Although it is obvious that the names of folders for computational chemistry projects do not affect the results, researchers are advised to chose names that make it easier to navigate inside a project. To this end, the following suggestions are made for working on projects that involve proteins:

Top folder

This should define the project so if the project involves working with a PDB file named "1ABC", then the the top folder should be named "1ABC" or "1ABC Mechanism" or "1ABC PM7 Mechanism" or something similar. When this is done, finding the project is relatively easy. Once inside the top-level folder, the project's name should not be used. Folder and file names should be as short as possible and should clearly indicate what is inside, so if the name of the project is in the folder name, there is no need to repeat it in the files and sub-folders.

Contents of Top Folder

Suggested names for a starting set of sub-folders are:

Literature: Reprints, original un-edited PDB files, research notes, correspondence, etc.
Sandbox or Work: A folder for testing ideas. The contents of this folder should be regarded as temporary. As soon as something works, it should be moved to another folder, and the folder emptied, so it's ready for the next idea.
Preparing Starting Model: All the steps involved in constructing the starting model. If the globule model is used, see "Construction of starting Globule system."
Starting model: A single-point calculation of the geometry of the starting system. This would be based on the results of "Preparing Starting Model."
Preparing Intermediate Model: All the steps involved in constructing an intermediate model.
Intermediate Model: A single-point calculation of the geometry of the intermediate. This would be based on the results of "Preparing Intermediate Model."

If JSmol is used, and its use is strongly recommended, then the jsmol folder should be in the top folder, and, to prevent it being accidentally deleted, should be hidden. The presence of this folder is essential for activating web-pages created by HTML.