Align Guide mode
|Opened on:||Sunday, October 9, 2011 - 14:27|
|Last modified:||Monday, June 3, 2013 - 08:02|
The current general Align guide tool (for the entire protein) rarely appears to help you out. Its current implementation to automatically re-align the guide when you click on it, is poor. Unless approximately 90% of the protein structure has already been manually aligned to the align guide (sometimes through hours of hard work), it will NOT correctly align to the majority of your protein structure when clicked. Since the Undo mechanism is apparently NOT related to the align tool, you cannot reset the align guide back to where it was, before the Align Guide button is clicked.
The local version of the tool is also not very helpful. When the user right-clicks on a particular segment to use the Align Guide tool relational to that segment, if the tool decides to work at all (sometimes it doesn't), it appears to align the guide in a completely different direction to where the majority of the protein structure lies at the time.
Apart from the recommendation to fix the Align Guide tool so that it is more user intuitive, I am going to suggest an Align Guide mode be implemented. Accessed through the Modes tab, the mode will allow the user to rotate and translocate the guide for the protein, to wherever he/she wishes. While some users will opt to have the guide sit directly on top of the majority of the protein structure, others may take a different approach, re-positioning the guide to the side of the protein structure as if it were a reverse mirror image, or silhouette of the structure.
An extension to this suggestion, is a Band Snap to Guide option, which could be enabled and disabled by the user, while using the Align Guide mode. Bands for each individual segment of a protein will automatically snap to the equivalent section on the guide, making it far easier to align the structure to the guide.
Please note that the alignment of the protein structure to the guide, and the alignment of the guide to the protein structure, are effectively two separate, yet equally important concepts presented here.