On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote:
Dear Users and Developers,
I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera?
Hi Arun, The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature- request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu