Talk:Task 7: MSUD - Structure-based mutation analysis
Revision as of 18:09, 17 November 2012 by Wagnerr (moved Talk:Task 7: MSUP - Structure-based mutation analysis to Talk:Task 7: MSUD - Structure-based mutation analysis)
A few comments
- in the mdp file settings you say: "(make molecule whole again)" - As far as I understand it, this just disables periodic boundary conditions
- the table with the foldX results needs a few explanations - or get rid of it on the mainpage if you only look at the total energy anyways.
- the plot of the runtime looks like you're integrating something - we are not interested in the area under the curve, just the time at a point. Really minor, but it confused me. ;)
Boidolj 14:56, 25 June 2012 (UTC)
An from me some more:
- you should probably render your pictures and choose colors which have a better contrast than blue and green if you want to show the overview... or even make the picture bigger! But thats just my opinion
- if you want to show the mutations, you should show them in more detail and not in cartoon mode... ANYthing is better than cartoon mode to compare the SNP changes, because as SNP suggests, its only ONE change whereas the structure is the same most of the time for the overall protein.
- As for minimise i am quite surprised, as you are the only group, where minimise increases the quality of the model almost all the time, but on a different matter, the plot of the energy is missing some of the basics like axis labels. Further Table 1 in minimise is rather weird, as i think you mixed the different energies from different methods. Or aren't you surprised about a 400 fold change in energy with just one run?
Hollizeck 19:57, 25 June 2012 (UTC)