Difference between revisions of "Talk:Structure-based mutation analysis (PKU)"
From Bioinformatikpedia
(→suggestions) |
(→suggestions) |
||
Line 13: | Line 13: | ||
*What exactly do you want to convey by "...left for the reader as exercise"? |
*What exactly do you want to convey by "...left for the reader as exercise"? |
||
+ | **yeah, kinda hard to compare the two figures. You should have enough colours for all three ;) -jonas |
||
*The SCWRL and FoldX energies (-> tables) could use some elaboration but you already know this. |
*The SCWRL and FoldX energies (-> tables) could use some elaboration but you already know this. |
||
*Very wild color :)..... a overall color-scheme could make the entry more straightforward |
*Very wild color :)..... a overall color-scheme could make the entry more straightforward |
||
das wars von mir, gute nacht --ali |
das wars von mir, gute nacht --ali |
||
− | * 'the color is chosen automatically by PyMol' |
+ | * 'the color is chosen automatically by PyMol'. This is a bit confusing, why not always colour the structures the same? -jonas |
+ | * You might have focussed too much on only the change of hydrogen bonds. What about clashes to neighbouring atoms, introduction or removal of charged residues that might have coorindated other charges nearby. What about things like pi-stacking, the possibilities are endless ;) -jonas |
||
+ | * I like how much emphasis you put on the surface considerations, however it felt like there was always the final step missing. You describe that e.g. there is a buldge created but what I really want to know in such a case is what is the effect of this. Is the binding pocket changed, is it at an interaction site (you have a multimer iirr), what about the case where a charge is removed from the surface. You would think there might be a reason if a strong charge is placed standing out on the surface. I am very much aware though that information like this is really hard and time-consuming to find. -jonas |
||
+ | |||
+ | ===Small stuff=== |
||
+ | coming later |
||
== urgent matters == |
== urgent matters == |
Revision as of 09:27, 26 June 2012
This is just a place to add criticism and or positive feedback so we Jonathan and Sebastian have a possibility to improve. Please note, that we wont be able to adress all matters immediately but we will address them eventually!
criticism
positive feedback
Again, everything very nice !--Meiera 23:51, 25 June 2012 (UTC)
suggestions
- What exactly do you want to convey by "...left for the reader as exercise"?
- yeah, kinda hard to compare the two figures. You should have enough colours for all three ;) -jonas
- The SCWRL and FoldX energies (-> tables) could use some elaboration but you already know this.
- Very wild color :)..... a overall color-scheme could make the entry more straightforward
das wars von mir, gute nacht --ali
- 'the color is chosen automatically by PyMol'. This is a bit confusing, why not always colour the structures the same? -jonas
- You might have focussed too much on only the change of hydrogen bonds. What about clashes to neighbouring atoms, introduction or removal of charged residues that might have coorindated other charges nearby. What about things like pi-stacking, the possibilities are endless ;) -jonas
- I like how much emphasis you put on the surface considerations, however it felt like there was always the final step missing. You describe that e.g. there is a buldge created but what I really want to know in such a case is what is the effect of this. Is the binding pocket changed, is it at an interaction site (you have a multimer iirr), what about the case where a charge is removed from the surface. You would think there might be a reason if a strong charge is placed standing out on the surface. I am very much aware though that information like this is really hard and time-consuming to find. -jonas
Small stuff
coming later
urgent matters
Just noticed that you used charmm27. When you use this force field the output from g energy misses angles. Also the number of the potential attribute is shifted 1 is Bond, 2 is "U-B" and 12 is "dont know right now". The potential is number 13. Im not sure what exactly U-B is but i think angle would be given when choosing the attributes Joerdensv
- Ahead of you: Fixed the potential energy, still trying to figure out the "angle" option. Thx anyway! Boidolj 14:14, 24 June 2012 (UTC)