Hello,
My question is related to optimization. I increased the default optimization in "model-full.py" using the following code:
# High VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 5000
Optimization does occur, however a few amino acids are changed from their L-isomeric forms to the D-isomers.
To check if this was caused by problems with the PDB file I was using, I used a file(2KDV) from the protein databank. The same thing happens to it as well. Also if a lower amount of optimization is used, the change from L to D forms does not occur.
Thank you in advance for the help, Abdullah Ahmed _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969
On 2/2/10 8:25 AM, abdullah ahmed wrote: > My question is related to optimization. I increased the default > optimization in "model-full.py" using the following code: > > # High VTFM optimization: > a.library_schedule = autosched.slow > a.max_var_iterations = 5000 > > Optimization does occur, however a few amino acids are changed from > their L-isomeric forms to the D-isomers.
Modeller contains a full description of the topology of the standard amino acids; the internal coordinates of these amino acids are for the L-isomers, so it will not produce D forms by default. However, since every optimization starts with a randomization, it is possible that that randomization produced a D-like residue which the optimizer is then unable to recover from, since it's a local minimum. This can happen at any optimization level.
The solution for problems like these is generally to build multiple models and then detect and discard "bad" models using the Modeller scoring function or an assessment score.
Ben Webb, Modeller Caretaker
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abdullah ahmed -
Modeller Caretaker