Packstat score in InterfaceAnalyzer

[Anonymous]

Why do I get a different packstat score after different runs of  Interface analyzer on the same structure ?

 

How is packstat value actually calculated? What does it signify?

[Anonymous]

You get different values because packstat has a large random component.  

You can use -packstat::oversample 100 to cause it to “run more” and be less random (I think this makes it run 100 times more, up from 1 cycle).  packstat is slow, although since this is a run-once step at the end of a run it won’t matter much.  That will reduce the variance significantly.

Packstat is not well documented.  It’s searching for the presence of non-solvent-accessible “voids”.  It reports on the range 0-1, where 1 is perfect.  I’ve seen “above 0.65” marked as “good enough”.  The scale was set with high-res crystal structures.

I usually turn packstat off for InterfaceAnalyzer – a lot of the things IA reports are there to test if they are useful; I found that packstat was not.

[Anonymous]

You get different values because packstat has a large random component.  

You can use -packstat::oversample 100 to cause it to “run more” and be less random (I think this makes it run 100 times more, up from 1 cycle).  packstat is slow, although since this is a run-once step at the end of a run it won’t matter much.  That will reduce the variance significantly.

Packstat is not well documented.  It’s searching for the presence of non-solvent-accessible “voids”.  It reports on the range 0-1, where 1 is perfect.  I’ve seen “above 0.65” marked as “good enough”.  The scale was set with high-res crystal structures.

I usually turn packstat off for InterfaceAnalyzer – a lot of the things IA reports are there to test if they are useful; I found that packstat was not.

[Anonymous]

You get different values because packstat has a large random component.  

You can use -packstat::oversample 100 to cause it to “run more” and be less random (I think this makes it run 100 times more, up from 1 cycle).  packstat is slow, although since this is a run-once step at the end of a run it won’t matter much.  That will reduce the variance significantly.

Packstat is not well documented.  It’s searching for the presence of non-solvent-accessible “voids”.  It reports on the range 0-1, where 1 is perfect.  I’ve seen “above 0.65” marked as “good enough”.  The scale was set with high-res crystal structures.

I usually turn packstat off for InterfaceAnalyzer – a lot of the things IA reports are there to test if they are useful; I found that packstat was not.

[Anonymous]

See also Protein Sci. 2009 Jan;18(1):229-39, which is the RosettaHoles paper.  Packstat is “RosettaHoles lite” (especially light in that it does not require an external secondary executable, dalphaball.

[Anonymous]

See also Protein Sci. 2009 Jan;18(1):229-39, which is the RosettaHoles paper.  Packstat is “RosettaHoles lite” (especially light in that it does not require an external secondary executable, dalphaball.

[Anonymous]

See also Protein Sci. 2009 Jan;18(1):229-39, which is the RosettaHoles paper.  Packstat is “RosettaHoles lite” (especially light in that it does not require an external secondary executable, dalphaball.

[Author]

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