Is there a way to calculate chi1 and chi1+chi differences between two structures?

[Anonymous]

Hi,

I looked up some of the options for various protocols to see if there is a way to calculate chi1 and chi1+chi2 measures for two structures. Essentially I want to compare the xray with that of the model predicted by Rosetta.

Thanks.

[Anonymous]

There isn’t a pre-made application that will already do this. I see several options:

Personally, I’d probably lean toward PyRosetta for this, though part of that is that I already know Python programming. It should be relatively straightforward to load up the structures in PyRosetta, query each chi angle for both structures, and then do whatever comparson you want to them.

If you prefer C++, you can also write your own Rosetta application that does basically the same thing, recompile Rosetta and now have your custom-build application. (We can provide more details if you decide to go this route.)

A third option is to use the FeaturesReporter framework in RosettaScripts. The ProteinResidueConformationFeatures is probably what you want. Using that properly will create an SQLite database which you can then use to query for specific residues, as well as do comparisons. (Generally, you would want to use a scripting language interface to the SQLite database – like those provided by Python or R – to do the analysis.)

[Anonymous]

There isn’t a pre-made application that will already do this. I see several options:

Personally, I’d probably lean toward PyRosetta for this, though part of that is that I already know Python programming. It should be relatively straightforward to load up the structures in PyRosetta, query each chi angle for both structures, and then do whatever comparson you want to them.

If you prefer C++, you can also write your own Rosetta application that does basically the same thing, recompile Rosetta and now have your custom-build application. (We can provide more details if you decide to go this route.)

A third option is to use the FeaturesReporter framework in RosettaScripts. The ProteinResidueConformationFeatures is probably what you want. Using that properly will create an SQLite database which you can then use to query for specific residues, as well as do comparisons. (Generally, you would want to use a scripting language interface to the SQLite database – like those provided by Python or R – to do the analysis.)

[Anonymous]

There isn’t a pre-made application that will already do this. I see several options:

Personally, I’d probably lean toward PyRosetta for this, though part of that is that I already know Python programming. It should be relatively straightforward to load up the structures in PyRosetta, query each chi angle for both structures, and then do whatever comparson you want to them.

If you prefer C++, you can also write your own Rosetta application that does basically the same thing, recompile Rosetta and now have your custom-build application. (We can provide more details if you decide to go this route.)

A third option is to use the FeaturesReporter framework in RosettaScripts. The ProteinResidueConformationFeatures is probably what you want. Using that properly will create an SQLite database which you can then use to query for specific residues, as well as do comparisons. (Generally, you would want to use a scripting language interface to the SQLite database – like those provided by Python or R – to do the analysis.)

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