SEEING’ THE MOTION CORRESPONDING TO A SELECTED PRINCIPAL COM- PONENT in dpca

[suji george]

 Hi,

 Is there a way to see the motion corresponding to a selected priniciple component in dihedral principle component analysis using carma. Although there is a way out for cartesian principle component analysis using the command

carma −verb −write −col −cov −eigen −play 1 −4 5 cluster _01.dcd CAs.psf

whether the same command can be used for dpca.

Any help will be appreciated

Thanking you

ss

[Nicholas M. Glykos]

> Is there a way to see the motion corresponding to a selected priniciple
> component in dihedral principle component analysis using carma. Although
> there is a way out for cartesian principle component analysis using the
> command
>
> carma −verb −write −col −cov −eigen −play 1 −4 5 cluster _01.dcd CAs.psf
>
> whether the same command can be used for dpca.

This is an interesting question. You want to perform an analysis in one
space (sin/cos of phi/psi), but visualize the results in another (unrelated)
space (Certesian). Interesting.

For now : carma as it is can not do that. Additionally, I am not aware of a
solution to this question. As I said, this is an interesting question.

As a temporary solution, you can try this : perform a cluster analysis using
dPCA, and then use the DCD/PSF pairs (for each dPCA cluster), to perform a
Cartesian PCA analysis, and, thus, visualize the Cartesian motion within each
dPCA-derived cluster. This will go much faster if you can use 'grcarma'.




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Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/