Documentation to improve

Documentation to improve core.find example plots read.pdb use of x11() in 'Example' sections ?bio3d ?plot.pca, ?plot.pca.headings, etc plot titles for example() plots go by to fast gap.inspect() ?read.dcd ?write.fasta & ?read.fasta ?entropy ?mktrj.pca ?pca.xyz Proof-reading Comments dm() atom.select() References section plot.new() and x11() fit.xyz() plot.pca() read.dcd() core.find.R plot.dmat.Rd write.dcd read.pdb() read.fasta.pdb() gap.inspect() typo

 

core.find

add example of using a trajectory for core finding. For example,

 

example plots

• Improve example graphs as they go by too fast.

Solution is to add a par(ask=TRUE) command and try example(plot) again

• Add a descriptive title to all example graphs.
• Add png format plots to website

 

read.pdb

change title of read.pdb (ad 'a')

 

use of x11() in 'Example' sections

Is is sensible to have the x11() calls within the examples? Will it not mess things up for those not using x-windows?

Going to try plot.new()

 

?bio3d

documentation is missing the core find step

but it does run in the example(bio3d)

 

?plot.pca, ?plot.pca.headings, etc

These contain no examples on the documentation, but have very nice example() code.

 

plot titles for example()

Titles for plots rendered during bio3d's examples would help, since the user may not be able to tell how or when each plot was generated

 

plots go by to fast

add a par(ask=TRUE) command

 

gap.inspect()

The example() and documentation contains a cute plot. It may be nice to add a ylab, like:

 

?read.dcd

This has no examples yet DONE ... HIVP.DCD

?write.fasta & ?read.fasta

In the example for both of these functions, the following command takes a very long time to run on ziggy:

The hiv example used in some of the other functions loads a lot faster. Changed for hivp_xray.fa

 

?entropy

In the examples for this function, are the following lines still needed? Yes, but I will take of the nf object

 

?mktrj.pca

This function is missing examples, but there already are examples for it in the bio3d package main documentation and in the pca.xyz documentation, which could simply be pasted in here.

 

?pca.xyz

When I run this function's examples one by one, the plots with the loadings look small, like they are using the columns/rows settings from the last plot (of the main pca results). When I run them through the examples(), the loadings graphs come out much bigger.

In the documentation, this is what the commands look like:

 

Proof-reading Comments

 

dm()

There is some inconsistency with the references. FIXED

 

atom.select()

Maybe a link to pymol url would be nice.

-http://pymol.sourceforge.net/- JUST REMOVED REFERENCE TO PYMOL

 

References section

Maybe remove the 'To be published', from all but the bio3d.dm LETS KEEP IT FOR NOW

 

plot.new() and x11()

Still showing up is some examples.

 

 

fit.xyz()

line 96 is missing example code. FIXED

 

plot.pca()

Arguments start.row and end.row are missing explanations.

• Barry Q. ARE THEY NEEDED???
• Ana A. I think so. Their descriptions are missing full stops.

 

read.dcd()

is missing some examples. <- DONE, added HIVP

 

core.find.R

Error as sum vol not less than 1A when stop.at=15

Error in which(ordered.vol < 1)1:length(ordered.vol)

NA/NaN argument

lower the stop.at value or put in a if (vol>1) inds=NULL catch

 

plot.dmat.Rd

example takes a long time on the mac

 

write.dcd

need a function for this!

 

read.pdb()

too slow

 

read.fasta.pdb()

only saves CA data why not more?? I had this with backbone and C-beta before??

Leave this for next version

 

gap.inspect() typo

the word columns is misspelled (as coloums) in the 'Details' section