Bug and Proposal: stride()

[Xinqiu Yao]

I got following warning message from calling stride()

pdb <- read.pdb("1tag")
sse <- stride(pdb)
#Warning message:
#In stride(pdb) : NAs introduced by coercion

But went well with dssp():

sse2 <- dssp(pdb)

Another issue is the inconsistency of returned class by dssp() and stride()

class(sse)
#"list"

class(sse2)
#"dssp"

Propose to return as "sse" class for both function. Accordingly, update print.dssp() to print.sse()

[Barry Grant]

Yes this would be good. Also I would like to see some consistency with the $helix and $sheet returned from read.pdb() when the input file has these REMARK sections. Note that there is no $length in the pdb versions currently. Not a big deal but could catch someone out later - most likely me!

Note that for vignettes etc. it would be best to take the sse from the pdb as then we done force a user to have dssp or stride installed...

[Xinqiu Yao]

How about returning pdb$sse by read.pdb(), where pdb$sse has the same attributes to "sse" object but data extracted from PDB file directly?

[Lars Skjærven]

On line 112 in plot.dccm2() we could then change

 sse$helix$length

to

 sse$helix$end - sse$helix$start +1

so that we can provide a pdb object as input to argument sse for that funtion. I'll add that unless you're editing this file already.

[Barry Grant]

I am not a big fan of this idea. I like keeping it simple with e.g.

plot.bio3d(x, sse=pdb)

I don't think we need, or want, to make the pdb version consistent in every way with the dssp and stride results as we don't want to waist time with $phi $acc etc. I guess just a $length is all that I would add to the pdb $helix and $sheet for now.

[Xinqiu Yao]

phi and acc are kind of problems for pdb$sse idea (maybe just NULL in this case). But I agree that currently we should focus on essential update and maybe leave the consistent check later.

[Barry Grant]

Hi Lars, there is a catch for the missing $length in my last commit and I moved plot.dccm2() to plot.dccm() so hopefully this should work with just a plot(cm, sse=pdb).

Unfortunately, there is a strange diagonal band of white that appears with your example 1C (see below) that may be related to smoothing???

pdb.full <- read.pdb("1sx4")
pdb.open <- trim.pdb(pdb.full, atom.select(pdb.full, chain = "A")) 
modes <- nma(pdb.open)
cm <- dccm(modes)
plot(cm, sse=pdb.open, contour=F)

# Annoying white band on diag
plot(cm, sse=pdb.open, contour=F, col.regions=bwr.colors(10))

On a related note I was looking at ggplot2 again earlier and I like its various grid based options for adding layers to a plot and being able to edit them after. I think this might be the best way to go in the future for such plots that demand extensive annotation.

[Lars Skjærven]

I still get this error at line 125 in the vignette when calling plot.dccm() with sse=pdb.

> plot(cm, sse=pdb.open, contour=F)
Error in unit(length - 0.5, "native") : 
  'x' and 'units' must have length > 0

I also see this diagonal white stripe and two vertical white stripes at position ~420 and ~510. hmm...

[Barry Grant]

I forgot to push the commit that fixed the missing sse$length from pdb fix - should be there now. The white line on the diag is related to the smoothing done in the contourplot() function. I still have not had a change to look into and fix this. Sorry. Generally I am getting fed up with lattice and am considering switching to ggplot2 for these kind of plots...

[Xinqiu Yao]

It seems solved