problem in visualizing results on pymol...

[jay]

I performed an ensemble NMA of 8 homologs of an enzyme from diff. organisms and made trajectory files for visualizing specific modes from each organism.

ids<-c("1","2","3","4","5","6","7","8") aln <- read.fasta("corrected.fasta") pdbs <- read.fasta.pdb(aln) modes<-nma(pdbs,rtb=FALSE,rm.gaps=FALSE,subset=10)

inds <- c(grep("1", ids)[1]) mktrj(modes, pdbs, m.inds=1, s.inds=inds[1], file="1-mode1.pdb")

Bio3D generates a file alright but I find only green dots in each frame when I open it in pymol. ...corresponding to C-alpha atoms only. The created file itself has only this info.

Similarly, the same kind of problem happens in the mode visualization of a single structure NMA.

mktrj(modes1, mode=7,file = "1_mode7_trj.pdb")

1_mode7_trj.pdb has only c-alpha coordinates.

I also tried to visualize deformation energies of the NMA on the single PDB structure by writing a output file by:

write.pdb(pdb="1.pdb", xyz=modes1$xyz, file="1_1st3_R-defor.pdb", b=defsums)

Again only c-alpha coordinates are only written to file.

What is the reason for the omission of other atomic coordinates?

Please help me in resolving this issue.

[Lars Skjærven]

You are performing c-alpha NMA. See help(nma) for more information. For all-atom NMA see function aanma().

[jay]

Perfectly logical...but just could not help wondering about how in the tutorials, trajectories are visualized with preceeding C-alpha nma. Please check up the following tutorial section links...

For eg.:

"Mode visualization" section in http://thegrantlab.org/bio3d/tutorials/normal-mode-analysis Fig 3 A

or in the "visualize modes" section in http://thegrantlab.org/bio3d/tutorials/ensemble-nma-part-2 - Fig 5

???

[jay]

In other words, is it impossible to visualize trajectory or visulize deformation energy profile on the structure from the results of C-alpha based NMA ?

Fig 3A (NMA) and Fig 5 (ensemble NMA-part 2) from tutorials - are they based on aanma ?

[Barry Grant]

View as “tube” in vmd for example. There are other representations such as “trace” etc.

More generally, you will likely want to read the documentation for whatever molecular viewer you are are using.

[jay]

Thank you Sir.

[jay]

resolved