Can't generate pdb aligned plot

[Former user]

Hi - I am following the viginette snippet here:

# read two G-protein structures
a <- read.pdb("4q21")
b <- read.pdb("4lhy")

# perform iterative alignment
aln <- struct.aln(a, b)

and I can see some files generated in a temp folder "fitlsq", but there are no 3d plots of the alignment. I have Muscle, PyMOL and VDS installed to a Windows machine and in my PATH. Any pointers? Thanks!

[Xinqiu Yao]

Hi,

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You need to open the structures manually from the command line using e.g. vmd -m fitlsq/*.pdb

[Xinqiu Yao]

Not a bug

[Arron Lacey]

Thanks very much - problem solved.