VMD-L Mailing List
From: thereal sisterdot (therealsisterdot_at_gmail.com)
Date: Tue Jan 31 2012 - 03:04:52 CST
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Dear all,
a total newby question:
i am trying to use structural alignment tools as provided in the pdb
workbench.
i am splitting up the models into separate pdb files and loading them as
new molecules into vmd.
in vmd: when using the vmd_calculate_structure i typically get two types of
error messages:
"Residue ....- is involved in 6 hydrogen bonds (5 are allowed)"
or
"No hydrogen bonds found"
depending on the tool.
any recommendations on how to visualize the structural alignments?
particular cartoon/ribbon modes are no good with the errors in stride?
do i need to use other 3d viewers- eg pymol?
thanks for any advice!
best
Maria
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