[Chimera-users] Bug (?) with EnsembleCluster

Francesco Pietra chiendarret at yahoo.com
Sat Jan 5 00:34:52 PST 2008

I was trying to carry out a cluster analysis from three mdcrd trajectories from
Amber 9.

I reported here yesterday that I was unable to input more that one mdcrd (in gz
form) to Chimera. Therefore, I combined the mdcrd files with ptraj in Amber 9,
while stripping all water molecules, all lipid, and box information, leaving
only the protein with ligand.

That combined mdcrd loaded perfectly into Chimera MD Movie saving a pdb file 
(there was no option "save all frames" suggested by Elaine's email; I did not
select anything else than "untranformed coordinates")

Opened successfully this pdb into Chimera, Tools, MD/EnsembleAnalysis,
EnsembleCluster, select the new file, finally click on OK:

that resulted in Chimera Error. This was a first trial, though I have right
taken the opportunity to submit an alleged bug from the window inviting to do
so. From a perusal of Reply Log, I was unable to grasp the nature of the
failure. In particular, lacking documentation for ksdssp, I was unable to run
it (to assign the lacking secondary structure of the protein) with different
parameters from used

energy cutoff -0.5
minimum helix length 3
minimum strand length 3

and commands as from Log.

Perhaps I should also mention that lack of secondary structure is typical of
the long procedure through different programs to carry our (1) model building,
(2) docking, (3) MD.


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