[Chimera-users] Bug (?) with EnsembleCluster
chiendarret at yahoo.com
Sat Jan 5 13:26:40 PST 2008
Although I could argue that the "Report Bug" window was misleading, I am better
saying that I was stupid enough.
--- Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Francesco,
> On Jan 5, 2008, at 12:34 AM, Francesco Pietra wrote:
> > 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")
> As I said in previous messages, you have to view all the frames you
> want to save (actually play through the trajectory) before you can
> save them. Even if the dialog says "N frames" the coordinates are
> not read until they are viewed. So if you didn't view them, there is
> no "save all frames" option, it won't save multiple structures, and
> the saved PDB will not work in the ensemble tools.
> > 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
> Probably your file did not contain multiple structures, as explained
> > 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.
> We realize this is a common situation, and that is why Chimera is
> able to calculate secondary structure automatically. The message
> about lack of secondary structure is not an error message or
> complaint about a problem. It is just an "informational message"
> that Chimera is automatically running ksdssp for you to calculate the
> secondary structure assignments since they weren't in the file.
> Thus, you do not need to run ksdssp yourself unless you wanted to,
> and I don't think ksdssp is involved in your problems here. However,
> you can run ksdssp with a command or from the Model Panel.
> If you choose Help... Search Documentation from the Chimera menu and
> search for "ksdssp" that is the top hit.
> I hope this clarifies things,
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