[Chimera-users] Bug (?) with EnsembleCluster

[Francesco Pietra]

Elaine:
Although I could argue that the "Report Bug" window was misleading, I am better
saying that I was stupid enough.
francesco

--- 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  
> above.
> 
> > 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.   
> Documentation:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html
> If you choose Help... Search Documentation from the Chimera menu and  
> search for "ksdssp" that is the top hit.
> 
> I hope this clarifies things,
> Elaine
> 



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