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@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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