That's definitely a bug. I missed a Numeric reference in MMTK when I did the Numeric->numpy conversion. It will be fixed in the next release, which should be up in a couple weeks. We will also try to get more recent snapshots with the bug fix up in the mean time. Sorry about that. Conrad Jean-Didier Marechal wrote:

Dear all,

I don't know whether my problem falls in "bug" or "user request" category, pcorry if I use the wrong list.

I am preparing a course where students will perform some protein-ligand dockings. I was thinking in minimizing the ligand in chimera using the "minimize structure" tool.

I have installed the 1.2356 (that's what I thought but the message in the "About UCSF Chimera" pop up window says 1.2376 actually) version of chimera on ubuntu 6.10 and when I try to minimize my ligand (a HIV protease inhibitor), I am stopped at the PARMCHK run. Chimera seems to have compatibility problems with numpy. I join here the message given in the reply log file:

.... Charges for residue U0E determined Total charge for #0: 1.0000 Running PARMCHK for U0E1.pdb command: /usr/local/chimera/bin/antechamber/exe/parmchk -i /tmp/tmpc6R8F8/parmchk.in.0 -f mol2 -o /tmp/tmpc6R8F8/frcmod.0 -p /usr/local/chimera/share/MMMD/parm/gaff.dat Finished PARMCHK for U0E1.pdbThis version of Chimera uses numpy for calculations. Numeric is only available in Chimera 1.2318 and earlier.

Is there an easy way to move around this problem or should I install a earlier version of chimera for the moment?

cheers, JD

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