[phenixbb] Elbow ligand building
Nigel W Moriarty
NWMoriarty at lbl.gov
Wed Nov 4 10:09:47 PST 2009
On 11/4/09 9:35 AM, Joe Krahn wrote:
> I have an accurate reference structure, but elbow seems to "regularize"
> the coordinates in a way the distorts the structure. Is there a way to
> disable this?
eLBOW will always run a simple optimisation unless you specify the final
geometry you like using
phenix.elbow --final-geometry accurate.pdb
Naturally, you are smart to use a better input format thus
phenix.elbow filename.sdf --final-geometry accurate.pdb
> With --opt, QM optimization should hopefully remove distortions, but it
> is not doing a very good job for this molecule. So, I decided to
> optimize using Gaussian, and a better basis set.
> It seems that the Gaussian interface is still fairly simple, and it
> seems that you have to edit the Gaussian.csh template. So, I did that,
> but got the "Gaussian does not seem to be installed" message.
> Unfortunately, elbow runs the Gaussian script with output to /dev/null,
> so there is no way to see any error messages. Maybe that should be done
> only when the --quiet flag is given.
Maybe I'll implement this with a --verbose flag.
> I edited the Python source to let errors go to the tty, and found that
> the problem is in the way the script is invoked using "csh -c %s.csh".
> That only works if "." is in your $PATH, which is often the case. It
> also invokes an extra instance of csh, because it is invoked as a system
> command. The correct way to run a shell script is to leave out the '-c'.
> Elbow makes the script executable, so an even better approach is to just
> leave out "csh", and do "os.system('./%s.csh' % project)". Then, the
> script can be in sh/bash/etc. Maybe the was the intent of using '-c'?
This is old code from before PHENIX had a smart module for running
commands. I'll update to code.
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty at LBL.gov
Web : CCI.LBL.gov
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