[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.
Good thinking.
> 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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