search

MDAnalysis / RotamerConvolveMD

Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
https://www.mdanalysis.org/RotamerConvolveMD
GNU General Public License v2.0
7 stars 4 forks source link

useNOelectron required for convolve-mtss-rotamers.py #31

Open yfichou opened 5 years ago

yfichou commented 5 years ago

Hello, I'm running rotamerConvolveMD 1.3.0 with Window.

I got the following error when trying to run convolve-mtss-rotamers.py. The script run fine if the --useNoelectron option is added though.

Yann

convolve-mtss-rotamers.py --resid 161 183 --histogramBins 0 80 1 --clashDistance 2.2 --output "testOutput" --plotname "plotname.pdf" --outputRawDistances "dataOut" --dcdfilename "testDCD" --dcdfilenameNoClashes "testDCD_noClash" 5o3l-o-t_resnr.pdb MDAnalysis : INFO MDAnalysis 0.19.2 STARTED logging to 'MDAnalysis.log' MDAnalysis.app: INFO Rotamer Convolve MD, release 1.3.0 --- Copyright (c) Philip W Fowler, Oliver Beckstein, Katrin Reichel, and AUTHORS 2011-2017 MDAnalysis.app: INFO Released under the GNU Public Licence, version 2 (or higher) MDAnalysis.app: INFO Please cite: LS Stelzl, PW Fowler, MSP Sansom, O Beckstein. J Mol Biol 426 (2014), 735-751, doi:10.1016/j.jmb.2013.10.024 MDAnalysis.app: INFO Loading trajectory data as Universe(5o3l-o-t_resnr.pdb) MDAnalysis.app: INFO Using rotamer library 'MTSSL 298K 2015' by Gunnar Jeschke MDAnalysis.app: INFO Please cite: Polyhach Y, Bordignon E, Jeschke G. Phys Chem Chem Phys. 2011; 13(6):2356-2366. doi: 10.1039/c0cp01865a MDAnalysis.app: INFO Starting rotamer distance analysis of trajectory 5o3l-o-t_resnr.pdb... MDAnalysis.app: INFO clashDistance = 2.2 A; rotamer library = 'MTSSL 298K 2015' Step 3/3 [100.0%] Traceback (most recent call last): File "C:\Users\Yann\Anaconda3\Scripts\convolve-mtss-rotamers.py", line 107, in useNOelectron=options.useNOelectron) File "C:\Users\Yann\Anaconda3\lib\site-packages\rotcon\convolve.py", line 194, in init distances.append(distance) UnboundLocalError: local variable 'distance' referenced before assignment

orbeckst commented 5 years ago

@katrinr any idea? – I think that might have happened when --useNOelectron was introduced.

katrinr commented 5 years ago

Thanks for using RotamerConvolveMD. Did you run the tests (e.g. https://github.com/MDAnalysis/RotamerConvolveMD/blob/master/tests/mtssl_2015/test_mtssl_2015.sh) and did it go smoothly? Are you using MTSL and what is the name of the atom (O1 in the pdb or sth. else)?

orbeckst commented 5 years ago

The tests all use --useNOelectron. I don't think we have tests without it with the alternative option.

-- Oliver Beckstein email: orbeckst@gmail.com

Am Jun 1, 2019 um 11:34 schrieb Katrin Reichel notifications@github.com:

Thanks for using RotamerConvolveMD. Did you run the tests (e.g. https://github.com/MDAnalysis/RotamerConvolveMD/blob/master/tests/mtssl_2015/test_mtssl_2015.sh) and did it go smoothly? Are you using MTSL and what is the name of the atom (O1 in the pdb or sth. else)?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.