Gajoe -p command line options

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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JoshB918
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Gajoe -p command line options

#1 Post by JoshB918 » 2017.07.21 11:58

Hi all,

I am doing a lot of runs using the gajoe -p option, however I was wondering If there was a way to run this without having to go through each step every time.

So rather than having to do this every time:
gajoe -p
******* ------------------------------------------------------ *******
******* GAJOE - version 2.1 - (r9453) *******
******* Copyright (c) ATSAS Team *******
******* EMBL, Hamburg Outstation, 2007 - 2015 *******
******* *******
******* For doubts/questions please visit SAXIER forum: *******
******* http://www.saxier.org/forum/viewforum.php?f=10 *******
******* *******
******* In case of bugs please refer to: *******
******* G. Tria, D.I. Svergun, EMBL BioSAXS group *******
******* atsas@embl-hamburg.de *******
******* ------------------------------------------------------ *******
---------------------------- ATTENTION ------------------------------
Using a pool of PDBs could take a while due to the CRYSOL computation
---------------------------------------------------------------------
Number of experimental curves to fit? (default: 1) ................... :
Experimental data file name 1? (*.dat) .............................. : file.dat
Directory containing the PDB files? (default: .) ..................... : ./directory
Number of harmonics (min. 10, max. 50)? (default: 15) ................ :
Maximum s value (min. 0.1, max. 0.5)? (default: 0.500) ............... :
Number of points (min. 10, max. 201)? (default: 51) .................. :
Number of generations (min. 10) (default: 1000) ...................... :
Number of ensembles (min. 10) (default: 50) .......................... :
Ensemble size fixed? (default: no) ................................... :
Maximum number of curves per ensemble (min. 1, max. 50) (default: 20) :
Minimum number of curves per ensemble (min. 1) (default: 5) .......... :
Curve repetition in the ensemble allowed? (default: yes) ............. :
Constant subtraction allowed? (default: yes) ......................... :
Number of times you want the genetic algorithm repeated (min. 1)
(default: 100) ....................................................... :

I was hoping to simply pass a command such as:
gajoe file.dat ./directory -p

or some variation just so I would be able to speed up the work flow.
Is there a way of doing this that I have just missed?
Or does anyone know of a quick way to do this?

Thanks,
Josh

Alex
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Re: Gajoe -p command line options

#2 Post by Alex » 2017.09.25 16:56

perhaps try to put all your answers in the text file and run, like: $> gajoe -p < myanswers.txt

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