CRYSON Bug in Batch Mode?

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA, PyMOL plugin SASpy
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freemans
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Joined: 2015.09.22 13:46

CRYSON Bug in Batch Mode?

#1 Post by freemans » 2016.07.09 17:21

Hello All,

I am currently experiencing a potential bug in CRYSON in the most recent version.

When I try to run the software in batch mode in a directory, for example:

Code: Select all

$ cryson *.pdb -sm 0.2
I am always met with the error "Error -- Wrong extension: 27 ON 09-JUL-2016 17:16:46
ERROR STOP"

CRYSOL works absolutely fine if I try the same command.

I am using OSX El Capitan but have found that CRYSON also fails to run in this mode in Windows 10. Any help would be much appreciated since I am pretty stuck at this point as I need curves for 10,000 structures!

Cheers

EDIT: I've just discovered that the batch mode does work but there's a catch... If I put more than 32 PDB files in the same directory and try to run I get the above error. Below that and it works just fine. Still not too helpful though!

Alex
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Location: Planet Earth

Re: CRYSON Bug in Batch Mode?

#2 Post by Alex » 2016.07.10 18:31

it is probably due to old way the command line is processed which was changed in CRYSOL but apparently not in CRYSON.
I assume you need it for running GAJOE?.. or.. Anyway, what I typically do is smth like this:
$>for i in *.pdb; do crysol $i datafile.dat myoptions -kp; do rm *.sav *.alm *.flm; done
If you don't need it for EOM then remove '-kp' and 'do rm *.sav *.alm *.flm'.

HTH, Alex

freemans
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Posts: 9
Joined: 2015.09.22 13:46

Re: CRYSON Bug in Batch Mode?

#3 Post by freemans » 2016.07.12 16:12

Alex wrote:it is probably due to old way the command line is processed which was changed in CRYSOL but apparently not in CRYSON.
I assume you need it for running GAJOE?.. or.. Anyway, what I typically do is smth like this:
$>for i in *.pdb; do crysol $i datafile.dat myoptions -kp; do rm *.sav *.alm *.flm; done
If you don't need it for EOM then remove '-kp' and 'do rm *.sav *.alm *.flm'.

HTH, Alex

I tried what you said and it worked perfectly.

Thanks for the advice.

ckerr
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Posts: 86
Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: CRYSON Bug in Batch Mode?

#4 Post by ckerr » 2016.07.14 17:11

Thanks for reporting this, the bug has been fixed and the fix will be included in the next version of ATSAS

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