ATSAS 3.0 damaver error

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
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jbhopkins
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Posts: 11
Joined: 2014.10.22 21:21
Location: BioCAT, Advanced Photon Source

ATSAS 3.0 damaver error

#1 Post by jbhopkins » 2019.11.07 18:21

Hi folks,

Congrats on the ATSAS 3.0 release! However, I've been trying to use it on Windows 10 and I can't get damaver to run. I've tried both from the command line and from Primus. If I install ATSAS 3.0 in the default directory (C:/Program Files (x86)/ATSAS 3.0.0) I get this error when I try to run damaver (from Primus):

>>> 11/12
>>> damaver --automatic=lysozyme- --symmetry=P1 lysozyme-1-1.pdb lysozyme-2-1.pdb lysozyme-3-1.pdb lysozyme-4-1.pdb lysozyme-5-1.pdb lysozyme-6-1.pdb lysozyme-7-1.pdb lysozyme-8-1.pdb lysozyme-9-1.pdb lysozyme-10-1.pdb
Read file .............................................. : lysozyme-1-1.pdb
Number of atoms ........................................ : 1781
Fineness of the structure .............................. : 2.600
Read file .............................................. : lysozyme-2-1.pdb
Number of atoms ........................................ : 1768
Fineness of the structure .............................. : 2.600

Initial Final
Orientation Distance Distance
1 1 1 0.5760 0.5447
1 1 -1 0.5498 0.5430
1 -1 1 0.5598 0.5360
1 -1 -1 0.5878 0.5636
-1 1 1 0.5486 0.5386
-1 1 -1 0.5620 0.5590
-1 -1 1 0.5668 0.5552
-1 -1 -1 0.5303 0.4966

Transformation matrix
-0.6135 0.7765 0.1437 -0.0225
0.1117 -0.0949 0.9892 0.0844
-0.7817 -0.6230 0.0285 0.1681
0.0000 0.0000 0.0000 1.0000

Wrote file ............................................. : lysozyme-2-1_aw_lysozyme-1-1.pdb
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.
'C:\Program' is not recognized as an internal or external command,
operable program or batch file.
error calling dam2alm
>>> An error occurred while running 'damaver' - aborted processing


If I install it in the old location (C:/atsas) I get a slightly different error (again run from Primus):

>>> 11/12
>>> damaver --automatic=lysozyme- --symmetry=P1 lysozyme-1-1.pdb lysozyme-2-1.pdb lysozyme-3-1.pdb lysozyme-4-1.pdb lysozyme-5-1.pdb lysozyme-6-1.pdb lysozyme-7-1.pdb lysozyme-8-1.pdb lysozyme-9-1.pdb lysozyme-10-1.pdb
Read file .............................................. : lysozyme-1-1.pdb
Number of atoms ........................................ : 1769
Fineness of the structure .............................. : 2.600
Read file .............................................. : lysozyme-2-1.pdb
Number of atoms ........................................ : 1767
Fineness of the structure .............................. : 2.600

Initial Final
Orientation Distance Distance
1 1 1 0.5371 0.5360
1 1 -1 0.5144 0.5018
1 -1 1 0.5046 0.5023
1 -1 -1 0.4828 0.4809
-1 1 1 0.5498 0.5482
-1 1 -1 0.5286 0.4975
-1 -1 1 0.5122 0.5102
-1 -1 -1 0.4988 0.4911

Transformation matrix
-0.5438 -0.8384 -0.0371 0.0090
0.6776 -0.4125 -0.6088 0.0363
0.4951 -0.3562 0.7924 0.1920
0.0000 0.0000 0.0000 1.0000

Wrote file ............................................. : lysozyme-2-1_aw_lysozyme-1-1.pdb
'C:\atsas\bin\dam2alm.exe" -ns 400 -lm 18 -sm 1.0 --modeltype=b "lysozyme-1-1.pdb' is not recognized as an internal or external command,
operable program or batch file.
'C:\atsas\bin\dam2alm.exe" -ns 400 -lm 18 -sm 1.0 --modeltype=b "lysozyme-2-1_aw_lysozyme-1-1.pdb' is not recognized as an internal or external command,
operable program or batch file.
error calling dam2alm
>>> An error occurred while running 'damaver' - aborted processing.


Either way it's not working. I suspect this is a bug, since it seems to be coming from an internal call from damaver to dam2alm, but if I'm doing something wrong please let me know.

- Jesse

han yin
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Posts: 3
Joined: 2019.10.11 13:30

Re: ATSAS 3.0 damaver error

#2 Post by han yin » 2019.11.13 23:31

I can confirm that i have encountered the exact same error when running DAMMIF from PRIMUS with ATSAS 3.0.0

I have tried to install 3.0.0 on different drives after a clean uninstall/install protocol. I have followed the PATH variable set up on this page here https://www.embl-hamburg.de/biosaxs/man ... stall.html, and i have tried on different computers. Same error occurs regardless.

This version also does not run on SCATTER BIOSIS despite i setting the path to ATSAS/bin.

This does not happen with 2.8.4. I was able to use that version to get DAMAVER running fine through PRIMUS and SCATTER Biosis.

Could dev look into this? seems like a bug is going on.

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AL
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Re: ATSAS 3.0 damaver error

#3 Post by AL » 2019.11.20 07:10

Indeed. Thank you for reporting this.

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