ATSAS 3.0 damaver error

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA, PyMOL plugin SASpy
Post Reply
Message
Author
jbhopkins
Active member
Posts: 15
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
Member
Posts: 5
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.

User avatar
AL
Administrator
Posts: 717
Joined: 2007.08.03 18:55
Location: EMBL Hamburg, Germany
Contact:

Re: ATSAS 3.0 damaver error

#3 Post by AL » 2019.11.20 07:10

Indeed. Thank you for reporting this.

Post Reply