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insane.py -rotate option doesn't work
- almeida
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8 years 1 month ago - 8 years 1 month ago #5433
by almeida
insane.py -rotate option doesn't work was created by almeida
Hello,
In insane.py, the option -rotate does not work. I am particularly interested in rotate a protein along the z axis, to have different angles with the membrane xy plane.
Best
Yasser
In insane.py, the option -rotate does not work. I am particularly interested in rotate a protein along the z axis, to have different angles with the membrane xy plane.
Best
Yasser
Last edit: 8 years 1 month ago by almeida.
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- peterkroon
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8 years 1 month ago #5434
by peterkroon
Replied by peterkroon on topic insane.py -rotate option doesn't work
Please provide your exact command, what you expected to find, and what you found instead. Otherwise we're all just guessing in the dark.
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- almeida
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8 years 1 month ago #5435
by almeida
Replied by almeida on topic insane.py -rotate option doesn't work
I tried:
insane.py -f protein.gro -o protein_DPPC.test_rotate.gro -pbc square -box 10,10,10 -d 1 -l DPPC -sol W -center -rotate angle 45
... and I got:
Traceback (most recent call last):
File "/home/hernandez/bin/insane.py", line 703, in <module>
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '45'
I've tried -rotate with 'random' and 'princ'. It seems that rotation is performed in the xy membrane plane, but I need to rotate in z axis, so the protein span through the membrane at different angles
insane.py -f protein.gro -o protein_DPPC.test_rotate.gro -pbc square -box 10,10,10 -d 1 -l DPPC -sol W -center -rotate angle 45
... and I got:
Traceback (most recent call last):
File "/home/hernandez/bin/insane.py", line 703, in <module>
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
KeyError: '45'
I've tried -rotate with 'random' and 'princ'. It seems that rotation is performed in the xy membrane plane, but I need to rotate in z axis, so the protein span through the membrane at different angles
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- tsjerk
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8 years 1 month ago #5436
by tsjerk
Replied by tsjerk on topic insane.py -rotate option doesn't work
The rotation capabilities are currently limited, although the fact that it doesn't take numbers should be corrected. If you need to rotate around other axes than the z-axis, you can preprocess using editconf -rotate.
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- almeida
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8 years 1 month ago #5437
by almeida
Replied by almeida on topic insane.py -rotate option doesn't work
Thanks, editconf -rotate solved my problem.
Best
Yasser
Best
Yasser
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