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Normal mode analysis from VMD #1467
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How did you install ProDy? |
I installed it manually by using the source code downloaded from this link. |
You downloaded those files and then did what? |
Why didn't you just use |
Well I was having problem with pip which may be due different python version. tar -xzf ProDy-x.y.z.tar.gz |
ok Have you checked whether you got the prody executables in your installation directory? You probably need to use build_ext too |
We usually recommend using anaconda to handle pip and all the other environment things so you may want to consider that. |
Yes I get that because previuosly when I installed PRODY in my system it was working fine with VMD. But I had to format it due some ubuntu repository problem and reinstalled. This time I am getting this problem. Thanks for your help. |
I'm not sure I've really helped yet but you're welcome anyway |
Ok |
We usually use build_ext. It should build the c extensions I think. We use it for development install (see http://prody.csb.pitt.edu/manual/devel/develop.html) |
Ok I will check this too and update. |
Great that the executables are there. I don't really know what the problem is then. It sounds like something to do with VMD not finding them. Is /usr/local/bin in your PATH? |
Yes /usr/local/bin is in PATH. |
Did you make sure that your prody python module is also in your PYTHONPATH? |
Any luck yet? Otherwise, we could arrange a video call to look at it. |
Actually I am out of my institute due to family issues so I am not able to look into it. Will contact you once I reach the institute. |
Ok, no worries. Hope everything is as ok as it can be |
I have installed PRODY. When I am running Normal mode wizard from VMD it show error message as following.
Traceback (most recent call last):
File "/usr/local/bin/prody", line 6, in
from pkg_resources import load_entry_point
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3088, in
@_call_aside
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3072, in _call_aside
f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3101, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 574, in _build_master
ws.require(requires)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 892, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 778, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ProDy==2.0.1' distribution was not found and is required by the application
Traceback (most recent call last):
File "/usr/local/bin/prody", line 6, in
from pkg_resources import load_entry_point
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3088, in
@_call_aside
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3072, in _call_aside
f(args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 3101, in _initialize_master_working_set
working_set = WorkingSet._build_master()
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 574, in _build_master
ws.require(requires)
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 892, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 778, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ProDy==2.0.1' distribution was not found and is required by the application
while executing
"exec $::NMWiz::pybin $::NMWiz::prody anm --quiet -s $selstr {}$args "$pdbfn""
(procedure "::NMWiz::prodySubmitANMjob" line 42)
invoked from within
"::NMWiz::prodySubmitANMjob"
(procedure "::NMWiz::prodySubmitJob" line 22)
invoked from within
"::NMWiz::prodySubmitJob"
invoked from within
".nmwizprody.submitFrame.prodySubmit invoke"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list $w invoke]"
(procedure "tk::ButtonUp" line 22)
invoked from within
"tk::ButtonUp .nmwizprody.submitFrame.prodySubmit"
(command bound to event).
Any suggestions would be appreciated.
THANKS
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