Unable to find Engines?

Hello to everyone involved in Avogadro; I look forward to using it in KDE4.
So, after having seen a program called Chem3D at school, I decided to
seriously look into Avogadro. I’m now trying to figure out how to actually
render anything, as I receive an error any time I try to open one of the test
files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I have
no engines in the list where I’ve seen them in the screenshots. Any advice on
what I should do?
Thanks,
Ben

My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1

Hi,

If you are compining from trunk try to copy the executable
/avogadro/src/avogadro to /usr/bin or /usr/local/bin/, I have to
do the same here in order to able it work… (the reason you have no
engines is because they are not from the same compilation process as
your executable.

Let me know if this helped…

Tim

On Dec 8, 2007 9:03 PM, Ben Lewis benjf5@gmail.com wrote:

Hello to everyone involved in Avogadro; I look forward to using it in KDE4.
So, after having seen a program called Chem3D at school, I decided to
seriously look into Avogadro. I’m now trying to figure out how to actually
render anything, as I receive an error any time I try to open one of the test
files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I have
no engines in the list where I’ve seen them in the screenshots. Any advice on
what I should do?
Thanks,
Ben

My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1


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I’ve tried all sorts of stuff, but nothing will allow me to open a file.
I just realised, I haven’t posted any specs at all… Kubuntu Gutsy (7.10) w/
a Pentium D 805…

~Ben
On Saturday 08 December 2007 14:07:57 you wrote:

Hi,

If you are compining from trunk try to copy the executable
/avogadro/src/avogadro to /usr/bin or /usr/local/bin/, I have to
do the same here in order to able it work… (the reason you have no
engines is because they are not from the same compilation process as
your executable.

Let me know if this helped…

Tim

On Dec 8, 2007 9:03 PM, Ben Lewis benjf5@gmail.com wrote:

Hello to everyone involved in Avogadro; I look forward to using it in
KDE4. So, after having seen a program called Chem3D at school, I decided
to seriously look into Avogadro. I’m now trying to figure out how to
actually render anything, as I receive an error any time I try to open
one of the test files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I
have no engines in the list where I’ve seen them in the screenshots. Any
advice on what I should do?
Thanks,
Ben

My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1


SF.Net email is sponsored by:
Check out the new SourceForge.net Marketplace.
It’s the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1

On Dec 8, 2007 9:18 PM, Ben Lewis benjf5@gmail.com wrote:

I’ve tried all sorts of stuff, but nothing will allow me to open a file.
I just realised, I haven’t posted any specs at all… Kubuntu Gutsy (7.10) w/
a Pentium D 805…

Have you installed the lastest version of openbabel trunk? And if so,
make sure it’s installed to the right location. Do you have openbabel
and/or avogadro in your /usr and /usr/local?

And have you tried another file format? Because methane.cml isn’t
working here too. testfiles/1CRN.pdb is working however. But you
should always be able to see the engines and tools if openbabel and
avogadro are installed correctly.

On Saturday 08 December 2007 14:07:57 you wrote:

Hi,

If you are compining from trunk try to copy the executable
/avogadro/src/avogadro to /usr/bin or /usr/local/bin/, I have to
do the same here in order to able it work… (the reason you have no
engines is because they are not from the same compilation process as
your executable.

Let me know if this helped…

Tim

On Dec 8, 2007 9:03 PM, Ben Lewis benjf5@gmail.com wrote:

Hello to everyone involved in Avogadro; I look forward to using it in
KDE4. So, after having seen a program called Chem3D at school, I decided
to seriously look into Avogadro. I’m now trying to figure out how to
actually render anything, as I receive an error any time I try to open
one of the test files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I
have no engines in the list where I’ve seen them in the screenshots. Any
advice on what I should do?
Thanks,
Ben

My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1


SF.Net email is sponsored by:
Check out the new SourceForge.net Marketplace.
It’s the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1

This is probably OpenBabel not finding the CML plugin. Probably your
BABEL_LIBDIR variable is not properly set. You can see on the Avogadro wiki
how to set it (adapt to your own case; notice that the path won’t be the same
depending of whether you use OpenBabel with or without installation).

Cheers,
Benoit

On Saturday 08 December 2007 21:03:26 Ben Lewis wrote:

Hello to everyone involved in Avogadro; I look forward to using it in KDE4.
So, after having seen a program called Chem3D at school, I decided to
seriously look into Avogadro. I’m now trying to figure out how to actually
render anything, as I receive an error any time I try to open one of the
test files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I
have no engines in the list where I’ve seen them in the screenshots. Any
advice on what I should do?
Thanks,
Ben

I can now open any of the files, as well as draw my own molecules, however I
have a slightly different problem in that I cannot save a file in a way that
is useful…

On Sunday 09 December 2007 01:10:28 you wrote:

This is probably OpenBabel not finding the CML plugin. Probably your
BABEL_LIBDIR variable is not properly set. You can see on the Avogadro wiki
how to set it (adapt to your own case; notice that the path won’t be the
same depending of whether you use OpenBabel with or without installation).

Cheers,
Benoit

On Saturday 08 December 2007 21:03:26 Ben Lewis wrote:

Hello to everyone involved in Avogadro; I look forward to using it in
KDE4. So, after having seen a program called Chem3D at school, I decided
to seriously look into Avogadro. I’m now trying to figure out how to
actually render anything, as I receive an error any time I try to open
one of the test files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I
have no engines in the list where I’ve seen them in the screenshots. Any
advice on what I should do?
Thanks,
Ben


My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1

Hm, that’s already better!
Can you be more specific about your file-saving problem?
Can you cut-and-paste and error message and the console output ?

On Sunday 09 December 2007 08:17:17 Ben Lewis wrote:

I can now open any of the files, as well as draw my own molecules, however
I have a slightly different problem in that I cannot save a file in a way
that is useful…

On Sunday 09 December 2007 01:10:28 you wrote:

This is probably OpenBabel not finding the CML plugin. Probably your
BABEL_LIBDIR variable is not properly set. You can see on the Avogadro
wiki how to set it (adapt to your own case; notice that the path won’t be
the same depending of whether you use OpenBabel with or without
installation).

Cheers,
Benoit

On Saturday 08 December 2007 21:03:26 Ben Lewis wrote:

Hello to everyone involved in Avogadro; I look forward to using it in
KDE4. So, after having seen a program called Chem3D at school, I
decided to seriously look into Avogadro. I’m now trying to figure out
how to actually render anything, as I receive an error any time I try
to open one of the test files, any of them. The error from within
Avogadro is: Cannot read file format of file
$HOME/svn/avogadro/testfiles/methane.cml. I’ve been running Avogadro
from Terminal, and no error appears there. I have no engines in the
list where I’ve seen them in the screenshots. Any advice on what I
should do?
Thanks,
Ben

Just wondering, is there a specific format I should be selecting? I would
imagine that some are better supported than others.
–EDIT:Whoops, forgot to CC the list…
On Sunday 09 December 2007 01:20:24 you wrote:

Hm, that’s already better!
Can you be more specific about your file-saving problem?
Can you cut-and-paste and error message and the console output ?

On Sunday 09 December 2007 08:17:17 Ben Lewis wrote:

I can now open any of the files, as well as draw my own molecules,
however I have a slightly different problem in that I cannot save a file
in a way that is useful…

On Sunday 09 December 2007 01:10:28 you wrote:

This is probably OpenBabel not finding the CML plugin. Probably your
BABEL_LIBDIR variable is not properly set. You can see on the Avogadro
wiki how to set it (adapt to your own case; notice that the path won’t
be the same depending of whether you use OpenBabel with or without
installation).

Cheers,
Benoit

On Saturday 08 December 2007 21:03:26 Ben Lewis wrote:

Hello to everyone involved in Avogadro; I look forward to using it in
KDE4. So, after having seen a program called Chem3D at school, I
decided to seriously look into Avogadro. I’m now trying to figure out
how to actually render anything, as I receive an error any time I try
to open one of the test files, any of them. The error from within
Avogadro is: Cannot read file format of file
$HOME/svn/avogadro/testfiles/methane.cml. I’ve been running Avogadro
from Terminal, and no error appears there. I have no engines in the
list where I’ve seen them in the screenshots. Any advice on what I
should do?
Thanks,
Ben


My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1

huh… maybe something hadn’t loaded properly… because now there’s no
problem at all… I don’t get it… but it works!
Thanks, and maybe that should go on the recommendations list? Actual formats,
instead of a catch-all Save-As window?
On Sunday 09 December 2007 01:33:52 you wrote:

Hm, I never used “save as…” and now I notice that there’s a problem: no
particular file formats are suggested.

Anyway, have you tried saving as .cml ? I tried here and it worked fine.

On Sunday 09 December 2007 08:25:55 you wrote:

Just wondering, is there a specific format I should be selecting? I would
imagine that some are better supported than others.

On Sunday 09 December 2007 01:20:24 you wrote:

Hm, that’s already better!
Can you be more specific about your file-saving problem?
Can you cut-and-paste and error message and the console output ?

On Sunday 09 December 2007 08:17:17 Ben Lewis wrote:

I can now open any of the files, as well as draw my own molecules,
however I have a slightly different problem in that I cannot save a
file in a way that is useful…

On Sunday 09 December 2007 01:10:28 you wrote:

This is probably OpenBabel not finding the CML plugin. Probably
your BABEL_LIBDIR variable is not properly set. You can see on the
Avogadro wiki how to set it (adapt to your own case; notice that
the path won’t be the same depending of whether you use OpenBabel
with or without installation).

Cheers,
Benoit

On Saturday 08 December 2007 21:03:26 Ben Lewis wrote:

Hello to everyone involved in Avogadro; I look forward to using
it in KDE4. So, after having seen a program called Chem3D at
school, I decided to seriously look into Avogadro. I’m now trying
to figure out how to actually render anything, as I receive an
error any time I try to open one of the test files, any of them.
The error from within Avogadro is: Cannot read file format of
file
$HOME/svn/avogadro/testfiles/methane.cml. I’ve been running
Avogadro from Terminal, and no error appears there. I have no
engines in the list where I’ve seen them in the screenshots. Any
advice on what I should do?
Thanks,
Ben


My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1

Yes, definitely. I won’t do that myself as, not being a chemist, I really
don’t know which formats should be suggested (though .cml is definitely one
of them).

Cheers,

Benoit

On Sunday 09 December 2007 08:37:18 Ben Lewis wrote:

huh… maybe something hadn’t loaded properly… because now there’s no
problem at all… I don’t get it… but it works!
Thanks, and maybe that should go on the recommendations list? Actual
formats, instead of a catch-all Save-As window?

On Sunday 09 December 2007 01:33:52 you wrote:

Hm, I never used “save as…” and now I notice that there’s a problem: no
particular file formats are suggested.

Anyway, have you tried saving as .cml ? I tried here and it worked fine.

On Sunday 09 December 2007 08:25:55 you wrote:

Just wondering, is there a specific format I should be selecting? I
would imagine that some are better supported than others.

On Sunday 09 December 2007 01:20:24 you wrote:

Hm, that’s already better!
Can you be more specific about your file-saving problem?
Can you cut-and-paste and error message and the console output ?

On Sunday 09 December 2007 08:17:17 Ben Lewis wrote:

I can now open any of the files, as well as draw my own molecules,
however I have a slightly different problem in that I cannot save a
file in a way that is useful…

On Sunday 09 December 2007 01:10:28 you wrote:

This is probably OpenBabel not finding the CML plugin. Probably
your BABEL_LIBDIR variable is not properly set. You can see on
the Avogadro wiki how to set it (adapt to your own case; notice
that the path won’t be the same depending of whether you use
OpenBabel with or without installation).

Cheers,
Benoit

On Saturday 08 December 2007 21:03:26 Ben Lewis wrote:

Hello to everyone involved in Avogadro; I look forward to using
it in KDE4. So, after having seen a program called Chem3D at
school, I decided to seriously look into Avogadro. I’m now
trying to figure out how to actually render anything, as I
receive an error any time I try to open one of the test files,
any of them. The error from within Avogadro is: Cannot read
file format of file
$HOME/svn/avogadro/testfiles/methane.cml. I’ve been running
Avogadro from Terminal, and no error appears there. I have no
engines in the list where I’ve seen them in the screenshots.
Any advice on what I should do?
Thanks,
Ben

I thought I fixed this? Is it not working again?

(Sat, Dec 08, 2007 at 09:07:57PM +0100) Tim Vandermeersch tim.vandermeersch@gmail.com:

Hi,

If you are compining from trunk try to copy the executable
/avogadro/src/avogadro to /usr/bin or /usr/local/bin/, I have to
do the same here in order to able it work… (the reason you have no
engines is because they are not from the same compilation process as
your executable.

Let me know if this helped…

Tim

On Dec 8, 2007 9:03 PM, Ben Lewis benjf5@gmail.com wrote:

Hello to everyone involved in Avogadro; I look forward to using it in KDE4.
So, after having seen a program called Chem3D at school, I decided to
seriously look into Avogadro. I’m now trying to figure out how to actually
render anything, as I receive an error any time I try to open one of the test
files, any of them. The error from within Avogadro is:
Cannot read file format of file $HOME/svn/avogadro/testfiles/methane.cml.
I’ve been running Avogadro from Terminal, and no error appears there. I have
no engines in the list where I’ve seen them in the screenshots. Any advice on
what I should do?
Thanks,
Ben

My PGP key (can be found on the Ubuntu Keyserver) is:
0x0E8BCAA1,
Fingerprint:
74D9 E4BE 2F95 3806 E2FA 7E04 8A71 5831 0E8B CAA1


SF.Net email is sponsored by:
Check out the new SourceForge.net Marketplace.
It’s the best place to buy or sell services for
just about anything Open Source.
http://sourceforge.net/services/buy/index.php


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel


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Check out the new SourceForge.net Marketplace.
It’s the best place to buy or sell services for
just about anything Open Source.
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