RE: [PyMOL] Transparent cartoons?

[DeLano, Warren]

Fred,

Not currently.  To the rest of the list:  How important is this to 
people?  Please send me an email directly if you think it would be an important 
feature to add.

Warren


--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D. 
Informatics Manager 
Sunesis Pharmaceuticals, Inc. 
341 Oyster Point Blvd. 
S. San Francisco, CA 94080 
(650)-266-3606 FAX:(650)-266-3501



> -Original Message-
> From: Fred Berkovitch [mailto:fr...@mit.edu]
> Sent: Monday, March 17, 2003 6:41 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Transparent cartoons?
> 
> 
> Hello everyone,
> 
> Can pymol make transparent cartoons?  If so, how?
> 
> -Fred
> 
> 
> 
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Re: [PyMOL] fink install fail: pymol-0.86-4

[Matt Stephenson]

On Wednesday, Mar 19, 2003, at 07:42 Australia/Sydney, DeLano, Warren 
wrote:



Kevin,

	It looks to me like you are missing Numeric Python.  Either you need 
to remove the _PYMOL_NUMPY option from the Rules.make, or you need 
Numpy installed.  There is likely a Fink package which contains it, 
but I suspect this dependency may have been missed in the creation of 
the Fink PyMOL package.


No this is a problem in the fink unstable tree due to python-2.3 and 
numeric being install in the wrong spot.


Cheers
Matt

Re: [PyMOL] fink install fail: pymol-0.86-4

[Matt Stephenson]

Do this,

fink install python-2.2.2

fink rebuild numeric

fink rebuild pmw

fink install pymol

Cheers
Matt



On Wednesday, Mar 19, 2003, at 05:58 Australia/Sydney, Kevin Gardner 
wrote:



Hi all:
I'll continue on a thread from a couple of weeks ago, re: failed
fink-based installs of pymol over the past month or so.  Here's the
machine setup:

- attempting to install pymol-0.86-4 onto OS 10.2.4
- python (2.3a2-1), python22 (2.2.2-4) and python22-shlibs
(2.2.4) all installed
- running Apple's X11 (v0.2 and now 0.3) w/SDK installed,
other X programs compiling OK

Output from the build attached below --- anyone have any insights
here?

Thanks,
Kevin

--

cd pyopengl;make
cc -ffast-math -no-cpp-precomp -g -I/sw/include 
-I/sw/include/python2.2 -I/usr/X11R6/include -D_HAVE_LIBPNG  
-D_PYMOL_MODULE -D_PYMOL_NUMPY -DHAVE_ARRAYOBJECT_H -c 
_glu_nummodule.c -DPythonTypes

In file included from _glu_nummodule.c:8:
_glumodule.c: In function `py_glu_NewTess':
_glumodule.c:346: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type

In file included from _glu_nummodule.c:8:
_glumodule.c:637:33: Numeric/arrayobject.h: No such file or directory
_glumodule.c: In function `py_glu_Build2DMipmaps':
_glumodule.c:723: `PyArrayObject' undeclared (first use in this 
function)

_glumodule.c:723: (Each undeclared identifier is reported only once
_glumodule.c:723: for each function it appears in.)
_glumodule.c:723: `ap' undeclared (first use in this function)
_glumodule.c:741: parse error before ')' token
_glumodule.c:744: parse error before ')' token
make[2]: *** [_glu_nummodule.o] Error 1
make[1]: *** [make-pyopengl] Error 2
make: *** [.contrib] Error 2
### execution of make failed, exit code 2
Failed: compiling pymol-0.86-4 failed

--
**
Kevin Gardner, Ph.D.  kevin.gard...@utsouthwestern.edu
Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
214-648-8916/FAX: -8947  http://freedom7.swmed.edu



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Re: [PyMOL] fink install fail: pymol-0.86-4

[Ian Robinson]

On 18/3/03 8:42 pm, "DeLano, Warren"  wrote:

> There is likely a Fink package which contains it, but I suspect this
> dependency may have been missed in the creation of the Fink PyMOL package.

I installed PyMOL using Fink Commander on MacOS X 10.2.4. Fink Commander
will download the source files and compile them automatically.

PyMOL works nicely under Apple's X11 beta.

Ian
-- 
Ian Robinson - Belfast - UK

RE: [PyMOL] fink install fail: pymol-0.86-4

[DeLano, Warren]

Kevin,

It looks to me like you are missing Numeric Python.  Either you need to 
remove the _PYMOL_NUMPY option from the Rules.make, or you need Numpy 
installed.  There is likely a Fink package which contains it, but I suspect 
this dependency may have been missed in the creation of the Fink PyMOL package.

A quick workaround would be to remove the _PYMOL_NUMPY define from the 
PyMOL Rules.make file.

Cheers,
Warren


--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D. 
Informatics Manager 
Sunesis Pharmaceuticals, Inc. 
341 Oyster Point Blvd. 
S. San Francisco, CA 94080 
(650)-266-3606 FAX:(650)-266-3501



> -Original Message-
> From: Kevin Gardner [mailto:kevin.gard...@utsouthwestern.edu]
> Sent: Tuesday, March 18, 2003 10:59 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] fink install fail: pymol-0.86-4
> 
> 
> Hi all:
>  I'll continue on a thread from a couple of weeks ago, re: failed
> fink-based installs of pymol over the past month or so.  Here's the
> machine setup:
> 
>   - attempting to install pymol-0.86-4 onto OS 10.2.4
>   - python (2.3a2-1), python22 (2.2.2-4) and python22-shlibs
>   (2.2.4) all installed
>   - running Apple's X11 (v0.2 and now 0.3) w/SDK installed,
>   other X programs compiling OK
> 
> Output from the build attached below --- anyone have any insights
> here?
> 
> Thanks,
> Kevin
> 
> --
> 
> cd pyopengl;make
> cc -ffast-math -no-cpp-precomp -g -I/sw/include 
> -I/sw/include/python2.2 
> -I/usr/X11R6/include -D_HAVE_LIBPNG  -D_PYMOL_MODULE -D_PYMOL_NUMPY 
> -DHAVE_ARRAYOBJECT_H -c _glu_nummodule.c -DPythonTypes
> In file included from _glu_nummodule.c:8:
> _glumodule.c: In function `py_glu_NewTess':
> _glumodule.c:346: warning: passing arg 3 of `gluTessCallback' from 
> incompatible pointer type
> _glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from 
> incompatible pointer type
> _glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from 
> incompatible pointer type
> _glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from 
> incompatible pointer type
> _glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from 
> incompatible pointer type
> In file included from _glu_nummodule.c:8:
> _glumodule.c:637:33: Numeric/arrayobject.h: No such file or directory
> _glumodule.c: In function `py_glu_Build2DMipmaps':
> _glumodule.c:723: `PyArrayObject' undeclared (first use in 
> this function)
> _glumodule.c:723: (Each undeclared identifier is reported only once
> _glumodule.c:723: for each function it appears in.)
> _glumodule.c:723: `ap' undeclared (first use in this function)
> _glumodule.c:741: parse error before ')' token
> _glumodule.c:744: parse error before ')' token
> make[2]: *** [_glu_nummodule.o] Error 1
> make[1]: *** [make-pyopengl] Error 2
> make: *** [.contrib] Error 2
> ### execution of make failed, exit code 2
> Failed: compiling pymol-0.86-4 failed
> 
> -- 
> **
> Kevin Gardner, Ph.D.  kevin.gard...@utsouthwestern.edu
> Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
> 214-648-8916/FAX: -8947
http://freedom7.swmed.edu



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[PyMOL] fink install fail: pymol-0.86-4

[Kevin Gardner]

Hi all:
I'll continue on a thread from a couple of weeks ago, re: failed
fink-based installs of pymol over the past month or so.  Here's the
machine setup:

- attempting to install pymol-0.86-4 onto OS 10.2.4
- python (2.3a2-1), python22 (2.2.2-4) and python22-shlibs
(2.2.4) all installed
- running Apple's X11 (v0.2 and now 0.3) w/SDK installed,
other X programs compiling OK

Output from the build attached below --- anyone have any insights
here?

Thanks,
Kevin

--

cd pyopengl;make
cc -ffast-math -no-cpp-precomp -g -I/sw/include -I/sw/include/python2.2 
-I/usr/X11R6/include -D_HAVE_LIBPNG  -D_PYMOL_MODULE -D_PYMOL_NUMPY 
-DHAVE_ARRAYOBJECT_H -c _glu_nummodule.c -DPythonTypes

In file included from _glu_nummodule.c:8:
_glumodule.c: In function `py_glu_NewTess':
_glumodule.c:346: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:347: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:348: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:349: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type
_glumodule.c:351: warning: passing arg 3 of `gluTessCallback' from 
incompatible pointer type

In file included from _glu_nummodule.c:8:
_glumodule.c:637:33: Numeric/arrayobject.h: No such file or directory
_glumodule.c: In function `py_glu_Build2DMipmaps':
_glumodule.c:723: `PyArrayObject' undeclared (first use in this function)
_glumodule.c:723: (Each undeclared identifier is reported only once
_glumodule.c:723: for each function it appears in.)
_glumodule.c:723: `ap' undeclared (first use in this function)
_glumodule.c:741: parse error before ')' token
_glumodule.c:744: parse error before ')' token
make[2]: *** [_glu_nummodule.o] Error 1
make[1]: *** [make-pyopengl] Error 2
make: *** [.contrib] Error 2
### execution of make failed, exit code 2
Failed: compiling pymol-0.86-4 failed

--
**
Kevin Gardner, Ph.D.  kevin.gard...@utsouthwestern.edu
Asst. Professor, Dept. of Biochemistry, UT Southwestern Medical Center
214-648-8916/FAX: -8947  http://freedom7.swmed.edu