pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Joe,

> Thanks for the code!  I find the prospect of using this pretty exciting, and
> hope Warren can incorporate the function and (a) way(s) to call it into the
> distributed code.
> 
> I hope to steal some time to try to try this out here, and to try to
> convince the folks who run the 3D printers on campus to let us print some
> things.
> 
> For future reference, with what version of PyMOL, running in which
> environment, have U Alberta used this code?  It looks pretty
> straightforward, but you never know.

I was running 0.90 compiled from a source tarball, running under
Debian Linux.

> Also, if you or your client would like to comment at all about the size of
> PyMOL files that have been printed (both in terms of output object
> dimensions as well as numbers-of-atoms or molecular weight), I'd be very
> interested in reading about it.  

The molecules were 2 serotonin receptors and 12 serotonin molecules.
Dr. Warren Gallin, the researcher that commisioned the print job,
has sent you some files and some more detailed info about the
science involved.

The actual sizes of the printed serotonin receptors were about
5" x 5" x 4" and the serotonin molecules were about 1" x 1" x 1/4".

A screenshot of one of the serotonin receptors in pymol is here:

http://bebop.cns.ualberta.ca/~cwant/wgallin-pymol.jpg

A picture of the printer output of the receptor with an
orientation roughly matching the screenshot, and a few
serotonin molecules, is here:

http://bebop.cns.ualberta.ca/~cwant/wgallin-3d-printed.jpg
(I hope this is the right molecule ... the 2 receptor
molecules were visually quite similar.)

The 8.5" x 11" paper underneath the molecule should give
a decent indication of the size of the output.

> (From reading the general description of your facility I can translate, for
> instance, size into print times, but whatever PyMOL-specific details you
> want to provide would be great.)

The size in the stl file doesn't matter -- the 3D printing
software allows scaling to any size desired that will
fit within the machine's build volume. The only
thing to note here is that we had to scale all of the
molecules by the same factor for the output to be meaningful.

Regards,
Chris


-- 
Chris Want
Research Computing Support
Computing & Network Services
University of Alberta
Tel: 1-780-492-9418

> Actually, I've encountered this problem myself -- very annoying...
>
> What happened is that you saved the Terminal window settings while you
> had a PyMOL session open, so OS X inferred that you were indicating a
> desire to have PyMOL open as a default preference.
>
> The only way I know of changing this is to text-edit
> $HOME/Library/Preferences/com.apple.Terminal.plist and remove the
> ExecutionString entry which contains PyMOL.  That means deleting those
> two lines: the one which contains ExecutionString and the one with the
> PyMOL launch command.

The OS X Terminal.app allows you to customize various terminal windows 
by saving different sets of preferences.  What happens is that you 
somehow accidently saved the pymol-specific ones as your default.

Probably the simplest thing to do is

rm ~/Library/Preferences/com.apple.Terminal.plist

and either replace it with your carefully backed up copy, or else just 
re-set all the preferences next time you open terminal.

You can also avoid this problem by invoking pymol at the command line.  
For convenience,

alias pymol /Applications/PyMOL/Darwin/pymol.com

and then just type pymol next time you start it.  You can also open pdf 
files and/or .pml scripts in one command, eg:

alias pymol /Applications/PyMOL/Darwin/pymol.com -q 
/Users/username/pymol/alias.pml

Finally if you also are running the X-windows version, you may want to 
alias one of these to a different name (npymol or xpymol).

Bill

Hi, I'm having a strange problem.   I'm trying to install pymol 0.90 on a 
new computer (Windows XP Home Edition).   So far everytime I try to run 
pymol, a window will pop-up briefly telling me that if pymol doesn't start 
up immediately, to hit ENTER.   If I'm quick enough to hit enter or not, 
either way the window will disappear, and pymol doesn't start.   I've tried 
all four options:
PyMOL Viewer Only
PyMOL Full Screen
PyMOL + Tk-Tcl GUI + Console
PyMOL + Tk-Tcl GUI
and all do the same thing.   I then uninstalled pymol, and tried the .90 
release that required python, downloading and installing each release of 
python (2.3, 2.2.3, 2.1.3) as needed.   All with no go.   Then I tried the 
.86 release (with the right version of python), with the same result.

What am I missing?!

Thanks.

_________________________________________________________________
Get MSN 8 and enjoy automatic e-mail virus protection.  
http://join.msn.com/?page=features/virus

Hi Guys,

Attached you find a nice piece of artwork produced by Pymol 0.90. This 
happens when I switch my screen under Linux RedHat 8.0 or when the 
screen saver starts, which is obvious on a 1944 frame movie ;) The 
images seem to get overlaid.
Rendering would be an option if only double transparencies rendered as 
they should, but somehow that doesn't work fine.

For now I'll just redo it again this evening, while turning the 
screensaver off, but I thought just to mention it so it is known and 
maybe can be tackled in a future release.

However, if anyone wants a higher resolution copy of this piece of work 
to hang on the wall, just give me a mail ;) Actually, I've got about 
1500 nice images more :)

Cheers,

Tsjerk


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Tsjerk A. Wassenaar, M.Sc.
-- :) 	Molecular Dynamics Group
-- :) 	Dept. of Biophysical Chemistry
-- :) 	University of Groningen
-- :) 	Nijenborgh 4
-- :) 	9747 AG Groningen
-- :) 	The Netherlands
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- :)
-- :) 	Hi! I'm a .signature virus!
-- :) 	Copy me into your ~/.signature to help me spread!
-- :)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I'm stuck using some OS X computers that do not allow installation of 
software.  Does anyone have (or can quickly build) PyMOL 0.9 as a single 
directory that I can launch pymol.com from without having to make any changes 
to the system?  Given the circumstances, I probably need to work out of /tmp.  
The Irix binary behaves similarly but I couldn't get the Mac version to work 
without installing it.

thanks,
Nat

On Wed, Aug 20, 2003 at 11:54:26AM -0600, Chris Want wrote:
> 
> I'm not a pymol user per se, but I have had a
> client who really liked the 'surface' visualization
> from pymol and wanted to print some molecules off
> on the 3D printer. Unfortunately, pymol lacks an
> export export option for the 'STL' format, so
> I crafted together a little hack that quietly dumps
> out an STL file when a surface is created, which I
> hope may be of use to other users (or perhaps somebody
> who finds it useful, and who also has an
> understanding of the pymol user interface
> code, can create a button for it).

Thanks for the code!  I find the prospect of using this pretty exciting, and
hope Warren can incorporate the function and (a) way(s) to call it into the
distributed code.

I hope to steal some time to try to try this out here, and to try to
convince the folks who run the 3D printers on campus to let us print some
things.

For future reference, with what version of PyMOL, running in which
environment, have U Alberta used this code?  It looks pretty
straightforward, but you never know.

Also, if you or your client would like to comment at all about the size of
PyMOL files that have been printed (both in terms of output object
dimensions as well as numbers-of-atoms or molecular weight), I'd be very
interested in reading about it.  

(From reading the general description of your facility I can translate, for
instance, size into print times, but whatever PyMOL-specific details you
want to provide would be great.)

Best Regards,

--Joe

-- 
D. Joe Anderson, Asst. Sci.                    2252 Molecular Biology Bldg.                    
BBMB Research Computing Support 
www.bb.iastate.edu/computing                   bbs...@ia...

try resizing it using:

viewport width, height

Jon Ostrem

----- Original Message ----- 
From: "Michael Ford" <mf...@cc...>
To: <pym...@li...>
Sent: Thursday, August 28, 2003 8:18 AM
Subject: [PyMOL] pymol - screen hog


> So when I run pymol 9.0 under XP on my laptop, the molecule screen takes 
> up the whole screen and can't be minimized.  The programs works, but I 
> can't access the menus.  Any ideas...?
> 
> 
> Mike Ford
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 

So when I run pymol 9.0 under XP on my laptop, the molecule screen takes 
up the whole screen and can't be minimized.  The programs works, but I 
can't access the menus.  Any ideas...?


Mike Ford

Yes, but you need to write in Python directly.  For example:

from pymol import cmd
cmd.select("mysel","none")
for i in range(10,20): cmd.select("mysel","mysel or resi %d"%i)

Would work in a ".py" file.

Cheers,
Warren

--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Shu-Hsien Sheu
> Sent: Wednesday, August 27, 2003 1:10 PM
> To: pym...@li...
> Subject: [PyMOL] Python commands and variables
> 
> Hi,
> 
> I am new to Pymol with some experiences with Python.
> I have a basic question which maybe a little stupid.
> Does Pymal take Python commands in selecting atoms?
> For instance:
> 
> i = range(1, 299)
> select resi i
> 
> or, further:
> for i in range(1, 299)
>     select  resi i
> 
> I understand the above can be easily done with:
> select resi 1-288
> 
> However, I am wondering if variables can work in Pymol in general.
> 
> Thanks!
> 
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi, 

I am new to Pymol with some experiences with Python.
I have a basic question which maybe a little stupid.
Does Pymal take Python commands in selecting atoms?
For instance:

i = range(1, 299)
select resi i

or, further:
for i in range(1, 299)
    select  resi i

I understand the above can be easily done with:
select resi 1-288

However, I am wondering if variables can work in Pymol in general.

Thanks!

Hello,

Ah, I see why now. I did do a full installation, during which the _cmd and
sglite extension files, etc. were copied to
C:\Python22\Lib\site-packages\pymol. According to comment in
C:\Python22\Lib\site.py, a path configuration file must exist in the
\site-packages directory indicating which sub-directories are to be appended
to sys.path. So I added a file, pymol.pth in \site-packages that contains:

# pymol package configuration
pymol

Now Python knows where to look for modules. And it works.

Thanks so much!

Tina


----- Original Message ----- 
From: "Warren L. DeLano" <wa...@de...>
To: "'Tina Li'" <th...@bi...>;
<pym...@li...>
Sent: Wednesday, August 27, 2003 2:32 PM
Subject: RE: [PyMOL] Re: cannot find _cmd module


| Tina,
|
| Did you do a full installation?  After running:
|
| python setup.py build install
| python setup2.py
|
| (in that order)
|
| pymol.bat should just work.  There shouldn't be any need to copy
| anything over, nor should you set PYMOL_PATH -- that is all taken care
| of automatically with this approach.
|
| Cheers,
| Warren
|
|
| --
| mailto:wa...@de...
| Warren L. DeLano, Ph.D.
| Principal Scientist
| DeLano Scientific LLC
| Voice (650)-346-1154
| Fax   (650)-593-4020
|
| > -----Original Message-----
| > From: pym...@li... [mailto:pymol-users-
| > ad...@li...] On Behalf Of Tina Li
| > Sent: Wednesday, August 27, 2003 8:34 AM
| > To: pym...@li...
| > Subject: [PyMOL] Re: cannot find _cmd module
| >
| > Hello,
| >
| > So I figured that in my $PYMOL_PATH\build\lib.win32-2.2\pymol, there
| is a
| > _cmd.pyd that's missing in $PYMOL_PATH\modules\pymol. I copied it
| over,
| > and
| > PyMOL started up, but said that it failed to import the xray module,
| which
| > however exists in $PYMOL_PATH\modules\pymol, so I don't understand why
| it
| > doesn't import that. Anyways, it seems to be up. I guess every time I
| > build
| > PyMOL, I'll have to copy the _cmd.pyd file over.
| >
| > Tina
| >
| > ----- Original Message -----
| > | From: "Tina Li" <th...@bi...>
| > | To: <pym...@li...>
| > | Date: Mon, 25 Aug 2003 11:57:27 -0400
| > | Subject: [PyMOL] cannot find _cmd module
| > |
| > | Hello,
| > |
| > | Eh, I think this is a rather basic question. So I built PyMOL on
| Win32,
| > tried
| > | to run pymol.bat, which calls python
| > $PYMOL_PATH/modules/pymol/__init__.py,
| > | which complained:
| > |
| > | Traceback (most recent call last):
| > |   File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py",
| line
| > 92, in
| > ?
| > |     import pymol
| > |   File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py",
| line
| > 300,
| > in
| > | ?
| > |     import _cmd
| > | ImportError: No module named _cmd
| > |
| > | I have PYTHONPATH set to $PYMOL_PATH/modules. Is it something
| obvious
| > I'm
| > | missing?
| > |
| > | Thanks much!
| > |
| > | Tina
| >
| >
| >
| >
| > -------------------------------------------------------
| > This sf.net email is sponsored by:ThinkGeek
| > Welcome to geek heaven.
| > http://thinkgeek.com/sf
| > _______________________________________________
| > PyMOL-users mailing list
| > PyM...@li...
| > https://lists.sourceforge.net/lists/listinfo/pymol-users
|

> I have a Mac TI powerbook running OSX.  Every time I launch a new
> terminal window, pymol launches.  For example, if I open 3 terminal
> windows, 3 pymol sessions also start.  How do I stop this?

What?  You don't want PyMOL to launch every possible opportunity?

Actually, I've encountered this problem myself -- very annoying...

What happened is that you saved the Terminal window settings while you
had a PyMOL session open, so OS X inferred that you were indicating a
desire to have PyMOL open as a default preference.

The only way I know of changing this is to text-edit
$HOME/Library/Preferences/com.apple.Terminal.plist and remove the
ExecutionString entry which contains PyMOL.  That means deleting those
two lines: the one which contains ExecutionString and the one with the
PyMOL launch command.

Sorry about this!

Cheers,
Warren

Tina,

Did you do a full installation?  After running:

python setup.py build install
python setup2.py 

(in that order)

pymol.bat should just work.  There shouldn't be any need to copy
anything over, nor should you set PYMOL_PATH -- that is all taken care
of automatically with this approach.  

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Tina Li
> Sent: Wednesday, August 27, 2003 8:34 AM
> To: pym...@li...
> Subject: [PyMOL] Re: cannot find _cmd module
> 
> Hello,
> 
> So I figured that in my $PYMOL_PATH\build\lib.win32-2.2\pymol, there
is a
> _cmd.pyd that's missing in $PYMOL_PATH\modules\pymol. I copied it
over,
> and
> PyMOL started up, but said that it failed to import the xray module,
which
> however exists in $PYMOL_PATH\modules\pymol, so I don't understand why
it
> doesn't import that. Anyways, it seems to be up. I guess every time I
> build
> PyMOL, I'll have to copy the _cmd.pyd file over.
> 
> Tina
> 
> ----- Original Message -----
> | From: "Tina Li" <th...@bi...>
> | To: <pym...@li...>
> | Date: Mon, 25 Aug 2003 11:57:27 -0400
> | Subject: [PyMOL] cannot find _cmd module
> |
> | Hello,
> |
> | Eh, I think this is a rather basic question. So I built PyMOL on
Win32,
> tried
> | to run pymol.bat, which calls python
> $PYMOL_PATH/modules/pymol/__init__.py,
> | which complained:
> |
> | Traceback (most recent call last):
> |   File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py",
line
> 92, in
> ?
> |     import pymol
> |   File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py",
line
> 300,
> in
> | ?
> |     import _cmd
> | ImportError: No module named _cmd
> |
> | I have PYTHONPATH set to $PYMOL_PATH/modules. Is it something
obvious
> I'm
> | missing?
> |
> | Thanks much!
> |
> | Tina
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Hello,

So I figured that in my $PYMOL_PATH\build\lib.win32-2.2\pymol, there is a
_cmd.pyd that's missing in $PYMOL_PATH\modules\pymol. I copied it over, and
PyMOL started up, but said that it failed to import the xray module, which
however exists in $PYMOL_PATH\modules\pymol, so I don't understand why it
doesn't import that. Anyways, it seems to be up. I guess every time I build
PyMOL, I'll have to copy the _cmd.pyd file over.

Tina

----- Original Message ----- 
| From: "Tina Li" <th...@bi...>
| To: <pym...@li...>
| Date: Mon, 25 Aug 2003 11:57:27 -0400
| Subject: [PyMOL] cannot find _cmd module
|
| Hello,
|
| Eh, I think this is a rather basic question. So I built PyMOL on Win32,
tried
| to run pymol.bat, which calls python $PYMOL_PATH/modules/pymol/__init__.py,
| which complained:
|
| Traceback (most recent call last):
|   File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py", line 92, in
?
|     import pymol
|   File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py", line 300,
in
| ?
|     import _cmd
| ImportError: No module named _cmd
|
| I have PYTHONPATH set to $PYMOL_PATH/modules. Is it something obvious I'm
| missing?
|
| Thanks much!
|
| Tina

	 
On 08/26/03 20:09:43, Malcolm Walker wrote:
> You are missing libz (which is strange, since libpng depends on libz)

Oops, sorry.  We fixed the problem.
Somehow libpng got built without linking to zlib.  Odd.

Many thanks for your help.
Austin

-- 
                         Austin Acton Hon.B.Sc.
              Synthetic Organic Chemist, Teaching Assistant
            Department of Chemistry, York University, Toronto
              MandrakeClub Volunteer (www.mandrakeclub.com)
                      homepage: www.groundstate.ca

On 08/26/03 20:09:43, Malcolm Walker wrote:
> You are missing libz (which is strange, since libpng depends on libz)
> You may need the development package too (zlib1-devel)

[austin@gamma373-165 austin]$ rpm -q zlib1
zlib1-1.1.4-8mdk

[austin@gamma373-165 austin]$ rpm -q zlib1-devel
zlib1-devel-1.1.4-8mdk

[austin@gamma373-165 austin]$ pymol.com
Traceback (most recent call last):
   File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 92, in ?
     import pymol
   File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 300, in ?
     import _cmd
ImportError: /usr/lib/libpng.so.3: undefined symbol: deflate

It must have something to do with the upgrade to python 2.3... but we rebuilt 
all python containing packages since.

Austin

-- 
                         Austin Acton Hon.B.Sc.
              Synthetic Organic Chemist, Teaching Assistant
            Department of Chemistry, York University, Toronto
              MandrakeClub Volunteer (www.mandrakeclub.com)
                      homepage: www.groundstate.ca

On Sat, 23 Aug 2003, Austin wrote:

> ImportError: /usr/lib/libpng.so.3: undefined symbol: deflate
>
> We're currently using python 2.3, pil 1.1.4, libpng 1.2.5.
>
> Any suggestions would be appreciated, as I'm supposed to have this working by
> Wednesday.  I'm not on the list, so a cc would also be appreciated.

You are missing libz (which is strange, since libpng depends on libz)

Try installing that first.
# urpmi zlib1

You may need the development package too (zlib1-devel)

Hello,

Eh, I think this is a rather basic question. So I built PyMOL on Win32, tried
to run pymol.bat, which calls python $PYMOL_PATH/modules/pymol/__init__.py,
which complained:

Traceback (most recent call last):
  File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py", line 92, in ?
    import pymol
  File "D:\thli\root\misc\pymol-0.90\modules\pymol\__init__.py", line 300, in
?
    import _cmd
ImportError: No module named _cmd

I have PYTHONPATH set to $PYMOL_PATH/modules. Is it something obvious I'm
missing?

Thanks much!

Tina

Hi Everyone,
I have a ligand containing aromatic rings (pyrroles, imidazoles). I'd like to 
show them as "filled" or "shaded" rings in the stick representation mode.
Could anyone suggest how to go about doing it in Pymol ?
Thanks very much,
Raji

Raji Edayathumangalam
Dept. of Biochemistry & Molecular Biology
Colorado State University
Fort Collins, CO 80523 USA
Tel:(970)491-4614
Fax:(970)491-0494

Hello,
I'm the maintainer for the pymol package in Mandrake Linux.
I recently updated it to 0.90, but it won't run now.  I'm not a python expert, 
so maybe someone here could help me interpret the following error?

[austin@gamma373-165 SOURCES]$ pymol.com
Traceback (most recent call last):
   File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 92, in ?
     import pymol
   File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 300, in ?
     import _cmd
ImportError: /usr/lib/libpng.so.3: undefined symbol: deflate

We're currently using python 2.3, pil 1.1.4, libpng 1.2.5.

Any suggestions would be appreciated, as I'm supposed to have this working by 
Wednesday.  I'm not on the list, so a cc would also be appreciated.

Thanks,
Austin
-- 
                         Austin Acton Hon.B.Sc.
              Synthetic Organic Chemist, Teaching Assistant
            Department of Chemistry, York University, Toronto
              MandrakeClub Volunteer (www.mandrakeclub.com)
                      homepage: www.groundstate.ca

Dear all:

I would like to know how to keep the back of a surface (cut via the slab)
dark rather than white (when using a wite background) once I ray trace the
image.

Thank you in advance

Jose

Tina,

	"layer0/MemoryCache.c" is missing from the list of sources in
the setup.py file.  If you add that in right after the
"layer0/MemoryDebug.c", it should build.

Sorry about that!

Cheers,
Warren


--
mailto:wa...@de...
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154 
Fax   (650)-593-4020

> -----Original Message-----
> From: pym...@li... [mailto:pymol-users-
> ad...@li...] On Behalf Of Tina Li
> Sent: Friday, August 22, 2003 10:31 AM
> To: pym...@li...
> Subject: [PyMOL] linker errors on win32?
> 
> Hello,
> 
> I was following instructions in setup/INSTALL.win32 (as in pymol-0_90-
> src.tgz)
> to build PyMOL. I have all the external components (glut, zlib,
libpng) in
> place. When I tried
> 
> python setup.py build
> 
> It generated linker errors:
> 
> C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe /DLL
/nologo
> /INCREME
> NTAL:NO /LIBPATH:win32/lib /LIBPATH:C:\Python22\libs opengl32.lib
> glu32.lib
> glut
> 32.lib libpng.lib zlib.lib /EXPORT:init_cmd
> build\temp.win32-2.2\Release\Block.o [...more .obj here...]
> ...
>    Creating library build\temp.win32-2.2\Release\_cmd.lib and object
> build\temp.win32-2.2\Release\_cmd.exp
> Map.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
> MemoryDebug.obj : error LNK2001: unresolved external symbol
> _MemoryCacheFree
> Basis.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
> Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
> Map.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
> MemoryDebug.obj : error LNK2001: unresolved external symbol
> _MemoryCacheMalloc
> Basis.obj : error LNK2001: unresolved external symbol
_MemoryCacheMalloc
> Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
> Map.obj : error LNK2001: unresolved external symbol _MemoryCacheCalloc
> MemoryDebug.obj : error LNK2001: unresolved external symbol
> _MemoryCacheRealloc
> main.obj : error LNK2001: unresolved external symbol _MemoryCacheDone
> main.obj : error LNK2001: unresolved external symbol _MemoryCacheInit
> build\lib.win32-2.2\pymol\_cmd.pyd : fatal error LNK1120: 6 unresolved
> externals
> 
> error: command '"C:\Program Files\Microsoft Visual
> Studio\VC98\BIN\link.exe"'
> failed with exit status 1120
> 
> I wonder if I'm missing a particular library.
> 
> 
> Thanks much,
> 
> Tina
> 
> 
> 
> 
> -------------------------------------------------------
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Hello,

I was following instructions in setup/INSTALL.win32 (as in pymol-0_90-src.tgz)
to build PyMOL. I have all the external components (glut, zlib, libpng) in
place. When I tried

python setup.py build

It generated linker errors:

C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe /DLL /nologo
/INCREME
NTAL:NO /LIBPATH:win32/lib /LIBPATH:C:\Python22\libs opengl32.lib glu32.lib
glut
32.lib libpng.lib zlib.lib /EXPORT:init_cmd
build\temp.win32-2.2\Release\Block.o [...more .obj here...]
...
   Creating library build\temp.win32-2.2\Release\_cmd.lib and object
build\temp.win32-2.2\Release\_cmd.exp
Map.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
MemoryDebug.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
Basis.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheFree
Map.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
MemoryDebug.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
Basis.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
Ray.obj : error LNK2001: unresolved external symbol _MemoryCacheMalloc
Map.obj : error LNK2001: unresolved external symbol _MemoryCacheCalloc
MemoryDebug.obj : error LNK2001: unresolved external symbol
_MemoryCacheRealloc
main.obj : error LNK2001: unresolved external symbol _MemoryCacheDone
main.obj : error LNK2001: unresolved external symbol _MemoryCacheInit
build\lib.win32-2.2\pymol\_cmd.pyd : fatal error LNK1120: 6 unresolved
externals

error: command '"C:\Program Files\Microsoft Visual Studio\VC98\BIN\link.exe"'
failed with exit status 1120

I wonder if I'm missing a particular library.


Thanks much,

Tina

Thanks for your code!

> P.S. I wish this mailing list had archives ...

But it does!

http://sourceforge.net/mailarchive/forum.php?forum_id=60

You can search by keyword.  Look for the text box upper-left.

Cheers,
Warren

Jan,

	Thanks for that -- copy hereby sent to the PyMOL list.  This is
a relief.  I was wondering why strange bounced email was coming back and
had become concerned that infection had occurred here despite every
precaution.	
	SMTP-based email is indeed a hopeless cause.  I vote for a
return to smoke signals and semaphores.

- Warren

Summary:	

	The current viruses add a bogus "From" field, so don't get upset
at the person who seemed to have sent that infected email to you since
it wasn't really them.  They are not infected -- someone else is.  

> -----Original Message-----
> From: Computational Chemistry List [mailto:che...@cc...]
On
> Behalf Of Dr. Jan K Labanowski
> Sent: Thursday, August 21, 2003 9:50 AM
> To: che...@cc...
> Cc: Dr. Jan K Labanowski
> Subject: CCL:E-mail worm is going around
> 
> Dear CCL,
> 
> Since I got few a questions, I will post an answer to the whole list
to
> cool you down...
> 
> There is a malicious Internet worm going on, which infects the (guess
> what...)
> Windows machines. It is an e-mail message which carries a virus with
it
> (so it is about 100kB large to be able to pack the virus executable).
> It grabs addresses from the victim address book, and resends itself
> to these addresses, and to make things worse, it also changes its
From:
> (i.e., the address from which the message is supposedly coming from)
> to some address from the victim's address book. Of course, according
to
> the old saying: "The worse, the better...". Microsoft will sell us
> upgraders, and improved products, and scoop millions of dollars in
> consulting hours from people who use their maintainance program.
> Hopefully events like this will revive economy and create new job
> opportunities.
> 
> Obviously, the che...@cc... is in many people address books, as
well
> as,
> my personal address. Many of you got the mail which is supposedly
coming
> from, say, che...@cc..., but it really did not come from this
> address.
> 
> If you want to know more about this malice, read on... The e-mail
message
> consist of header and body. The header should contain the information
> about
> intended recipients, message origin, path which message traveled
> (gateways)
> before it got to you and the information about the type and methods of
> encoding used for the body of the message. The message body is the
actual
> pay-load of the e-mail message). But make no mistake... Header is not
the
> envelope of your mail. It is not used by mail software (mail transfer
> agent - MTA) to deliver your mail. Header has only an "informational"
> (or lately often "dis-informational") value.
> 
> The problem is that you can put anything you want in the header
(beside
> maybe the top Received: header line, which is usually added by your
own
> computer or mail gateway). The top Received: line (depending on the
way
> your
> mail is configured) contains the information about the IP address of
the
> machine which had sent you the the message, and the destination of the
> message
> (i.e., in most cases it lists your own machine and sometimes your user
id,
> or
> mail alias). However, beside the first Received: line (or maybe more,
if
> the mail was traveling to you via some trusted gateways as each
legitimate
> MTA should add its Received: line to the header -- SHOULD, but DOES
NOT
> HAVE TO!!!), all other header lines can be set by the mail originators
to
> anything they want. Most importantly: the To:, From:, Cc: do not have
to
> be
> real, and THESE FIELDS ARE NOT USED IN DELIVERING THE MESSAGE !!!.
> 
> To be more precise, if you use a legitimate mail composing program,
> the destination of your mail message will be taken from the To: and/or
> Cc: lines, and the From: line will point to you, when your
> message is passed to your own mail transfer agent. BUT THE BAD GUYS
> DO NOT USE STANDARD AND LEGITIMATE MAIL COMPOSERS AND TRANSFER
AGENTS!!!
> Note that the mail is delivered to your mail server by a special
protocol
> (SMTP), where the recipient's and originator's address is given to
your
> local
> mail server as a part of delivery process, and THEY DO NOT HAVE TO BE
EVEN
> CLOSE to what is being given on the To: and From: lines of your
message.
> 
> At the same time, what is displayed in your e-mail browsing tool as
> message
> origin, is the From: line from header. CURRENTLY, THERE IS NO WAY TO
> ESTABLISH
> THE IDENTITY OF THE PERSON WHO HAD SENT MAIL TO YOU!!! The only thing
> which
> can be (in most cases!!!, not always!!!) established is the IP address
> of the machine which forwarded you the message (this can be guessed
from
> inspecting the top Received: line of the header). In most cases the IP
> address
> of the originating machine is a TOTALLY USELESS information, since it
> gives
> you the pointer to the machine which was:
> 
>    1)  either hacked by spammers,
>    2)  or infected by the virus (i.e., a victim like you),
>    3)  or represents an open relay machine (made an open relay either
>        intentionally or not)
> 
> We badly need a new electronic mail protocol, where the originator of
the
> mail can be either reliably identified, or the message is not
delivered.
> As always, there are scores of proposed protocols, none of them
popular
> or widely used, and all of them would require some kind of trusted
> authority (e.g., digital certificate authority) which will verify that
> a person on a From: line is really an originator of e-mail. Once
something
> of this kind gets adopted (years...) we will:
> 
>   1) loose our privacy,
>   2) will need to pay for it,
>   3) the poor countries will not have money to support needed
> infrastructure.
> 
> Some of the older folks on the list remember when we used "finger" to
> check,
> if we should call someone at work or at home, and if he/she had read
our
> mail message...  So long for "kindler and gentler Internet"...
> 
> Panta rei, but unfortunately usually down the sewer...
> 
> Yours,
> Jan
> 
> Jan K. Labanowski         |  phone: 614-292-9279,  FAX: 614-292-7168
> Ohio Supercomputer Center |  E-mail: jk...@os...
> 1224 Kinnear Rd,          |  http://www.osc.edu/~jkl
> Columbus, OH 43212-1163   |  http://www.ccl.net/    http://asdn.net/
> 
> 
> 
> -= This is automatically added to each message by mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your
Subject:
> line
> and send your message to:  CHE...@cc...
> 
> Send your subscription/unsubscription requests to: CHEMISTRY-
> RE...@cc...
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs
> 
> If your mail is bouncing from CCL.NET domain send it to the
maintainer:
> Jan Labanowski,  jk...@os... (read about it on CCL Home Page)
>
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> 
> 
>