[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 t...@bioinformaticssolutions.com | To: pymol-users@lists.sourceforge.net | 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
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:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Tina Li Sent: Wednesday, August 27, 2003 8:34 AM To: pymol-users@lists.sourceforge.net 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 t...@bioinformaticssolutions.com | To: pymol-users@lists.sourceforge.net | 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 $PYMOL_PATH/modules. Is it something obvious I'm | missing? | | Thanks much! | | Tina --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] problems updating Mandrake packages
On 08/26/03 20:09:43, Malcolm Walker wrote: You are missing libz (which is strange, since libpng depends on libz) You may need the development package too (zlib1-devel) [aus...@gamma373-165 austin]$ rpm -q zlib1 zlib1-1.1.4-8mdk [aus...@gamma373-165 austin]$ rpm -q zlib1-devel zlib1-devel-1.1.4-8mdk [aus...@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
Re: [PyMOL] Re: cannot find _cmd module
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 war...@delanoscientific.com To: 'Tina Li' t...@bioinformaticssolutions.com; pymol-users@lists.sourceforge.net 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:war...@delanoscientific.com | Warren L. DeLano, Ph.D. | Principal Scientist | DeLano Scientific LLC | Voice (650)-346-1154 | Fax (650)-593-4020 | | -Original Message- | From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- | ad...@lists.sourceforge.net] On Behalf Of Tina Li | Sent: Wednesday, August 27, 2003 8:34 AM | To: pymol-users@lists.sourceforge.net | 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 t...@bioinformaticssolutions.com | | To: pymol-users@lists.sourceforge.net | | 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 | PyMOL-users@lists.sourceforge.net | https://lists.sourceforge.net/lists/listinfo/pymol-users |
[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!
RE: [PyMOL] Python commands and variables
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:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Shu-Hsien Sheu Sent: Wednesday, August 27, 2003 1:10 PM To: pymol-users@lists.sourceforge.net 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 PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
