Re: [PyMOL] Using PyMol as a library - no GUI
On Fri, Oct 17, 2003 at 09:41:24AM -0700, Warren L. DeLano wrote: > > Truls A. Tangstad wrote: > > I'm very interested in using alot of the functionality that PyMol > > offers programmatically from Python, i.e. without using a GUI at > > all. The chempy package seems to cover alot of my needs, loading > > different file formats etc. even though it doesn't seem to be > > documented. > > > > Is it also possible to use the rest of the functionality in PyMol from > > other Python scripts? Right now, just importing the pymol package > > seems to force the GUI to open. > If you've got PyMOL configured to open on > > import pymol > pymol.finish_launching() > > You can suppress the GUI feature and suppress startup output by > providing command line arguments as follows. Before importing PyMOL, > set a "pymol_argv" list in the __main__ namespace. PyMOL will interpret > this as a sys.argv styled list of command line arguments. > > import __main__ > __main__.pymol_argv['pymol','-qc'] > > import pymol > pymol.finish_launching() Thanks, seems to work like a charm in scripts after adding the assignment operator: __main__.pymol_argv = ['pymol', '-qc'] # adding miss Somehow it segfaults when trying the same thing in an interactive python interpreter though, right after importing pymol. This might be due to a shoddy install on my part, but I'm including a gdb backtrace: #0 0x41d7b21a in SettingGetGlobal_f () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #1 0x41d7c683 in SettingGet () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #2 0x41d6296d in OrthoAddOutput () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #3 0x41d679a5 in PCatchInit () from /usr/lib/python2.3/site-packages/pymol/_cmd.so #4 0x4006d74d in PyCFunction_Call () from /usr/lib/libpython2.3.so.1.0 #5 0x40045e37 in PyObject_Call () from /usr/lib/libpython2.3.so.1.0 #6 0x400a2a4a in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.3.so.1.0 #7 0x4000 in PyFile_WriteObject () from /usr/lib/libpython2.3.so.1.0 #8 0x400556e6 in PyFile_WriteString () from /usr/lib/libpython2.3.so.1.0 #9 0x400d56b6 in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #10 0x400d4b2c in PySys_WriteStderr () from /usr/lib/libpython2.3.so.1.0 #11 0x400d2c74 in Py_AtExit () from /usr/lib/libpython2.3.so.1.0 #12 0x40101043 in _PyUnicode_TypeRecords () from /usr/lib/libpython2.3.so.1.0 Any idea why it shouldn't work interactively? I'm using PyMol 0.90 and Python 2.3.2 on Debian unstable. -- Truls - kerfue+pymol-us...@herocamp.org
Re: [PyMOL] Segment Identifiers
How do I know what the segids are? How do I create segids? Thanks, Jon - Original Message - From: "Nat Echols" To: "Jonathan Ostrem" Cc: "PyMol User Group" Sent: Friday, October 17, 2003 12:08 AM Subject: Re: [PyMOL] Segment Identifiers > > if 'foo' is the segid of your kinase, > > PyMOL> select kinase, segi foo > PyMOL> color green, segi foo > > it doesn't seem to care about any leading or lagging spaces, as far as I > can tell. > > > On Thu, 16 Oct 2003, Jonathan Ostrem wrote: > > > How are segment identifiers used. I have a PDB file with a kinase domain and an inhibitor. How can I select the inhibitor and not the kinase domain residues? > > > > Thanks, > > Jon > > > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > >
[PyMOL] new error
I just started to get this error mac-osx 10.2.6. Could it be correlated with a recent installation of the python-based molecular visualization programs from the MGL at Scripps. I have reinstalled the program and I get the same error. Traceback (most recent call last): File "/Applications/PyMOL/Darwin/modules/pymol/__init__.py", line 58, in ? import threading File "/Applications/PyMOL/Darwin/ext/lib/python2.2/threading.py", line 4, in ? import time ImportError: No module named time Thanks, -Tom -- __ Tom Thompson, Ph.D.PH 847-467-4049 Northwestern University 2205 Tech Drive Evanston IL 60208-0001
RE: [PyMOL] recommendations for G5
Wataru, I would tend to go with the 9800 if cost is not an issue -- it is a faster card than the 9600. Both work great with flat panels (though you'll need a CRT for stereo). Also, I've found that the 9600 does not support antialiased lines on the G5, much to my disappointment. I do now know whether or not the 9800 suffers this same limitation. Perhaps others can comment? There were some glitches with Stereo on the ATI series of cards, but these may have been fixed by now. 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 wkag...@jota.gsc.riken.go.jp > Sent: Friday, October 17, 2003 12:50 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] recommendations for G5 > > Dear staff (and pymol users): > > I am looking for some suggestions on the power mac G5 hardware to run > pymol and other 3D applications without problems. > Between the two graphic cards offered by Apple (ATI Radeon 9600 pro or > 9800 pro), which do you recommend? Is it too risky to buy the 9800 pro > because of compatibility problems? How well does the Apple's flat > panel display work with those graphic cards? What are other flat panel > displays that work with those graphic cards? > > I'm sorry these questions are not directly related to pymol, but I > appreciate any suggestions. > > Wataru Kagawa > > > > --- > This SF.net email sponsored by: Enterprise Linux Forum Conference & Expo > The Event For Linux Datacenter Solutions & Strategies in The Enterprise > Linux in the Boardroom; in the Front Office; & in the Server Room > http://www.enterpriselinuxforum.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Using PyMol as a library - no GUI
If you've got PyMOL configured to open on import pymol pymol.finish_launching() You can suppress the GUI feature and suppress startup output by providing command line arguments as follows. Before importing PyMOL, set a "pymol_argv" list in the __main__ namespace. PyMOL will interpret this as a sys.argv styled list of command line arguments. import __main__ __main__.pymol_argv['pymol','-qc'] import pymol pymol.finish_launching() 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 Truls A. Tangstad > Sent: Friday, October 17, 2003 4:48 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Using PyMol as a library - no GUI > > I'm very interested in using alot of the functionality that PyMol > offers programmatically from Python, i.e. without using a GUI at > all. The chempy package seems to cover alot of my needs, loading > different file formats etc. even though it doesn't seem to be > documented. > > Is it also possible to use the rest of the functionality in PyMol from > other Python scripts? Right now, just importing the pymol package > seems to force the GUI to open. > > -- > Truls - kerfue+pymol-us...@herocamp.org > > > --- > This SF.net email is sponsored by: SF.net Giveback Program. > SourceForge.net hosts over 70,000 Open Source Projects. > See the people who have HELPED US provide better services: > Click here: http://sourceforge.net/supporters.php > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Using PyMol as a library - no GUI
I'm very interested in using alot of the functionality that PyMol offers programmatically from Python, i.e. without using a GUI at all. The chempy package seems to cover alot of my needs, loading different file formats etc. even though it doesn't seem to be documented. Is it also possible to use the rest of the functionality in PyMol from other Python scripts? Right now, just importing the pymol package seems to force the GUI to open. -- Truls - kerfue+pymol-us...@herocamp.org
[PyMOL] recommendations for G5
Dear staff (and pymol users): I am looking for some suggestions on the power mac G5 hardware to run pymol and other 3D applications without problems. Between the two graphic cards offered by Apple (ATI Radeon 9600 pro or 9800 pro), which do you recommend? Is it too risky to buy the 9800 pro because of compatibility problems? How well does the Apple's flat panel display work with those graphic cards? What are other flat panel displays that work with those graphic cards? I'm sorry these questions are not directly related to pymol, but I appreciate any suggestions. Wataru Kagawa
Re: [PyMOL] Segment Identifiers
if 'foo' is the segid of your kinase, PyMOL> select kinase, segi foo PyMOL> color green, segi foo it doesn't seem to care about any leading or lagging spaces, as far as I can tell. On Thu, 16 Oct 2003, Jonathan Ostrem wrote: > How are segment identifiers used. I have a PDB file with a kinase domain and > an inhibitor. How can I select the inhibitor and not the kinase domain > residues? > > Thanks, > Jon
