Re: [PyMOL] movie script
Hi Hasan, Start with the structures superimposed and translate/rotate one/both away from the/each other. Glue the images together in reversed order and no one will see the difference... By the way, it might be nice to start with small translations/rotations and have them increase quadratically in size, so that when you play it in reverse, it seems to slow down, as if you were being more careful and precise aligning the things... ;) Hope it helps, Tsjerk On 8/14/07, Demirci, Hasan wrote: > > Hi, > I have two pdb files that I want to superimpose them onto each other. (I know > how to do this part) > however, at the same time i want to generate a movie showing those two pdb > files going into each other. > Does anyone know how to do it? > Thanks in advance. > > Hasan Demirci > Department of Molecular Biology, Cellular Biology & Biochemistry > Brown University > 69 Brown Street > Providence, RI02912 > > (401) 863-3652 lab > (401) 226-7852 cell > > hasan_demi...@brown.edu > > > - > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
[PyMOL] Why can't I get to sys.argv on Linux?
Hi, I'm using PyMOL as a front end to a few scripts. So, I need to get my hands on sys.argv to process the command-line arguments. On OS X, everything works just like I'd expect. However, on Linux, I can't get sys.argv. Here's a very simple Python script: #!/usr/bin/env python import sys print dir(sys) print sys.argv When I run pymol -cr ./my_script.py on Linux, I get this: PyMOL>run ./x.py,main ['__displayhook__', '__doc__', '__excepthook__', '__name__', '__stderr__', '__stdin__', '__stdout__', '_getframe', 'api_version', 'builtin_module_names', 'byteorder', 'call_tracing', 'callstats', 'copyright', 'displayhook', 'exc_clear', 'exc_info', 'exc_type', 'excepthook', 'exec_prefix', 'executable', 'exit', 'exitfunc', 'getcheckinterval', 'getdefaultencoding', 'getdlopenflags', 'getfilesystemencoding', 'getrecursionlimit', 'getrefcount', 'hexversion', 'maxint', 'maxunicode', 'meta_path', 'modules', 'path', 'path_hooks', 'path_importer_cache', 'platform', 'prefix', 'setcheckinterval', 'setdlopenflags', 'setprofile', 'setrecursionlimit', 'settrace', 'stderr', 'stdin', 'stdout', 'version', 'version_info', 'warnoptions'] Traceback (most recent call last): File "/users/mlerner/src/pymol/modules/pymol/parser.py", line 287, in parse parsing.run_file(exp_path(args[nest][0]),__main__.__dict__,__main__.__dict__) File "/users/mlerner/src/pymol/modules/pymol/parsing.py", line 407, in run_file execfile(file,global_ns,local_ns) File "./x.py", line 4, in ? print sys.argv AttributeError: 'module' object has no attribute 'argv' PyMOL: normal program termination. While pawing around in the PyMOL sources, I found that pymol_argv shows up. It seems to be what I want, but I don't know how stable it is. Am I supposed to use it instead of sys.argv? Thanks, -michael -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner
Re: [PyMOL] Why can't I get to sys.argv on Linux?
Michael, Hmm...I see. This problem arises from the differences which exist between running PyMOL with an embedded interpreter -- PyMOL should do more to smooth out these differences... But in the meantime, as a workaround, fall back on __main__.pymol_argv if sys.argv is not defined. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Michael Lerner > Sent: Tuesday, August 14, 2007 2:35 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Why can't I get to sys.argv on Linux? > > Hi, > > I'm using PyMOL as a front end to a few scripts. So, I need > to get my hands on sys.argv to process the command-line > arguments. On OS X, everything works just like I'd expect. > However, on Linux, I can't get sys.argv. Here's a very simple > Python script: > > #!/usr/bin/env python > import sys > print dir(sys) > print sys.argv > > When I run pymol -cr ./my_script.py on Linux, I get this: > > PyMOL>run ./x.py,main > ['__displayhook__', '__doc__', '__excepthook__', '__name__', > '__stderr__', '__stdin__', '__stdout__', '_getframe', > 'api_version', 'builtin_module_names', 'byteorder', > 'call_tracing', 'callstats', 'copyright', 'displayhook', > 'exc_clear', 'exc_info', 'exc_type', 'excepthook', > 'exec_prefix', 'executable', 'exit', 'exitfunc', > 'getcheckinterval', 'getdefaultencoding', 'getdlopenflags', > 'getfilesystemencoding', 'getrecursionlimit', 'getrefcount', > 'hexversion', 'maxint', 'maxunicode', 'meta_path', 'modules', > 'path', 'path_hooks', 'path_importer_cache', 'platform', > 'prefix', 'setcheckinterval', 'setdlopenflags', 'setprofile', > 'setrecursionlimit', 'settrace', 'stderr', 'stdin', 'stdout', > 'version', 'version_info', 'warnoptions'] Traceback (most > recent call last): > File "/users/mlerner/src/pymol/modules/pymol/parser.py", > line 287, in parse > > parsing.run_file(exp_path(args[nest][0]),__main__.__dict__,__m > ain__.__dict__) > File "/users/mlerner/src/pymol/modules/pymol/parsing.py", > line 407, in run_file > execfile(file,global_ns,local_ns) > File "./x.py", line 4, in ? > print sys.argv > AttributeError: 'module' object has no attribute 'argv' > PyMOL: normal program termination. > > While pawing around in the PyMOL sources, I found that > pymol_argv shows up. It seems to be what I want, but I don't > know how stable it is. Am I supposed to use it instead of sys.argv? > > Thanks, > > -michael > > -- > Biophysics Graduate Student > Carlson Lab, University of Michigan > http://www.umich.edu/~mlerner > > -- > --- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and > a browser. > Download your FREE copy of Splunk now >> > http://get.splunk.com/ ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
