From: William S. <wg...@ch...> - 2004-07-16 00:47:06
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The best way to overcome this is to compile it, so that you don't have to depend on someone's dynamic library. Fink doesn't build the g77 dynamic library, which allows you to avoid this problem. If you use g77 3.4.1 (which is what is currently in fink) with gcc 3.3 you will have some linking errors. I could not get the LDFLAG to let me do this (i.e., I coudn't figure out how to do this the "right way"), so I instead did the following: 1. start up zsh (to make use of its recursive globbing capability) 2. configure 3. perl -pi -e 's|\-L/usr/local/|\-lcc_dynamic \-L/usr/local/|g' **/Makefile make; make install On Jul 15, 2004, at 5:03 PM, pym...@li... wrote: > I downloaded the Mac APBS binary, but I'm seeing this error when trying > to run it: > > % ./apbs-0.3.1-g4 > dyld: ./apbs-0.3.1-g4 can't open library: /usr/local/lib/libg2c.0.dylib > (No such file or directory, errno = 2) > Trace/BPT trap > > Anyone else see this or know how to overcome it? > > Thanks, > Doug William G. Scott Associate Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA phone: +1-831-459-5367 (office) +1-831-459-5292 (lab) fax: +1-831-459-3139 (fax) url: http://chemistry.ucsc.edu/~wgscott/ movie: http://www.apple.com/trailers/lions_gate/fahrenheit_911/ |
From: Michele F. <mfu...@me...> - 2004-07-16 17:42:07
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Hi, I compiled APBS successfully. Now when I try the plugin and click on Set Grid I get: --- Error: 1 ValueError Exception in Tk callback Function: <function <lambda> at 0x81205f0> (type: <type 'function'>) Args: () Traceback (innermost last): File "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ None File "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwDialog.py", line 153, in <lambda> None File "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwDialog.py", line 132, in _doCommand None File "/Volumes/Prugna/Science/PyMOL/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1046, in execute self.runPsize() File "/Volumes/Prugna/Science/PyMOL/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", line 1087, in runPsize size.runPsize(pdb_filename) File "/Volumes/Hofdi/Unix/Software/apbs-0.3.1/tools/manip/psize.py", line 257, in runPsize self.parseInput(filename) File "/Volumes/Hofdi/Unix/Software/apbs-0.3.1/tools/manip/psize.py", line 106, in parseInput self.q = self.q + float(words[3]) ValueError: invalid literal for float(): 1.00103.81 --- any help? Thanks Michele -- -- Michele Fuortes, M.D., Ph.D. Assistant Professor Department of Surgery Department of Cell and Developmental Biology Cornell University - Weill Medical College E-mail: mfu...@me... |
From: James R. G. <jam...@ma...> - 2004-07-16 18:05:23
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On Jul 16, 2004, at 1:41 PM, Michele Fuortes wrote: > I compiled APBS successfully. > Now when I try the plugin and click on Set Grid I get: i was able to compile it on my macs as well (after installing the fortran compiler). now, i just have to wait for the next version of macpymol in order to use the plug-in. ;) james |
From: Michael G. L. <ml...@um...> - 2004-07-16 18:20:18
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Hi, That sounds like APBS's psize.py is having trouble with your input data .. you could try going to the "APBS Location" tab and deleting the path to psize.py .. then it'll use my code instead. For some reason, it's reading "1.00103.81" where it expects a floating point number .. it's possible that there's trouble with your PDB file. -michael -- This isn't a democracy;| _ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mlerner@umich On Fri, 16 Jul 2004, Michele Fuortes wrote: > Hi, > > I compiled APBS successfully. > Now when I try the plugin and click on Set Grid I get: > > --- > Error: 1 > ValueError Exception in Tk callback > Function: <function <lambda> at 0x81205f0> (type: <type 'function'>) > Args: () > Traceback (innermost last): > File > "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwBase.py", > line 1747, in __call__ > None > File > "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwDialog.py", > line 153, in <lambda> > None > File > "/Users/delwarl/pymol/products/PyMOLX11Hybrid.app/py23/lib/python2.3/Pmw/Pmw_1_2/lib/PmwDialog.py", > line 132, in _doCommand > None > File > "/Volumes/Prugna/Science/PyMOL/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", > line 1046, in execute > self.runPsize() > File > "/Volumes/Prugna/Science/PyMOL/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs_tools.py", > line 1087, in runPsize > size.runPsize(pdb_filename) > File "/Volumes/Hofdi/Unix/Software/apbs-0.3.1/tools/manip/psize.py", line > 257, in runPsize > self.parseInput(filename) > File "/Volumes/Hofdi/Unix/Software/apbs-0.3.1/tools/manip/psize.py", line > 106, in parseInput > self.q = self.q + float(words[3]) > ValueError: invalid literal for float(): 1.00103.81 > --- > > > any help? > > Thanks > > Michele > > > > -- > > > -- > Michele Fuortes, M.D., Ph.D. > Assistant Professor > Department of Surgery > Department of Cell and Developmental Biology > Cornell University - Weill Medical College > E-mail: mfu...@me... > > > > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop > FREE Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Jianghai Z. <zh...@pu...> - 2004-07-16 02:54:24
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I still can't compile it with scott's method. Do you mind share your binary with us? Jianghai ========================== Jianghai Zhu Molecular Biology & Biochemistry Purdue University ========================== On Jul 15, 2004, at 7:47 PM, William Scott wrote: > The best way to overcome this is to compile it, so that you don't have > to depend on someone's dynamic library. > > Fink doesn't build the g77 dynamic library, which allows you to avoid > this problem. > > If you use g77 3.4.1 (which is what is currently in fink) with gcc 3.3 > you will have some linking errors. > > I could not get the LDFLAG to let me do this (i.e., I coudn't figure > out how to do this the "right way"), so I instead did the following: > > 1. start up zsh (to make use of its recursive globbing capability) > > 2. configure > > 3. perl -pi -e 's|\-L/usr/local/|\-lcc_dynamic \-L/usr/local/|g' > **/Makefile > > make; make install > |
From: Christopher Y. <chr...@sy...> - 2004-07-16 04:10:57
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The previous suggestion about downloading g77 and installing it from hpc.sourceforge.net worked for me - at least I didn't get an error when I ran APBS.... On Jul 15, 2004, at 10:54 PM, Jianghai Zhu wrote: > I still can't compile it with scott's method. Do you mind share your > binary with us? > > Jianghai > ========================== > Jianghai Zhu > Molecular Biology & Biochemistry > Purdue University > ========================== > On Jul 15, 2004, at 7:47 PM, William Scott wrote: > >> The best way to overcome this is to compile it, so that you don't >> have to depend on someone's dynamic library. >> >> Fink doesn't build the g77 dynamic library, which allows you to >> avoid this problem. >> >> If you use g77 3.4.1 (which is what is currently in fink) with gcc >> 3.3 you will have some linking errors. >> >> I could not get the LDFLAG to let me do this (i.e., I coudn't figure >> out how to do this the "right way"), so I instead did the following: >> >> 1. start up zsh (to make use of its recursive globbing capability) >> >> 2. configure >> >> 3. perl -pi -e 's|\-L/usr/local/|\-lcc_dynamic \-L/usr/local/|g' >> **/Makefile >> >> make; make install >> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop > FREE Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > Christopher M. Yip, Ph.D., P.Eng. Associate Professor - Canada Research Chair in Molecular Imaging Department of Chemical Engineering and Applied Chemistry Department of Biochemistry Institute of Biomaterials and Biomedical Engineering University of Toronto 407 Rosebrugh Building 4 Taddle Creek Rd Toronto, Ontario, CANADA M5S 3G9 (416) 978-7853 (416) 978-4317 (fax) chr...@ut... http://bigten.ibme.utoronto.ca |