Re: [PyMOL] ContactsNCONT script error
Hi, The first line is okay, but the rest seems to have an extra space, indeed. You can remove it from the script using: sed -i 's/^ //' script.py Hope it helps, Tsjerk On Thu, May 26, 2011 at 4:33 AM, Michael Lerner wrote: > Hi Ivan, > There's definitely a bug in that script. It looks like most of the file has > one extra space of indentation. I don't feel comfortable changing it at the > moment, as I'm not on a machine that has ccp4, but perhaps someone else can > fix and test it. If not, I'll fix it tomorrow. > Cheers, > -Michael > On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan > wrote: >> >> Dear All, >> >> >> I would like to compare the intermolecular crystal contacts in seven >> crystal forms of the same enzyme. >> I produced a list of contacts for each crystal form using the program >> NCONT from CCP4 and I found the ContactsNCONT script in the PyMOL Wiki >> (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a >> lot of time. >> Unfortunately, when I run the ContactsNCONT script, I always have the >> following message with different PCs running different OS (Windows, RedHat >> or Mac): >> >> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", >> line 338, in parse >> parsing.run_file(path,self.pymol_names,self.pymol_names) >> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", >> line 455, in run_file >> execfile(file,global_ns,local_ns) >> File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3 >> def parseContacts( f ): >> ^ >> IndentationError: unexpected indent >> >> >> Any suggestion will be more than appreciated. >> >> >> Thank you in advance, >> >> Regards >> >> Ivan Campeotto >> Centre for Molecular Microbiology and Infection >> Imperial College London >> >> >> -- >> vRanger cuts backup time in half-while increasing security. >> With the market-leading solution for virtual backup and recovery, >> you get blazing-fast, flexible, and affordable data protection. >> Download your free trial now. >> http://p.sf.net/sfu/quest-d2dcopy1 >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > > -- > vRanger cuts backup time in half-while increasing security. > With the market-leading solution for virtual backup and recovery, > you get blazing-fast, flexible, and affordable data protection. > Download your free trial now. > http://p.sf.net/sfu/quest-d2dcopy1 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] ContactsNCONT script error
Hi Ivan, There's definitely a bug in that script. It looks like most of the file has one extra space of indentation. I don't feel comfortable changing it at the moment, as I'm not on a machine that has ccp4, but perhaps someone else can fix and test it. If not, I'll fix it tomorrow. Cheers, -Michael On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan wrote: > Dear All, > > > I would like to compare the intermolecular crystal contacts in seven > crystal forms of the same enzyme. > I produced a list of contacts for each crystal form using the program > NCONT from CCP4 and I found the ContactsNCONT script in the PyMOL Wiki ( > http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a > lot of time. > Unfortunately, when I run the ContactsNCONT script, I always have the > following message with different PCs running different OS (Windows, RedHat > or Mac): > > File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", > line 338, in parse >parsing.run_file(path,self.pymol_names,self.pymol_names) > File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", > line 455, in run_file >execfile(file,global_ns,local_ns) > File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3 > def parseContacts( f ): >^ > IndentationError: unexpected indent > > > Any suggestion will be more than appreciated. > > > Thank you in advance, > > Regards > > Ivan Campeotto > Centre for Molecular Microbiology and Infection > Imperial College London > > > -- > vRanger cuts backup time in half-while increasing security. > With the market-leading solution for virtual backup and recovery, > you get blazing-fast, flexible, and affordable data protection. > Download your free trial now. > http://p.sf.net/sfu/quest-d2dcopy1 > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] ContactsNCONT script error
Dear All, I would like to compare the intermolecular crystal contacts in seven crystal forms of the same enzyme. I produced a list of contacts for each crystal form using the program NCONT from CCP4 and I found the ContactsNCONT script in the PyMOL Wiki (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a lot of time. Unfortunately, when I run the ContactsNCONT script, I always have the following message with different PCs running different OS (Windows, RedHat or Mac): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 338, in parse parsing.run_file(path,self.pymol_names,self.pymol_names) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", line 455, in run_file execfile(file,global_ns,local_ns) File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3 def parseContacts( f ): ^ IndentationError: unexpected indent Any suggestion will be more than appreciated. Thank you in advance, Regards Ivan Campeotto Centre for Molecular Microbiology and Infection Imperial College London -- vRanger cuts backup time in half-while increasing security. With the market-leading solution for virtual backup and recovery, you get blazing-fast, flexible, and affordable data protection. Download your free trial now. http://p.sf.net/sfu/quest-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
