Dear Pavan, PyMOL has a command line where you need to type in the commands which are provided by those scripts. Consider this example:
# fetch some example structures fetch 1e4y 1ake 4ake 3hpq, async=0 remove chain B # use 1ake as reference for superpositioning super_all 1ake Not all script can be installed as "plugins". If installation as plugin fails please use "File > Run..." from the menu. PyMOL version 0.97 is quite old, please consider upgrading. Also have a look at http://pymolwiki.org where you can find lots of documentation and useful scripts. Cheers, Thomas PAVAN PAYGHAN wrote, On 12/27/11 13:27: > Dear Mr. Thomas Holder , > > Thanks for the reply .According to you the plugin has been installed > properly.Can you briefly mention > 1.how to define the reference object for using super command > 2.how to use super command with multiple structures to align with the > suitable example. > I have started using pymol recently so it will be worth working for me. > > Pavan Payghan > > > On Tue, Dec 27, 2011 at 5:41 PM, Thomas Holder > wrote: > > Hi Pavan, > > > I want to install the plugins like super_all.py, > align_all_to_all.py ,build_seq.py etc in the PyMol version > +v0.97 but I am unable to do so. > As I mentioned earlier also , even after getting the success > message of plugin has been installed, please restart PyMol to > begin use failed to use the commands . > I got following error message - AttributeError: 'NoneType' > object has no attribute 'lower( for super_all.py ). > > > Provide the name of the reference object as first argument. All > other arguments have default values. > > > Also i want to know whether installing the plugin will add them > to be displayed in plugin list compulsorily for the above > mentioned or all the plugins. > > > The above mentioned scripts do not add plugin menu items, they only > provide new commands. > > Cheers, > Thomas > > Pavan Payghan > > > On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller > <j-kell...@fsm.northwestern.edu> wrote: > > You can try the "alignto" command as an alternative, if you want. > > JPK > > On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN > <pavana...@gmail.com <mailto:pavana...@gmail.com> > <mailto:pavana...@gmail.com <mailto:pavana...@gmail.com>>> wrote: > > Dear PyMol Users, > > > > I am using PyMol +v0.97 version on Windows XP .I have > downloded > > super_all.py and tried to install the plugin by using install > Plugin option > > menu. > > Then I got the message that the plugin was installed but after > > re-initialization I dont find the Plugin for the same in > Plugin > list,also > > was unable to run > > super command .So will you please help me to solve this > problem.Is there > > any incompatibility issues for OS XP? > > Please help me in solving this problem.Or suggest the > proper way > of doing > > the same as I am new user . > > > > Pavan > > > > > > -- > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > email: j-kell...@northwestern.edu > ******************************************* -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ 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
