While using  super_all command I am getting following error message 
valueError: list.remove(x): x not in list.
To mention how I have tried to use this command ..
1.I have loaded  structures(say 4 pdb files) using file> load option.
2. Then super_all xyz.pdb 
after this I got the above mentioned valueError message.

Pavan Payghan

On Tue, Dec 27, 2011 at 7:37 PM, Thomas Holder <> wrote:
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 where you can find lots of documentation and useful scripts.


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 to define the reference object  for using super command 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, , 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 ).

   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.


       Pavan Payghan

                On Tue, Dec 27, 2011 at 2:17 AM, Jacob Keller
       <> wrote:

          You can try the "alignto" command as an alternative, if you want.


          On Mon, Dec 26, 2011 at 12:45 PM, PAVAN PAYGHAN
       < <>
          < <>>> wrote:
           > Dear PyMol Users,
           > I am using PyMol +v0.97 version on Windows XP .I have
           >  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
           > 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

Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen