Dear,
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 <
spel...@users.sourceforge.net> 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 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-keller2@fsm.northwestern.**edu <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
>
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