ADL: 1AIK structure

Gavin Seddon home at gavsed.net
Thu Sep 30 02:37:38 PDT 2010


Andreas,
remember if you use an editor;
a.  the rest of the mol is wrong unless you reminimise with md.  This my 
be a good idea anyway.
b.  One has to be careful not to 'chop' anything crucial, yes this 
applies to a gui editor also.
c.  the best protein editor tools are YASARA and WHATIF.  These will 
also check your final structure.

Gav.

On 30/09/10 08:54, Kukol, Andreas wrote:
> I am not sure about removing side chains, but the most easy way to remove parts of the protein including side chains is with a text editor, such as WordPad or Notepad++.
>
> Andreas
>
>    
>> -----Original Message-----
>> From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
>> Behalf Of chandra shekhar
>> Sent: 30 September 2010 08:00
>> To: autodock at scripps.edu
>> Subject: Re: ADL: 1AIK structure
>>
>> use pymol for removing side chains
>>
>> On Thu, Sep 30, 2010 at 12:27 PM, Onur Alten
>> <onuralten1983 at hotmail.com>wrote:
>>
>>      
>>> Hello everyone. I have used the protein structure 1AIK for docking. I
>>> download it as a biological unit from rscb. It contains 3 N-helix and 3
>>> C-helix. I want to remove one of the C-helix.
>>> How can I make it with autodock?
>>> Many thanks
>>> ________________________________________________
>>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>>
>>>        
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>      
> ________________________________________________
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>
>    

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