VMD-L Mailing List
From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Jul 23 2014 - 14:37:01 CDT
If you mean that you have already run MDFF and now want to extract just a
part of the structure, look at using VMD's 'atomselect' command to select
the part you want and the 'writepdb' command to save it to a pdb file.
On Tue, Jul 22, 2014 at 3:25 PM, Anjela Manandhar <anjelamanandhar_at_gmail.com
> Thanks Ryan.
> So now I have a fitted structure. I only need a part of it. How can do
> Anjela Manandhar
> Graduate Student
> Biochemistry Program
> Graduate Center, City University of New York
> 365 Fifth Avenue, NY-10016, USA
> On Mon, Jul 21, 2014 at 3:49 PM, Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
>> MDFF is not used for initial docking. Instead you should use another
>> program like 'colores' in Situs (http://situs.biomachina.org/). After
>> the subunits are docked, you can then run MDFF.
>> On Mon, Jul 21, 2014 at 2:05 PM, Anjela Manandhar <
>> anjelamanandhar_at_gmail.com> wrote:
>>> I need to dock multiple subunits of a protein into a whole EM map. Does
>>> MDFF has this function
>>> Anjela Manandhar