On Fri, Oct 16, 2015 at 9:29 AM, anu chandra <anu80125.gmail.com> wrote:
> Hello Jason,
>
> Thanks for your prompt reply. Since my protein have quiet a lot of flexible
> loop regions, all I am trying to do here is to find a better alignment
> before doing RMSD calculation. Hence, I hoping that
>
> 'rms reference out RMSD.dat time 2 :1-604.CA,N,C,O' basically doing the
> alignment along whole (604 residues) backbone and calculate the total RMSD.
>
>
> Then, with ' rms reference out RMSD_mainloop.dat time 2
> :10-40,52-74,86-223,237-287,302-318,352-372,387-485,504-528,546-600.CA
> ,N,C,O
> ' , I am trying to align the regions other than few long loops and
> calculate the total RMSD .
>
> Afterwards, with ' rms reference out RMSD_allLoop.dat time 2
>
> :10-20,25-30,34-40,52-61,66-74,86-125,130-139,147-152,157-165,174-175,180-186,193-199,207-211,217-223,239-244,249-255,260-265,282-286,303-307,
>
> 313-318,353-358,368-371,389-392,397-405,415-421,430-434,437-461,467-484,504-512,515-524,547-564,568-585.CA
> ,N,C,O
> ' , I am trying to align regions other than all the loop regions and
> calculate the total RMSD.
>
> Am I making sense here?
>
Then I think your commands are doing what you expect them to do (that is,
they align to the mask for each rmsd command).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 16 2015 - 09:00:03 PDT
