VMD-L Mailing List

From: Mert Gür (gurmert_at_gmail.com)
Date: Mon Jun 14 2010 - 16:24:44 CDT

Thanks a lot it works!!
Johns solution sounded easier so I used it first. But thank you Genie
for your suggestion.
Best,
Mert

On Mon, Jun 14, 2010 at 11:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> From your description, it sounds like you're just wanting to replace
> the coordinates of one with the coordinate from the other, in which case
> you would do this:
>  $s1 set {x y z} [$s2 get {x y z}]
>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Mon, Jun 14, 2010 at 10:26:14PM +0300, Mert Gür wrote:
>> Dear all,
>> I want to change only the carbon alpha coordinates of my vilin pdb
>> file. The reason of doing that is to use the CA coordinates from a
>> different pdb file as Targeted Molecular Dynamic target coordinates.
>> I have two pdb files vilin.pdb which has all the initial coordinates
>> and CA.pdb which only has the target CA coordinates. The residue index
>> for the CA atoms is the same in both pdb file. However, atom indexes
>> are different.
>> Can anyone help me to change the CA coordinates in vilin.pdb to the
>> ones in CA.pdb?
>> Best,
>> Mert
>>
>> mol load pdb vilin.pdb
>> mol load pdb CA.pdb
>>
>> set s1 [atomselect 0 "name CA"]
>> set s2 [atomselect 1 "name CA"]
>> set s3 [atomselect 0 "protein"]
>>
>> I cant figure out the next step.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>