VMD-L Mailing List

From: Xing (stecue_at_gmail.com)
Date: Tue Sep 15 2015 - 22:10:11 CDT

Dear Axel,

Now I've figured it out. Thanks!

On 9/15/2015 4:41 PM, Axel Kohlmeyer wrote:
>
>
> On Tue, Sep 15, 2015 at 1:08 PM, Xing <stecue_at_gmail.com
> <mailto:stecue_at_gmail.com>> wrote:
>
> Dear John,
>
> Thanks! I did use VMD 1.9.1. It's much better with VMD 1.9.2 now. :)
> But there is still a problem in VMD 1.9.2. It seems that VMD will
> ignore the orders of atoms in the atom selection text, and I can
> only align the molecules properly after I updated the order of
> atoms in the pdb files manually. Is there a way to force VMD to
> use the input order of atom section text instead of the internal
> orders in the pdb files in "atom pairing" (that is, 5-->7, 4-->6,
> 6-->4 in my sample script) ?
>
>
> ​the measure fit command takes an optional "order" flag, which allows
> to provide an altered order of the indices as a list. please see the
> user's guide for details.
>
> axel.​
>
>
>
> Best wishes,
> Xing
>
>
> On 09/15/2015 11:58 AM, John Stone wrote:
>
> Hi,
> There was a limitation in older revs of VMD with regard to
> alignment of less than 4 atoms. I'm guessing that if you're
> having a problem that you must be runnig an older version of
> VMD and not VMD 1.9.2 or later.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu <mailto:vmd_at_ks.uiuc.edu>
>
> On Tue, Sep 15, 2015 at 11:34:25AM -0400, Xing wrote:
>
> Dear all,
>
> I'm trying to reproduce the step 2 of AMBER A1 tutorial
> with VMD.
> (http://ambermd.org/tutorials/advanced/tutorial1/section2.htm)
> because
> Sirius is no longer available. However VMD can never
> superposition the
> "anchor atoms" and the two structures (linker and dye)
> cannot be aligned as
> shown in the tutorial. I tried to increase the number of
> anchor atoms and
> the problem still exists. The script is as
>
> set anc_linker [atomselect 4 "index 5 4 6"]
> set anc_dye [atomselect 3 "index 7 6 4"]
> set linker_to_dye [measure fit $anc_linker $anc_dye]
> set all_linker [atomselect 4 "all"]
> $all_linker move $linker_to_dye
>
> Is there something wrong in the script or VMD just cannot
> align only a few
> atoms?
>
> --
> Sincerely yours
> Xing
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
Xing