VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 15 2015 - 15:41:30 CDT

On Tue, Sep 15, 2015 at 1:08 PM, Xing <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
>>
>> 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  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.