VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Fri May 20 2011 - 09:04:53 CDT

Dear VMD Users

I tried to align using index number & backbone for both the protein, but it
doesn't align poperly.

These are the commands I tried to align

set sel1 [atomselect 0 "index 1 to 4720"]
set sel2 [atomselect 1 "index 1 to 4720 "]
set transformation_matrix [measure fit $sel1 $sel2] (by choosing exact
number, i can able to get transforming co-ordinates)
set move_sel [atomselect 1 "all"]
$move_sel move $transformation_mat

Kindly advice.

Many Thanks
Balaji

On Fri, May 20, 2011 at 12:37 PM, ban arn <ban.arn_at_gmail.com> wrote:

> Dear VMD user
>
> Kindly help me how to get new co-ordinate values for transforming matrix
> for aligning two proteins of different atom numbers.
>
> Say for example like this..
>
> set transformation_matrix [measure fit $sel1 $sel2]
> Info) {0.971188 0.00716391 0.238206 -13.2877}
> {0.0188176 0.994122 -0.106619 3.25415} {-0.23757 0.108029 0.965345 -2.97617}
> {0.0 0.0 0.0 1.0}
>
> Balaji
>
>
>
> On Fri, May 20, 2011 at 11:47 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>> On Fri, May 20, 2011 at 5:23 AM, ban arn <ban.arn_at_gmail.com> wrote:
>> > Dear VMD users
>> >
>> > Thanks for reply.
>> >
>> > I tried to align two protein trajectories of varying atom numbers using
>> > transformation matrix, its shows error as " the selection should have
>> same
>> > atom numbers"
>> >
>> > For example, I defined my selection as
>> >
>> > set sel1 [atomselect 0 "backbone"]
>> > set sel2 [atomselect 2 "backbone"]
>> > set transformation_matrix [measure fit $sel1 $sel2]
>> >
>> > "Measure fit" commands requires that the selection should have same atom
>> > number.
>> >
>> > Kindly advice.
>>
>> kindly _follow_ the advice that has been given to you.
>>
>> search the mailing list archives for how to handle this.
>>
>> axel.
>>
>>
>>
>> >
>> > Many Thanks
>> > Balaji
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Thu, May 19, 2011 at 6:07 PM, Eduard Schreiner
>> > <eduard.schreiner_at_gmail.com> wrote:
>> >>
>> >> Axel's reply would work for that one too
>> >> eddi
>> >>
>> >> On Thu, May 19, 2011 at 6:37 PM, ban arn <ban.arn_at_gmail.com> wrote:
>> >>>
>> >>> Dear VMD users
>> >>>
>> >>> Thnaks for reply.
>> >>>
>> >>> It works fine.
>> >>>
>> >>> I can pose the question in another way.
>> >>>
>> >>> Is it possible to align the trajectories of two proteins of varying
>> atom
>> >>> numbers according to backbone in VMD.
>> >>>
>> >>> Many Thanks
>> >>> Balaji
>> >>>
>> >>> On Thu, May 19, 2011 at 5:31 PM, Joseph Bylund <
>> joseph.bylund_at_gmail.com>
>> >>> wrote:
>> >>>>
>> >>>> The stamp structural alignment in extensions->analysis->multiseq
>> sounds
>> >>>> like what you're looking for.
>> >>>>
>> >>>> On 05/19/2011 11:43 AM, ban arn wrote:
>> >>>>>
>> >>>>> Dear VMD users
>> >>>>>
>> >>>>> Is it possible to align two proteins of varying atom numbers
>> according
>> >>>>> to backbone in vmd.
>> >>>>>
>> >>>>> Kindly advice
>> >>>>>
>> >>>>> Many Thanks
>> >>>>> Balaji
>> >>>>>
>> >>>
>> >>
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>
>