VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Sun May 22 2011 - 16:25:11 CDT

Dear VMD users

I tried to all possibilities and i'm mentioning the exact same number of CA
atoms (for aligning) even though my proteins have different atom numbers.

I'm not getting the exact structural alignment.

Kindly advice.

Many Thanks
Balaji

On Fri, May 20, 2011 at 5:26 PM, Gianluca Interlandi <
gianluca_at_u.washington.edu> wrote:

> You are not aligning by the backbone atoms. You should try something like:
>
> set sel1 [atomselect 0 "backbone and resid xx to yy"]
> set sel2 [atomselect 1 "backbone and resid xx to yy"]
>
> where you should replace xx and yy with the resid numbers of the regions
> that you want to align.
>
> Also, the VMD manual is of great great help to learn about selections:
>
>
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node87.html#ug:topic:selections
>
> Gianluca
>
>
> On Fri, 20 May 2011, ban arn wrote:
>
> 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.
>>
>>
>>
>>
>>
>>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Postdoc at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------