VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 20 2011 - 05:47:18 CDT

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.