VMD-L Mailing List

From: ban arn (ban.arn_at_gmail.com)
Date: Fri May 20 2011 - 04:23:12 CDT

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.

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
>>>>
>>>>
>>
>