VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Aug 18 2016 - 17:01:15 CDT

Thanks everyone!

On Thu, Aug 18, 2016 at 6:00 PM, Crystal Liu <sixian_at_ualberta.ca> wrote:
> Hi Olya,
> Try using the command "serial" instead of index, in order to obtain obtain
> atom numbers starting from zero.
>
> Cheers,
> Crystal
>
>
> On Thursday, 18 August 2016, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>
>> Hi all,
>>
>> this is probably a simple thing, but I can't figure out how to write a
>> selection correctly. I would like to print out indices for all CA
>> atoms in certain chains in my pdb file. Here is a selection that I
>> make:
>>
>> set sel [atomselect top "chain A B C and name CA]
>> $sel list
>>
>> (or $sel get index)
>>
>> Then when printed all indices are shifted by 1 from the number it
>> supposed to be. The line in the pdb file looks like this:
>>
>> ATOM 5 CA THR A 1 60.252 86.999 118.788 0.00 0.00 A
>> ..
>> ..
>> ATOM 19 CA SER A 2 62.852 89.569 117.619 0.00 0.00 A
>>
>> and so on, but the numbers I get printed out in the tcl shell are like
>> this:
>>
>> 4 18 ... etc.
>>
>> So when I call list or index the atoms are numbered starting from 0.
>>
>> Is there a way to make atomselect print the actual index (in my case.
>> 5, 19... and so on) ?
>>
>> Thanks in advance!
>>
>>
>> Olga
>>
>