VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Tue Jul 17 2007 - 20:35:19 CDT

Arneh Babakhani wrote:
> Yes, the last is definitely what I'm looking for, thanks! (my protein
> example was a little too simple, I was just trying to illustrate the
> concept)
>
> Peter Freddolino wrote:
>> Hi Arneh,
>> there are three ways to do this:
>>
>> -make a compound selection:
>> set IndoleNitrogen [atomselect top "protein and name NE1"]
>>
>> -Define an atomselect macro:
>> atomselect macro prot {protein}
>> set IndoleNitrogen [atomselect top "protein and name NE1"]
>>
>> -Access the text of a previous selection in a new selection:
>> set prot [atomselect top protein]
>> set IndoleNitrogen [atomselect top "[$prot text] and name NE1"]
>>
>> All should be equivalent. The last may be closest to what you were
>> looking for.
>>
>> Best,
>> Peter
>>
>> Arneh Babakhani wrote:
>>
>>> Once I've made a selection, how do I use the name of that selection in
>>> making another selection??? Here's what I mean:
>>>
>>>
>>>> Main< 137 % set Peptide [atomselect top "all protein"]
>>>>
>>> atomselect17053
>>>
>>>> Main< 139 % set IndoleNitrogen [atomselect top "$Peptide and name
>>>>
>>> NE1"]
>>> atomselect: cannot parse selection text: atomselect17053 and name NE1
>>>
>>>> Main< 140 % set IndoleNitrogen [atomselect top "@Peptide and name
>>>>
>>> NE1"]
>>> atomselect: cannot parse selection text: @Peptide and name NE1
>>>
>>>
>>>
>>> How do I get it to parse the 'Peptide' selection??? Do I need
>>> brackets somewhere?
>>> Thanks,
>>>
>>> Arneh
>>>
>>
>>
>