Re: [PyMOL] Selecting ASP and GLU

[Hongbo Z. <hon...@bi...>]

I believe the confusion is caused by the simplified selection expression 
in PyMOL (and some other visualization tools as well). I remember that 
one of my colleagues once questioned strongly the reason of using OR 
instead of AND in such situation.

The expression:

select resn GLU or resn ASP

actually means

select (resn == GLU) or (resn == ASP)

The reason of using Boolean operator *or* is very clean when the two 
operands are stated completely. But when the operands are simplified, 
our first reaction is to use *and* because it is very natural to say

"I want GLU *and* ASP"

if you want both GLU and ASP.

And it is even more confusing in Jmol :

select 110 or 112 (select resno==110 or resn==112)

if want you really want is 110 *and* 112 :)

hongbo

On 03/01/2011 05:43 PM, Jason Vertrees wrote:
> Hi Martin,
>
> To select all ASPs and GLUs just type,
>
> select resn GLU+ASP
>
> or
>
> select resn GLU or resn ASP
>
> or, if you need parentheses,
>
> select ((resn GLU) or (resn ASP))
>
>
> Maybe this will help:
>
> # fetch a test protein
>
> fetch 1rsy, async=0
>
> # color all ASPs and GLUs red
>
> color tv_red, (resn ASP or resn GLU)
>
>
> While the boolean 'and' works, the following will fail to select and
> color any atoms:
>
> color tv_red, (resn ASP and resn GLU)
>
> because there will be no _single atom_ in both an ASP and a GLU.  The
> boolean 'and' in "(resn ASP and resn GLU)" requests an atom that is in
> any ASP _and_ in any GLU--which is impossible.
>
> Cheers,
>
> -- Jason
>
>
>
> On Tue, Mar 1, 2011 at 7:44 AM, Martin Hediger<ma...@bl...>  wrote:
>> Dear all
>> What is the selection syntax to select all GLU and ASP residues within an
>> object?
>>
>> I'm trying it the way its written on the wiki:
>>
>> remove resn hoh    # remove water
>> h_add              # add hydrogens
>>
>> as surface
>> color grey90
>>
>> color slate, resn lys       # lysines in light blue
>> color paleyellow, resn cys  # cysteines in light yellow
>> color tv_red, (resn asp or(resn glu))  # aspartic and glutamic acid in light
>> red
>>
>> but, the selection kind of does not work for me (I'm assuming the operator
>> for the logical AND is 'and').
>> What is it that I need to do differently?
>>
>> Kind regards
>> Martin
>>
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>
>

-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail:  hongbo.zhu at biotec
Webpage: www.biotec.tu-dresden.de