## Re: [PyMOL] Selecting ASP and GLU

 Re: [PyMOL] Selecting ASP and GLU From: Martin Hediger - 2011-03-02 21:03:51 ```Hey Hongbo, good way of putting it. Indeed, I think thats what seemed most intuetively to me in the beginning, and so I ended up trying to figure out why 'AND' was not giving me the expected selection. Remembering my boolean algebra lecture from back in the days, I suddendly realized that it has to be 'OR', right now I'm wondering why this is not expressed as 'v' (as opposed to 'AND', which then would of course be '^'). But you're right, the Jmol example is really making the point of how weird this can appear to be. Martin Am 02.03.11 11:06, schrieb Hongbo Zhu: > 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 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 >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search& Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> _______________________________________________ >>> PyMOL-users mailing list (PyMOL-users@...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@... >>> >> >> ```