On 03/02/2011 10:07 PM, Tsjerk Wassenaar wrote: > Hey :) > > It's good to note that programs are written by programmers, using > programmer's logic.
First of all, I was not complaining about the logic of the PyMOL programmers. I tried to help find out the reason that might cause Martin's script to break based on the similar complains I had received. It is true that programs are written by programmers. But I guess many users actually hate that fact so much because they see again and again that some programmers just presume that all users will think the same way as they think. (Of course after these users become programmers they start to do the same ;) The confusion is not so much caused by the > simplified expression, but by users with little background in > mathematics/logic assessing 'and' and 'or' from a linguistic > background.In computer science and mathematics OR := union, AND := > intersection. It's covered quite well in > http://www.pymolwiki.org/index.php/Selection_Algebra I disagree. I think it is caused by the simplified expression to the users who think intuitively instead of immediately mathematically when they try to write down the first line of selection script, no matter how much mathematics/logic they have (the colleague I mentioned is a computer scientist). After staring at the unexpected outcome for a while, they will try to think mathematically or google-ly ;). I can not think of a good way to address this small issue for new users. Maybe a more informative hint to the users is helpful rather than just print "0 atoms selected". For example, PyMOL can print the selection result of each operand, or print the complete selection expression translated from the the simplified selection expression. > > Cheers, > > Tsjerk > > On Wed, Mar 2, 2011 at 11:06 AM, Hongbo Zhu > <hongbo....@biotec.tu-dresden.de> wrote: >> 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....@bluewin.ch> 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@lists.sourceforge.net) >>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>>> >>> >>> >>> >> >> -- >> 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 >> >> ------------------------------------------------------------------------------ >> 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@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > -- 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 ------------------------------------------------------------------------------ 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@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
