yeah, its true. We should work out a tutorial for this kind of things. Something where there is only one line of instruction and one line of command, like:
1) Download a file fetch pdb1.pdb 2) Select all ASP or GLU residues: select acids, resn ASP+GLU 3) Suggestions? Am 02.03.11 22:36, schrieb Hongbo Zhu: > 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 >>> >> >> ------------------------------------------------------------------------------ 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. 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