From: Abhinav V. <abh...@gm...> - 2007-02-02 10:09:01
|
Hallo, I have an annoying problem. I have pdb file with Na+ atoms defined as ATOM 1 Na+ Na+ 53 -1.106 7.854 52.244 1.00 0.00 Na ATOM 2 Na+ Na+ 54 -0.106 3.854 27.244 1.00 0.00 Na ATOM 3 Na+ Na+ 55 1.894 -6.146 62.244 1.00 0.00 Na ATOM 4 Na+ Na+ 56 8.894 -5.146 42.244 1.00 0.00 Na ATOM 5 Na+ Na+ 57 -4.106 4.854 13.244 1.00 0.00 Na ATOM 6 Na+ Na+ 58 -10.106 -6.146 42.244 1.00 0.00 Na ATOM 7 Na+ Na+ 59 -7.106 5.854 35.244 1.00 0.00 Na ATOM 8 Na+ Na+ 60 4.894 4.854 49.244 1.00 0.00 Na ATOM 9 Na+ Na+ 61 9.894 -3.146 22.244 1.00 0.00 Na now if want to select these Na+ with PyMOL>select n. na+ Selector: selection "sele" defined with 0 atoms. Any ideas how to select them? I tried renaming them to Na and then select n. na which works. So I assume the problem is "+" which is used for add in pymol. I also tried n. "na+" which did not work either. thanks in advance, Abhi. |
From: Tsjerk W. <ts...@gm...> - 2007-02-02 10:22:56
|
Hi Abhi, Actually, it was a bit surprising to me to see you're right. Now, for showing/hiding, it has been dealt with in the code, by allowing the "+" to be left out. However, for selecting (and alter_ing) that doesn't go, apparently. A workaround is to use cmd.select("selectionname","r. na\+") or cmd.select("selectionname","n. na\+") Alternatively, you can change the residue/atomnames using: cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'") All of these worked for me. Of course, it would be good to have this dealt with properly in the same way as for showing/hiding. Hope it helps, Tsjerk On 2/2/07, Abhinav Verma <abh...@gm...> wrote: > Hallo, > I have an annoying problem. I have pdb file with Na+ atoms defined as > > ATOM 1 Na+ Na+ 53 -1.106 7.854 52.244 1.00 0.00 Na > > now if want to select these Na+ with > > PyMOL>select n. na+ > Selector: selection "sele" defined with 0 atoms. > > Any ideas how to select them? > > I tried renaming them to Na and then select n. na which works. So I assume > the problem is "+" which is used for add in pymol. > I also tried n. "na+" which did not work either. > > > thanks in advance, > Abhi. > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |
From: DeLano S. <de...@de...> - 2007-02-02 19:34:21
|
Tsjerk & Abhinav, > Actually, it was a bit surprising to me to see you're right. + is the default list separator in selections. For example: select posi, ARG+HIS+LYS/ select backbone, n. N+CA+C+O That is why it needs to be escaped with a backslash. Commas can also be used, but only within parentheses -- otherwise the parser gets confused, since commas are also used to separate command arguments. select backbone, (n. N,CA,C,O) Also, be aware when using backslashes inside a Python string that they are also a string escape character, so it is best to use two of them "\\+". However, a single slash happens to work in this case for some bizzare reason. In other words, the PyMOL command: select selectionname, r. na\+ has a true Python equivalent of cmd.select("selectionname","r. na\\+") not cmd.select("selectionname","r. na\+") which actually works, but probably shouldn't. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:de...@de... > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of Tsjerk Wassenaar > Sent: Friday, February 02, 2007 2:23 AM > To: Abhinav Verma > Cc: pym...@li... > Subject: Re: [PyMOL] selecting Na+ in pymol > > Hi Abhi, > > Actually, it was a bit surprising to me to see you're right. > Now, for showing/hiding, it has been dealt with in the code, > by allowing the "+" to be left out. However, for selecting > (and alter_ing) that doesn't go, apparently. A workaround is to use > > cmd.select("selectionname","r. na\+") or > cmd.select("selectionname","n. na\+") > > Alternatively, you can change the residue/atomnames using: > > cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'") > > All of these worked for me. Of course, it would be good to > have this dealt with properly in the same way as for showing/hiding. > > Hope it helps, > > Tsjerk > > On 2/2/07, Abhinav Verma <abh...@gm...> wrote: > > Hallo, > > I have an annoying problem. I have pdb file with Na+ atoms > defined as > > > > ATOM 1 Na+ Na+ 53 -1.106 7.854 52.244 > 1.00 0.00 Na > > > > now if want to select these Na+ with > > > > PyMOL>select n. na+ > > Selector: selection "sele" defined with 0 atoms. > > > > Any ideas how to select them? > > > > I tried renaming them to Na and then select n. na which works. So I > > assume the problem is "+" which is used for add in pymol. > > I also tried n. "na+" which did not work either. > > > > > > thanks in advance, > > Abhi. > > > > > ---------------------------------------------------------------------- > > --- Using Tomcat but need to do more? Need to support web services, > > security? > > Get stuff done quickly with pre-integrated technology to > make your job > > easier. > > Download IBM WebSphere Application Server v.1.0.1 based on Apache > > Geronimo > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216 > > 42 _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > > -------------------------------------------------------------- > ----------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on > Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057& dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Tsjerk W. <ts...@gm...> - 2007-02-02 20:56:07
|
Hi Warren, Actually, I tried to use select .., r. na\+ as the second option, but that didn't work for me (Pymol 0.99b on Suse 9.2). Oh, and I owe you an elaborate answer still on the mail from a while ago. But that got a bit buried.. sorry ;) Tsjerk On 2/2/07, DeLano Scientific <de...@de...> wrote: > > Tsjerk & Abhinav, > > > Actually, it was a bit surprising to me to see you're right. > > + is the default list separator in selections. For example: > > select posi, ARG+HIS+LYS/ > select backbone, n. N+CA+C+O > > That is why it needs to be escaped with a backslash. > > Commas can also be used, but only within parentheses -- otherwise the parser > gets confused, since commas are also used to separate command arguments. > > select backbone, (n. N,CA,C,O) > > Also, be aware when using backslashes inside a Python string that they are > also a string escape character, so it is best to use two of them "\\+". > However, a single slash happens to work in this case for some bizzare > reason. > > In other words, the PyMOL command: > > select selectionname, r. na\+ > > has a true Python equivalent of > > cmd.select("selectionname","r. na\\+") > > not > > cmd.select("selectionname","r. na\+") > > which actually works, but probably shouldn't. > > Cheers, > Warren > > -- > DeLano Scientific LLC > Subscriber Support Services > mailto:de...@de... > > > -----Original Message----- > > From: pym...@li... > > [mailto:pym...@li...] On Behalf > > Of Tsjerk Wassenaar > > Sent: Friday, February 02, 2007 2:23 AM > > To: Abhinav Verma > > Cc: pym...@li... > > Subject: Re: [PyMOL] selecting Na+ in pymol > > > > Hi Abhi, > > > > Actually, it was a bit surprising to me to see you're right. > > Now, for showing/hiding, it has been dealt with in the code, > > by allowing the "+" to be left out. However, for selecting > > (and alter_ing) that doesn't go, apparently. A workaround is to use > > > > cmd.select("selectionname","r. na\+") or > > cmd.select("selectionname","n. na\+") > > > > Alternatively, you can change the residue/atomnames using: > > > > cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'") > > > > All of these worked for me. Of course, it would be good to > > have this dealt with properly in the same way as for showing/hiding. > > > > Hope it helps, > > > > Tsjerk > > > > On 2/2/07, Abhinav Verma <abh...@gm...> wrote: > > > Hallo, > > > I have an annoying problem. I have pdb file with Na+ atoms > > defined as > > > > > > ATOM 1 Na+ Na+ 53 -1.106 7.854 52.244 > > 1.00 0.00 Na > > > > > > now if want to select these Na+ with > > > > > > PyMOL>select n. na+ > > > Selector: selection "sele" defined with 0 atoms. > > > > > > Any ideas how to select them? > > > > > > I tried renaming them to Na and then select n. na which works. So I > > > assume the problem is "+" which is used for add in pymol. > > > I also tried n. "na+" which did not work either. > > > > > > > > > thanks in advance, > > > Abhi. > > > > > > > > ---------------------------------------------------------------------- > > > --- Using Tomcat but need to do more? Need to support web services, > > > security? > > > Get stuff done quickly with pre-integrated technology to > > make your job > > > easier. > > > Download IBM WebSphere Application Server v.1.0.1 based on Apache > > > Geronimo > > > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216 > > > 42 _______________________________________________ > > > PyMOL-users mailing list > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > Junior UD (post-doc) > > Biomolecular NMR, Bijvoet Center > > Utrecht University > > Padualaan 8 > > 3584 CH Utrecht > > The Netherlands > > P: +31-30-2539931 > > F: +31-30-2537623 > > > > -------------------------------------------------------------- > > ----------- > > Using Tomcat but need to do more? Need to support web > > services, security? > > Get stuff done quickly with pre-integrated technology to make > > your job easier. > > Download IBM WebSphere Application Server v.1.0.1 based on > > Apache Geronimo > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057& > dat=121642 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 |
From: Abhinav V. <abh...@gm...> - 2007-02-05 07:34:19
|
Hi Warren & Tsjerk, Thanks a lot for the explaination select r. na\+ did work for me (Pymol 0.99rc6 on Suse 10.1) cheers, Abhi. On 2/2/07, Tsjerk Wassenaar <ts...@gm...> wrote: > > Hi Warren, > > Actually, I tried to use select .., r. na\+ as the second option, but > that didn't work for me (Pymol 0.99b on Suse 9.2). > > Oh, and I owe you an elaborate answer still on the mail from a while > ago. But that got a bit buried.. sorry ;) > > Tsjerk > > On 2/2/07, DeLano Scientific <de...@de...> wrote: > > > > Tsjerk & Abhinav, > > > > > Actually, it was a bit surprising to me to see you're right. > > > > + is the default list separator in selections. For example: > > > > select posi, ARG+HIS+LYS/ > > select backbone, n. N+CA+C+O > > > > That is why it needs to be escaped with a backslash. > > > > Commas can also be used, but only within parentheses -- otherwise the > parser > > gets confused, since commas are also used to separate command arguments. > > > > select backbone, (n. N,CA,C,O) > > > > Also, be aware when using backslashes inside a Python string that they > are > > also a string escape character, so it is best to use two of them "\\+". > > However, a single slash happens to work in this case for some bizzare > > reason. > > > > In other words, the PyMOL command: > > > > select selectionname, r. na\+ > > > > has a true Python equivalent of > > > > cmd.select("selectionname","r. na\\+") > > > > not > > > > cmd.select("selectionname","r. na\+") > > > > which actually works, but probably shouldn't. > > > > Cheers, > > Warren > > > > -- > > DeLano Scientific LLC > > Subscriber Support Services > > mailto:de...@de... > > > > > -----Original Message----- > > > From: pym...@li... > > > [mailto:pym...@li...] On Behalf > > > Of Tsjerk Wassenaar > > > Sent: Friday, February 02, 2007 2:23 AM > > > To: Abhinav Verma > > > Cc: pym...@li... > > > Subject: Re: [PyMOL] selecting Na+ in pymol > > > > > > Hi Abhi, > > > > > > Actually, it was a bit surprising to me to see you're right. > > > Now, for showing/hiding, it has been dealt with in the code, > > > by allowing the "+" to be left out. However, for selecting > > > (and alter_ing) that doesn't go, apparently. A workaround is to use > > > > > > cmd.select("selectionname","r. na\+") or > > > cmd.select("selectionname","n. na\+") > > > > > > Alternatively, you can change the residue/atomnames using: > > > > > > cmd.alter("r. na\+","resn='Na'") or cmd.alter("n. na\+","name='Na'") > > > > > > All of these worked for me. Of course, it would be good to > > > have this dealt with properly in the same way as for showing/hiding. > > > > > > Hope it helps, > > > > > > Tsjerk > > > > > > On 2/2/07, Abhinav Verma <abh...@gm...> wrote: > > > > Hallo, > > > > I have an annoying problem. I have pdb file with Na+ atoms > > > defined as > > > > > > > > ATOM 1 Na+ Na+ 53 -1.106 7.854 52.244 > > > 1.00 0.00 Na > > > > > > > > now if want to select these Na+ with > > > > > > > > PyMOL>select n. na+ > > > > Selector: selection "sele" defined with 0 atoms. > > > > > > > > Any ideas how to select them? > > > > > > > > I tried renaming them to Na and then select n. na which works. So I > > > > assume the problem is "+" which is used for add in pymol. > > > > I also tried n. "na+" which did not work either. > > > > > > > > > > > > thanks in advance, > > > > Abhi. > > > > > > > > > > > ---------------------------------------------------------------------- > > > > --- Using Tomcat but need to do more? Need to support web services, > > > > security? > > > > Get stuff done quickly with pre-integrated technology to > > > make your job > > > > easier. > > > > Download IBM WebSphere Application Server v.1.0.1 based on Apache > > > > Geronimo > > > > > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216 > > > > 42 _______________________________________________ > > > > PyMOL-users mailing list > > > > PyM...@li... > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > Junior UD (post-doc) > > > Biomolecular NMR, Bijvoet Center > > > Utrecht University > > > Padualaan 8 > > > 3584 CH Utrecht > > > The Netherlands > > > P: +31-30-2539931 > > > F: +31-30-2537623 > > > > > > -------------------------------------------------------------- > > > ----------- > > > Using Tomcat but need to do more? Need to support web > > > services, security? > > > Get stuff done quickly with pre-integrated technology to make > > > your job easier. > > > Download IBM WebSphere Application Server v.1.0.1 based on > > > Apache Geronimo > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057& > > dat=121642 > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > |