From: Tsjerk W. <ts...@gm...> - 2007-10-09 11:04:17
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Hi Gillean, Frieda, The versions posted on the wiki should work for older versions of Python/Pymol. Don't see why it shouldn't. Anyway, in my implementation, the pop(i) throws out the element which is the same as the next one, for each element. After that, sslist contains exactly what is requested. Maybe there should've been a 'print sslist' as the final statement. Cheers, Tsjerk On 10/9/07, gilleain torrance <gil...@gm...> wrote: > > Hi Tsjerk, Frieda, > I made a different solution (I can't get Tsjerk's to work, oddly - it > looks like it should step through sses correctly, but I can't see why the " > sslist.pop(i)" gives what it should). > > Anyway, my 'versions' :) are on the wiki as: > > http://www.pymolwiki.org/index.php/Ss > > which is what was asked for. Also, there is a more tricky implementation, > that takes a function and applys it to each sse. I don't know if these > programs are compatible with very early versions of python, bytheway. > > http://www.pymolwiki.org/index.php/Iterate_sses > > They were fun to code, anyway. > > gilleain torrance > > On 10/9/07, Tsjerk Wassenaar < ts...@gm...> wrote: > > > > Hi Frieda, > > > > In addition to my previous mail, the following works for me: > > > > sslist=[] > > iterate n. ca, sslist.append( [resn,resi,ss] ) > > > > /i=1, j=len(sslist)-1 > > /while i<j:\ > > if sslist[i][2] == sslist[i+1][2]:\ > > sslist.pop[i]\ > > j = j - 1\ > > else:\ > > i=i+2 > > > > Hope it helps, > > > > Tsjerk > > > > On 10/9/07, Tsjerk Wassenaar < ts...@gm...> wrote: > > > > > > Hi Frieda, > > > > > > There's no such command. You'll have to parse the output you get > > > through a script which filters it in the way you want. This isn't difficult > > > though (good python exercise :p). > > > > > > Best, > > > > > > Tsjerk > > > > > > On 10/9/07, Frieda Reichsman < fr...@ns...> wrote: > > > > > > > Hi, > > > > > > > > > > > > I would like to get secondary structure information from a PyMOL > > > > file. I searched the list and found this: > > > > > > > > > > > > > > > > > > > > > I need a list of the secondary structure assigned to each residue > > > > by dss in > > > > > pymol. Is there a simple way to write this information to a file, > > > > or dump it > > > > > to the screen? > > > > > > > > To dump it to the screen, try: > > > > > > > > iterate <object name> & n. ca, print resn,resi,ss > > > > > > > > > > > > > > > > and it works, but the output is a long list of every residue. Is > > > > there a command to get the output more succinctly, such as > > > > > > > > 1-5 L > > > > 6-10 H > > > > 11-15 S > > > > > > > > Thanks, > > > > Frieda > > > > > > > > /////////////////////////////////////////// > > > > > > > > > > > > Frieda Reichsman > > > > > > > > Molecules in Motion > > > > > > > > Interactive Molecular Structures > > > > > > > > http://www.moleculesinmotion <http://www.moleculesinmotion.com> .com<http://www.moleculesinmotion.com> > > > > > > > > > > > > ////////////////////////////// ///////////// > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by: Splunk Inc. > > > > Still grepping through log files to find problems? Stop. > > > > Now Search log events and configuration files using AJAX and a > > > > browser. > > > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > > _______________________________________________ > > > > PyMOL-users mailing list > > > > PyM...@li...urceforge <PyM...@li...>.net<PyM...@li...> > > > > https://lists.sourceforge.net<https://lists.sourceforge.net/lists/listinfo/pymol-users> > > > > /lists/listinfo/pymol-users<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 > > > > > > > > > > -- > > 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 > > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Splunk Inc. > > Still grepping through log files to find problems? Stop. > > Now Search log events and configuration files using AJAX and a browser. > > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li...urceforge <PyM...@li...> .net<PyM...@li...> > > https://lists.sourceforge.net<https://lists.sourceforge.net/lists/listinfo/pymol-users>/lists/listinfo/pymol-users<https://lists.sourceforge.net/lists/listinfo/pymol-users> > > > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > 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 |