Thanks Markus, I'll try to examine it!
Jed,
the main problem with the profit is that I need to superimpose structures
in loop which are not always has the same sequence length. Is it possible
to superimpose each structure based on some common criterium found for each
mobile and reference automatically?
Kind regards,
James
2014-09-08 20:32 GMT+04:00 Markus Heller <mhel...@cdrd.ca>:
> Shot in the dark, based on reading “ensemble of the structures” and
> “ProFit”:
>
>
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828896/
>
>
>
> CARON – Average RMSD of NMR structure ensemble
>
>
>
> Hope that helps!
>
>
>
> Markus
>
>
>
> *From:* James Starlight [mailto:jmsstarli...@gmail.com]
> *Sent:* Monday, September 08, 2014 6:52 AM
> *To:* pymol-users
> *Subject:* Re: [PyMOL] Access to pymol commands from the terminal
>
>
>
> Ok, ProFit has been passed :D
>
> Now I'm looking for some software which could do the same least-square
> fitting for the ensemble of the structures taken it as the separate pdbs
> from the work dir (I'm not sure if the mustang software could be useful for
> this task)=> because looping using ProFit might be not good for me because
> each time I need to provide new atom selection for the superimposition for
> each model in the ProFit's script file.
>
> James
>
>
>
> 2014-09-07 11:11 GMT+02:00 Maciek Dziubiński <pona...@gmail.com>:
>
> Boo
> 7 wrz 2014 09:26 "Jamesno Starligois ht" <jmsstarli...@gmail.com>napisał
> napisał(a):
>
>
> >
> > Thomas,thanks for help- I'll try to test your script!
> >
> > Jed, many thanks too!
> >
> > if I understood correctly align.profit should contain thefollowing lines:
> >
> > # using ProFIT to align the model to 2hi4
> > open $PROFIT, "> align.profit" or die "Cannot open file
> align.profit\n";
> > print $PROFIT "ATOMS CA\n";
> > print $PROFIT "ZONE 34-513:1-480\n";
> > print $PROFIT "FIT\n";
> > print $PROFIT "WRITE $folder/$dir/$pdbnew\n";
> > close $PROFIT;
> >
> > shouldn't it?
> >
> > that that file is provided to 1 command line
> > `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
> $folder/$dir/$pdbnew`;
> > where 2hi4.pdb is my ref
> > $pdbnew variable assosiated with the target pdb
> >
> > one question about align.profit: will the output aligned mobile.pdb
> consist of all atoms? I've found that only CA atoms are used for the
> superimposition
> > print $PROFIT "ATOMS CA\n";
> >
> >
> > James
> >
> >
>
> >
> ------------------------------------------------------------------------------
> > Slashdot TV.
> > Video for Nerds. Stuff that matters.
> > http://tv.slashdot.org/
> > _______________________________________________
> > 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
>
> 7 wrz 2014 09:26 "James Starlight" <jmsstarli...@gmail.com> napisał(a):
>
> Thomas,thanks for help- I'll try to test your script!
>
> Jed, many thanks too!
>
>
>
> if I understood correctly align.profit should contain thefollowing lines:
>
>
>
> # using ProFIT to align the model to 2hi4
> open $PROFIT, "> align.profit" or die "Cannot open file
> align.profit\n";
> print $PROFIT "ATOMS CA\n";
> print $PROFIT "ZONE 34-513:1-480\n";
> print $PROFIT "FIT\n";
> print $PROFIT "WRITE $folder/$dir/$pdbnew\n";
> close $PROFIT;
>
>
>
> shouldn't it?
>
>
>
> that that file is provided to 1 command line
>
> `profit -f align.profit -h /home/jedgold/modelling/NAMD/2hi4.pdb
> $folder/$dir/$pdbnew`;
>
> where 2hi4.pdb is my ref
>
> $pdbnew variable assosiated with the target pdb
>
>
>
> one question about align.profit: will the output aligned mobile.pdb
> consist of all atoms? I've found that only CA atoms are used for the
> superimposition
>
> print $PROFIT "ATOMS CA\n";
>
>
>
>
>
> James
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Slashdot TV.
> Video for Nerds. Stuff that matters.
> http://tv.slashdot.org/
> _______________________________________________
> 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
>
>
>
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