I guess I've passed superimpoition- it works great - with the one
exception- after fitting to ref.pdb the last colum (consisted of the atom
names like C, N, O etc) from the each fitted mobile.pdb has been removed. I
need to keep this column on the resulted pdb because I'll use this pdb as
the initial structure for the autodock docking (actually I do
superimposition because I have had all input docking parameters including
XYZ of the cavity for the ref structure). If the last column is missed I
have promblems with the pdb2pdbqt conversion of the mobile_fit.pdb using
babel. I'll thankful to everyone who have faced with the same problem and
could provide me with some suggestions.
Thank for help,
James
2014-09-09 12:35 GMT+04:00 James Starlight <jmsstarli...@gmail.com>:
> 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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