Hey,
I've occasionally deleted my profit script which do superimposition
automatically so I'll be very thankful if someone remind me profit input
script syntax
for my case
profit -h -f script.txt ref.pdb tar.pdb
should do actual superimposition where in script.txt;
ATOMS CA
ZONE 2-290:2-290
FIT
WRITE fitted.pdb
unfortunately this end with the error
Starting script: 'new.profit'
Unrecognised keyword: FIT
Error==> Fitting has not yet been performed.
Finished script: 'new.profit'
althought those commands made from the profit command line works perfect
ProFit>FIT
Fitting structures...
RMS: 7.134
Where I made error?
James
2014-09-12 9:13 GMT+02:00 James Starlight <jmsstarli...@gmail.com>:
> Hi Jared,
>
> yes from pymol it's OK, here I've mentioned about ProFit :) but this also
> have been solved. ;)
>
> James
>
> 2014-09-11 19:43 GMT+02:00 Sampson, Jared <jared.samp...@nyumc.org>:
>
> Hi James -
>>
>> What version of PyMOL are you using? For me, using Open Source PyMOL
>> 1.7.2.0, a typical PDB file I tested ends up with more information in that
>> column, not less, after saving from PyMOL:
>>
>> Before:
>> ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61
>> N
>>
>> After:
>> ATOM 1312 NH1 ARG A 198 0.544 14.093 19.655 1.00 34.61
>> N1+
>>
>> Are you sure the column is there in your input file, and hasn’t been
>> removed before loading into PyMOL?
>>
>> Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>>
>>
>>
>>
>>
>>
>> On Sep 11, 2014, at 5:36 AM, James Starlight <jmsstarli...@gmail.com>
>> wrote:
>>
>> 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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>
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