Dear all,
I still need some help regarding some algorithm for structural
superimposition of my mobile structures regarding one specified reference
using some fitting method (to avoid changing in the position of the
reference.pdb which is very important for me!)=>something like super
command in pymol. Using ProFit I have faced with some errors during
superimposition regarding the chosing reference (in case where there were
some differences in the positions of ref and mob structures its alignment
was not perfect (the mob had not been fully aligned on the ref) obtaining
very big RMSD (20 A!) as the result although its actual value should be in
range of 2-5 A. I'll be thankful for possible sollutions of this problem
using Profit is there are users experienced with this software (mb it
should to define fitting zones or atom subsets more accurately but I have
no ideas here ) or any other alternatives which could be used as parts of
the shell script.
James
2014-09-15 18:52 GMT+04:00 James Starlight <jmsstarli...@gmail.com>:
> 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
>>>>> >
>>>>> >
>>>>>
>>>>> >
>>>>> ------------------------------------------------------------------------------
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>>>>>
>>>>> 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.
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>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
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>>
>
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