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 :
> 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 :
>
> 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
>> 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 :
>>
>>> 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 :
>>>
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 :
Boo
7 wrz 2014 09:26 "Jamesno Starligois ht" 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 th
