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<mailto: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<mailto: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<mailto: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<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<mailto:pona...@gmail.com>>:
Boo
7 wrz 2014 09:26 "Jamesno Starligois ht"
<jmsstarli...@gmail.com<mailto: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<mailto: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<mailto: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<mailto: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
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk_______________________________________________
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
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
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
