Hi Daniel,
You say you used "split_states", so all your conformations have the same
topology (are the same molecule). In that case, I suggest to use cmd.rms
instead of cmd.align, which will be more efficient. You also don't need to
split the structures, but call the function with the correct "m
, 20 Oct 2014 11:38:41 -0400
>> To: patrick.coss...@inbox.com
>> Subject: Re: [PyMOL] RMSD
>>
>> Hi Cedric,
>>
>> you probably include random waters with "name o". Try adding "... and
>> polymer" to your selection string.
>>
>>
: Mon, 20 Oct 2014 11:38:41 -0400
> To: patrick.coss...@inbox.com
> Subject: Re: [PyMOL] RMSD
>
> Hi Cedric,
>
> you probably include random waters with "name o". Try adding "... and
> polymer" to your selection string.
>
> Cheers,
> Thomas
>
Hi Cedric,
you probably include random waters with "name o". Try adding "... and polymer"
to your selection string.
Cheers,
Thomas
On 20 Oct 2014, at 11:16, Cedric wrote:
> Hi,
>
> I was comparing two very similar structures and I got the following results:
>
> align pdb1, pdb2, cycles=0
Hi Nidhi -
The “Align” feature in the GUI uses PyMOL's `align` command, which performs a
sequence alignment to use as the basis for structural alignment. It only uses
those residues which match exactly, which can throw off the RMSD. Try using
`super` or `cealign` instead, which are structural
angstrom
J
On Dec 12, 2013, at 3:41 AM, Ahmet yıldırım wrote:
> Dear users,
>
> What is the unit of RMSD in pymol? Nanometer or angstrom?
>
> PyMOL>align structure1 & n. ca, structure2 & n. ca
>
> --
> Ahmet Yıldırım
>
> -
Thanks for the clarification.
Osvaldo.
On Thu, Nov 28, 2013 at 2:11 PM, Tsjerk Wassenaar wrote:
> Hi Osvaldo,
>
> The problem can be understood from the description of 'super'.
>
> #-
> PyMOL>help super
>
> DESCRIPTION
>
> NOTE: This feature is experimental and unsu
Hi Osvaldo,
The problem can be understood from the description of 'super'.
#-
PyMOL>help super
DESCRIPTION
NOTE: This feature is experimental and unsupported.
"super" performs a residue-based pairwise alignment followed by a
structural superposition,
One should emphasize that this alignment is a *sequence* alignment in
case of the "align" command.
Cheers,
Thomas
On 11/30/2011 11:19 AM, Tsjerk Wassenaar wrote:
> Hi Martin,
>
> It does an alignment, finding matching pairs of atoms, removing
> outliers and calculating the RMSD over the remai
Hi Martin,
It does an alignment, finding matching pairs of atoms, removing
outliers and calculating the RMSD over the remaining matches.
Cheers,
Tsjerk
On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger wrote:
> How does PyMOL calculate the RMSD between two structures where the
> number of atoms
How does PyMOL calculate the RMSD between two structures where the
number of atoms is different?
Martin
Am 11.11.11 14:59, schrieb Thomas Holder:
> Hi Martin,
>
> is it the transform=0 argument what you are looking for?
>
> http://pymolwiki.org/index.php/Align#PYMOL_API
>
> x = cmd.align('fo
Hi Martin,
It should be RMSD indeed. Mind that the final RMSD from align is obtained
after optimizing the fit by leaving out outliers.
Cheers,
Tsjerk
On Nov 29, 2011 10:07 AM, "Martin Hediger" wrote:
Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin
Am 11.11.11 14:
Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin
Am 11.11.11 14:59, schrieb Thomas Holder:
> Hi Martin,
>
> is it the transform=0 argument what you are looking for?
>
> http://pymolwiki.org/index.php/Align#PYMOL_API
>
> x = cmd.align('foo', 'bar', transform=0)
> print '
Hi Martin,
is it the transform=0 argument what you are looking for?
http://pymolwiki.org/index.php/Align#PYMOL_API
x = cmd.align('foo', 'bar', transform=0)
print 'RMSD:', x[0]
About the "some kind of refinement": There are arguments "cutoff" and
"cycles" that control this behaviour.
Cheers,
Thank you all for your help. Looks like both ProFit and rms_cur will do
just what I needed.
Thanks!
Tom
--
Thomas D. Grant
Graduate Research Assistant
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203
On Fri, Jul 22, 2011 at 10:59 AM, Michael Lerner wrote:
>
PyMOL's rms_cur command will do what you want. E.g.
fetch 1rx1
fetch 1ra1
# reports "Executive: RMS = 34.329 (159 to 159 atoms)"
# because the structures still need to be translated and rotated
rms_cur (1rx1 and name CA), (1ra1 and name CA)
# reports "Executive: RMS =0.862 (159 to 159 atom
Tom-
Try ProFit
http://www.bioinf.org.uk/software/profit/
Jed
Thomas Grant wrote:
> Dear all,
>
> I'm attempting to align a series of structures using the CEAlign
> plug-in in PyMOL due to a lack of any detectable sequence homology.
> CEAlign does a good job of aligning and the fits are very
Hi Angelo,
instead of calculating RMSD you could monitor pairwise helix angles
over states. See attached script, it depends on the
http://www.pymolwiki.org/index.php/AngleBetweenHelices script.
Cheers,
Thomas
On Thu, Mar 10, 2011 at 12:05 AM, Angelo Rossi
wrote:
> Hello:
>
> I have a protein
rms and fit gave you different values? They have never given me different
values.
Example:
from pymol import cmd
cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j
rms_val = cmd.rms
Hi Renuka,
With a little bit of Python programming and better understanding of
structure alignment in PyMOL you should be able to complete your task.
First, check out the structure alignment category on the PyMOLWiki (
http://www.pymolwiki.org/index.php/Category:Structure_Alignment). Read the
dif
Jason,
When I use optAlign I get the same value as with ProFit (4.615214 A.),
that's why I suspected that 'align' omits some distant CA atoms when
calculating the RMSD. In fact I just noticed that the last 2 residues
are not assigned an asterisk or a dot in the alignment. So, when I
exclud
Thomas,
If PyMOL has paired two atoms for alignment, then they will be used in
the calculation of the RMSD.
Also, this sounds like you should be using 'fit' or 'optAlign' to be
superposing the molecules. (If you already know the atom pairings, no
'alignment' step is necessary.)
Possibly helpful
>Dear all,
>
>i have multiple conformations files (multi pdb) and would like to
>compute for each one, the rmsd for each snapshot against the first
>snapshot.
>Is it possible with pymol to do such a task ?
>
>thank you in advance for the gain of time ... :-)
>
>nicolas floquet
Yes, using a short P
Hi all,
I coded a little plugin that performs what Horacio asked for:
It takes 2 selections with the same number of residues
calculates RMSD for the backbone atoms and assigns each backbone atom's
b-factor the corresponding RMSD. (assigns 0.0 to non-backbone atoms)
(It only work for aminoacidic
Dear Horacio --
On 21 Sep 2008, at 18:38, Horacio Sánchez wrote:
Given two very similar pdb structures, do you know if it is
possible to
colour them in relationship with the RMSD between the 2 structures ?
I guess it might be possible to do it by using the same trick as for
the ConSurf rep
Siddharth,
align obj1CA, obj2CA, cycles=0
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of
siddha...@
Horacio,
PyMOL cannot currently superimpose small molecules unless:
1. either the identifiers match between the two molecules (fit commmand)
or
2. the pairwise correspondance between the two is explicitly specified
(pair_fit command or pair fitting wizard)
Cheers,
Warren
--
DeLano Scientific
Marcela,
Sorry, PyMOL can only compute rmsds on pairs of structures, not ensembles.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
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