Dear All,
I have multiple aligned PDB files loaded in PyMOL, each representing
different conformations of the same protein. I'm interested in
creating a graph displaying RMSD per residue, similar to those shown
at
https://www.ks.uiuc.edu/Training/Tutorials/science/aars/aars_html.bak/node22.html
I have been using VMD for most of my MD analysis, but I am trying to learn
PyMol now. I know how to load a pdb and a dcd onto that pdb. But how do I
measure the RMSD of each frame in the DCD aligned to the starting structure,
and then output a graph like of RMSD vs frame? Doing this through
Hello PyMOL users,
I was wondering does PyMol have a RMSD based clustering tool.
Many thanks,
Neena
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Dear All,
I am relative new with PyMol and I am having trouble finding my way around. I
wish to perform a rmsd for each atom from
1) a boundle of 20 conformers
2) two different align structures, in PyMol such that the results of each atom
pair can be displayed or plotted as a function of the
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
Hi!
I have a group of structures (168 in total) and I want to align all of them
to the first one in order to know the RMSD calculation. For that purpose I
use the following:
f=open('rmsd.txt','w')
rms2=cmd.align('structure_0002 and name ca','structure_0001 and name ca')
.
. (NOTE: I got all of
Hi,
I was comparing two very similar structures and I got the following results:
align pdb1, pdb2, cycles=0
0.38
align pdb1, pdb2 and name ca, cycles=0
0.05
align pdb1, pdb2 and name ca+cb+c+n, cycles=0
0.07
align pdb1, pdb2 and name ca+cb+c+n+o, cycles=0
9.8
I wonder why the addition of
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 patrick.coss...@inbox.com wrote:
Hi,
I was comparing two very similar structures and I got the following results:
align
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
On 20 Oct 2014, at 11:16, Cedric patrick.coss...@inbox.com wrote:
Hi,
I
...@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
On 20 Oct 2014, at 11:16, Cedric patrick.coss...@inbox.com wrote:
Hi,
I was comparing two very similar structures
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
Dear Sir/Madam
I have generated five models for a protein and I wanted to check the RMSD
of only the binding site residues. I have the list of binding site
residues. I tried using this through graphics by selecting the residues and
then aligning by selection but somehow its giving me a higher
Dear users,
What is the unit of RMSD in pymol? Nanometer or angstrom?
PyMOLalign structure1 n. ca, structure2 n. ca
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Ahmet Yıldırım
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Rapidly troubleshoot problems before they affect your business. Most IT
Hi,
I am trying to use the comand cmd.super() to calculate the rmsd between the
sidechains of two proteins using
cmd.super('%s and not name ca+c+o+n' % obj0, '%s and not name ca+c+o+n' %
obj1)
And I get this error
ExecutiveAlign: invalid selections for alignment.
It seems to me that the
Hi Osvaldo,
The problem can be understood from the description of 'super'.
#-
PyMOLhelp super
DESCRIPTION
NOTE: This feature is experimental and unsupported.
super performs a residue-based pairwise alignment followed by a
structural superposition,
Thanks for the clarification.
Osvaldo.
On Thu, Nov 28, 2013 at 2:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Osvaldo,
The problem can be understood from the description of 'super'.
#-
PyMOLhelp super
DESCRIPTION
NOTE: This feature is experimental
Dear PyMol users!
I'm looking for python script which would perform the
1- loading ensemble of the pdbs to the pymol (assuming that it could be
done by loadDir script)
2- Perform structural alighnemnt of all loaded structures against reference
0.pdb by means of buit-in TMalighn module
this
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 remaining
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 'RMSD:',
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 ma@bluewin.ch wrote:
Is the RMS the same as RMSD? PyMOL writes RMS when using align.
Martin
Dear List.
When aligning two structures using the PyMOL align command, one gets a
final RMS value indicating some kind of convergence i would say. Can I
somehow access the function for calculating this value directly from the
pymol prompt without aligning?
Thanks for hints
Martin
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,
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 reasonable. However, the RMSD
that is calculated is based only on the c-alphas that were
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
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 atoms)
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
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
angelo.raymond.ro...@gmail.com wrote:
Hello:
I have a protein with several helices and believe only one of them (the one
closest to that active center) moves significantly during a simulation.
Can someone suggest a way to use pymol to highlight the movement of the
helices in this protein. I want to select 20 structures from a
Hi All Pymol users
I have a set of 40 X-ray
crystallographic structures complexed with inhibitors belonging to a
specific family of kinases. Binding site residues within 5 angstrom
from the inhibitor were selected for each PDB
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
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 =
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
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
Dear pymol users,
I'm trying to understand how align command measures the RMSD between 2
homologues and explain the discrepancy between that value and the one
obtained from ProFit. The sequence alignments produced by both
programs are continuous and match, but the RMS values are 1.781 and
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 Python
Hello,
I am using PyMOL 1.1beta4 Education Edition to calculate the RMSD among
each individual sidechain in two structures. The two structures have
the same number of residues and types, and are just two forms of the
protein. When I use 'align':
PyMOLalign protein1, protein2
it does move
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
Hi,
I think Leo's is the right way. In a little variant, you could change the
b-factor value directly from pymol, instead of manipulating PDB. It should not
be difficult prepare an script that ask for two selections (already
superimposed and with the same number of residues) get the RMSDs and
Hi,
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
mean that for instance the backbone is practically the same in both
proteines, so it gets some same color in both, but for some chains which
are
...@iitg.ernet.in
Sent: Wednesday, June 04, 2008 3:15 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RMSD Calculations
Hi everyone,
I needed to know how to calculate the RMSD for 2 homologous structures over
the entire structure (For C-alpha atoms). Currently, PyMol performs sequence
Hi everyone,
I needed to know how to calculate the RMSD for 2 homologous structures
over the entire structure (For C-alpha atoms). Currently, PyMol performs
sequence alignment and then gives the RMSD values for only those regions
which are matching. But, as I mentioned before, I need RMSD values
Hi,
I need to calculate the RMSD between two ligands (around 50 atoms). For
proteins works very well but it seems that for small molecules it gives
errors. I looked through the forum and I did not find any useful info. I
tried rms , rms_cur and so between the atoms selections but I get errors
@lists.sourceforge.net
Subject: [PyMOL] RMSD between two ligands
Hi,
I need to calculate the RMSD between two ligands (around 50
atoms). For proteins works very well but it seems that for
small molecules it gives errors. I looked through the forum
and I did not find any useful info. I tried
Hello everybody!
I would like to calculate the backbone atoms rmsd of homologous structures
(more than two structures at the time), selecting for each one the structured
region.
Command as fit, rms, pair_fit do it only for pair of structures. Does Pymol has
the possibility to do rmksd
, or employer.
Thank you for participating!
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Marcela
NUNEZ
Sent: Wednesday, January 03, 2007 6:46 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] rmsd calculation
Hi frnds
Can any one please tell me the commands for
calculating the atom by atom RMSD of two pdb
structures in Pymol? Both the structure has same no.
of residues.
chiradip
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