Hi Ecem -
If I understand correctly, you first want to align on one set of residues
and calculate their RMSD, then to calculate the RMSD for the remaining
residues without moving the structures. This is straightforward using
PyMOL's internal command line.
```
# Create two selections called "sel1
Dear Pymol community,
I have a question about alignment module of Pymol. I have two different pdb
ids and each have about 100 amino acid long. I would like to align the
specific parts of these proteins and see both how the rest of the proteins
and also these specific parts superimpose with each ot
Hi Abhik,
Try this (with PyMOL 2.1 or newer):
load avg.pdb
loadall frame*.pdb
extra_fit (frame*) & guide, avg
multifilesave {name}-aligned.pdb, frame*
https://pymolwiki.org/index.php/load
https://pymolwiki.org/index.php/loadall
https://pymolwiki.org/index.php/extra_fit
https://pymolwiki.org/inde
Original Message
Subject: alignment of frame
From:abhik.gh...@bose.res.in
Date:Thu, August 9, 2018 3:02 pm
To: pymol-users@lists.sourceforge.net
--
Hello a
Hello all
I want to align each frame pdb w.r.t a specific frame pdb. Let assume i
have 10 pdb files.I have another file "avg.pdb". I want to align each pdb
w.r.t "avg.pdb" file. I can do it manually using align command i.e align
1, avg. But is there any code or anything by which i can produce align
question.
You might be looking for this:
http://pymolwiki.org/index.php/Align
Cheers,
Thomas
On 24 Aug 2016, at 09:10, Clarisa Alvarez wrote:
> Hello!
> could someone help me to download a pymol alignment? and know with which
> score it makes the alignment.
> Thanks in advance
Hello!
could someone help me to download a pymol alignment? and know with which
score it makes the alignment.
Thanks in advance.
Clarisa.
--
___
PyMOL-users mailing list (PyMOL
Hello!
could someone help me to download a pymol alignment? and know with which
score it makes the alignment.
Thanks in advance.
Clarisa.
--
___
PyMOL-users mailing list (PyMOL
Hi Amin,
It worked. Many Thanks
Cheers
Mohsen
From: a...@imtech.res.in [mailto:a...@imtech.res.in]
Sent: Thursday, 25 February 2016 10:24 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Alignment of two proteins
Hi. I think
align 4mt1 & chain A, 3aob & chain B
sho
Hi. I think
align 4mt1 & chain A, 3aob & chain B
should work.
Amin.
On 2016-02-25 17:02, Mohsen Chitsaz wrote:
> Hi Julian,
>
> I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A
> of 4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or
>
Hi Julian,
I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of
4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of
a protein, in my case chain A of 4mt1, to a specific chain or part of another
protein, in my case chain B of 3aob?
Cheers
Mo
Mike Marchywka wrote:
>
> > From: ccp4...@hotmail.com
> > To: pymol-users@lists.sourceforge.net
> > Date: Fri, 8 Nov 2013 19:53:50 -0600
> > Subject: [PyMOL] alignment of metal coordination
> >
> > Hi,
> >
> > Is it possib
> From: ccp4...@hotmail.com
> To: pymol-users@lists.sourceforge.net
> Date: Fri, 8 Nov 2013 19:53:50 -0600
> Subject: [PyMOL] alignment of metal coordination
>
> Hi,
>
> Is it possible to align two structure based on metal
Hi,
Is it possible to align two structure based on metal coordination or
metal-coordinating residues? What is good way to do it?I appreciate your
guidance.
ThanksSDY
--
November W
Hi Sasi,
for "pair_fit" you have to match all atom pairs manually. I guess what
you want is "align" on the full monomers and then "rms_cur" (or just
distance measure) on each CA pair.
Have a look at the "rmsd_b.py" script from
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
It writes per
dear pymol users,
i have a homodimer, with two identical monomers. i would like to know the
rmsd of each residue in the first monomer with respect to each residue in
the second monomer.
i guess pair_fit should give the rmsd.
is there a better command to look at the per residue rmsd.
thank you.
> Dear Jason,
>
> ""super" does pairwise residue alignments followed by a superposition.
> It also does refinements to improve the overall quality."
>
> Could you elaborate a little more on this? Do you mean that it
> calculates all pairwise distances and does a least squares fit with
> refinement
Hi Mike,
PyMOL has quite a few structure alignment and structure fitting
options. If you want CE, check out CEalign on the PyMOLWiki
(http://www.pymolwiki.org/index.php/Cealign). It's a script for
PyMOL. I might build it into newer releases of PyMOL, if anyone's
interested (let me know).
"alig
Dear PyMOL users,
I have browsed the wiki and the first 300 mailing list messages in the
archive (the sourceforge archive does not seem to have a search set up
for the archive... arg!), but did not find any details about the
algorithms behind 'fit' and 'super.' I understand how align works,
and i
On Fri, Sep 11, 2009 at 1:59 PM, Maia Cherney wrote:
> Is it posible in pymol to select all residues of a certain type
> automatically, like all arginines or all lysines + arginines in a chain?
select resnam arg
select chain A and (resnam lys or resnam arg)
-
Maia,
select all_arg_lys, resn arn+lys
Cheers,
Warren
> -Original Message-
> From: Maia Cherney [mailto:ch...@ualberta.ca]
> Sent: Friday, September 11, 2009 2:03 PM
> To: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Alignment Objects
>
> Hi,
> I
Hi,
Is it posible in pymol to select all residues of a certain type
automatically, like all arginines or all lysines + arginines in a chain?
Maia
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30
Hi David
On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall
wrote:
> Is there any documentation on getting information out of alignment objects
> into scripts? I tried looking around the wiki, but I didn't see anything.
>
> I'm just wondering things like if I have a residue in one object, find
Is there any documentation on getting information out of alignment objects into
scripts? I tried looking around the wiki, but I didn't see anything.
I'm just wondering things like if I have a residue in one object, finding the
residue in another object that has been aligned.
Thanks,
David
Hi All,
I'm having some trouble fitting to sets of residues in Pymol (1.2r0 -
installed with Fink on MacOSX 10.5.8). I'm also having almost
identical trouble using MacPymol as well (the version based on Pymol
1.1).
I'm trying to align 2 sets of 4 cysteine residues. I have tried align,
sup
set line_color, white, ligs3d, 1
set line_color, red, ligs3d, 2
Cheers,
Warren
From: Young-Tae Lee [mailto:yt...@scripps.edu]
Sent: Tue 4/14/2009 10:21 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Alignment of states
Well, this was easily figured
Well, this was easily figured out by just aligning all intermediate
states onto the very initial structure.
By the way, can I select specific states to change their color?
Thanks,
Young-Tae
On Apr 13, 2009, at 6:41 PM, Young-Tae Lee wrote:
Dear all,
I am working on making a movie showing p
Dear all,
I am working on making a movie showing protein movements, for example
from A -> B -> C -> D. I obtained calculated intermediate states
between A-B, B-C, C-D from the morph server at Yale. Unfortunately,
the last coordinate from one morphing step and the first coordinate
from the
0)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Douglas Kojetin
> Sent: Thursday, March 02,
Hi All-
If I have a protein with 150 residues (three 50 residue repeats;
1-50, 51-100, 101-150), and I want to align the first 100 residues
(resi 1-100) to the last 100 (51-150) ... and try to run the
following commands:
load structure.pdb
create s1, resi 1-100 and structure
create s2, re
:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Marc Bruning
> Sent: Tuesday, September 20, 2005 6:42 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] alignment question
>
> hello,
>
> is there any possibility to get a list of the pairs of atoms
> that are ma
hello,
is there any possibility to get a list of the pairs of atoms that are matched
using the align command?
cheers,
marc
r...
Cheers,
Warren
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Andreas Henschel
> Sent: Friday, January 28, 2005 9:18 AM
> To: pymol-users@lists.sourceforge.net
> Subject:
Dear PyMOL community,
I am trying to use the align command (from within python)
and want to evaluate the pairwise matches.
the command
cmd.align(sel1, sel2, object="alignment")
should do. Sorry for this stupid question,
but how do I get hold of the "alignment" object, and what is its
function
>1. Alignment and Translations/Rotations (Joshua L. Adelman)
> rotation of the protein). Ideally what I want to do is do a single
> alignment of the last frame of the first sequence with the first frame
> of the second sequence (they should be nearly identical structures)
> and
> then get the
I am trying to string together several sequences of PDB files outputted
from the Yale Morph Server in order to make a movie. Basically there
are 3 groups of trajectories and I want to make a continuous movie. The
problem is that the Morph Server rotated one set of structures relative
to the oth
Hey all, and especially Warren,
I've been playing around with alignment recently and was wondering what
exactly is going on when I run the command 'align'. As I understand it,
a combination of sequence and structural alignment is performed. Here
is my output from a recent alignment:
Match: rea
37 matches
Mail list logo
