Superb. Let me know how it goes.
On Sun, Mar 21, 2010 at 5:40 AM, Kersten Schroeder wrote:
> Bob,
>
>
> Thank you. I think that I will use both the atom-based
> coordinate-coordinate least-squares optimization (as in PyMol) and
> quaternion-based orientation-orientation least-squares optimizatio
Bob,
Thank you. I think that I will use both the atom-based coordinate-coordinate
least-squares optimization (as in PyMol) and quaternion-based
orientation-orientation least-squares optimization (your innovation) in our
website. Then, people could decide for themselves which fit they like. For
Kersten,
The COMPARE command is illustrated at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=103
I've used your Kt38/Kt7 comparison as an example. Hope you like it! The
example illustrates both atom-based coordinate-coordinate least-squares
optimization (as in PyMol) and quaterni
Excellent questions. Just the normal learning curve, I think. That's what
this list is for. Keep asking. I want this to work flawlessly for you.
I've just uploaded new files to
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
answers below...
On Thu, Mar 18, 2010 at 11:48 AM, Kersten
Bob,
I tried the new COMPARE script and it worked alot better for me than the
previous ALIGN script. I used this command the following command:
compare {2.1} {1.1} ATOMS {77-82 and a} {41-46 and a} {92-100 and a}
{27-35 and a} ROTATE TRANSLATE
I tried with a few other molecules and it gave me re
OK! We're in. So, that wasn't so bad -- just needed to add a bit of code
that set up an eigenvalue problem.
Jmol 11.9.34 does the equivalent of PyMol's "pair_fit" (without the
capability to determine atom-atom matchings a priori or to throw out poor
matches).
The COMPARE command does atom-based o
Let's go with COMPARE instead of ALIGN. That way we can have all sorts of
flexibility, anywhere from just reporting orientational or coordinate
superposition RMSD, doing just the rotation, doing just the translation,
etc.
Bob
On Mon, Mar 15, 2010 at 2:58 PM, Robert Hanson wrote:
> essentially.
essentially. Any situation where you can describe orientations.
Carbohydrates, for example, could be quite amenable.
On Mon, Mar 15, 2010 at 2:42 PM, wrote:
> On Mon, 15 Mar 2010 14:33:08 -0500, Robert Hanson
> wrote:
> > "Spacial" doesn't really describe it.
> >
> > The method goes like this:
On Mon, 15 Mar 2010 14:33:08 -0500, Robert Hanson
wrote:
> "Spacial" doesn't really describe it.
>
> The method goes like this:
>
> --Identify pairs of matched residues (as opposed to atoms).
>
So not of general use but limited to the special cases of nucleic acids
and proteins.
Rich
---
"Spacial" doesn't really describe it.
The method goes like this:
--Identify pairs of matched residues (as opposed to atoms).
--At each residue identify a characteristic reference frame. That's
effectively an xyz axis "frame" that can be compared between the structures.
For example, we have three
On Mon, 15 Mar 2010 13:48:19 -0500, Robert Hanson
wrote:
[snip]
>
> Be that as it may, I'm also quite happy to change the name to anything
> reasonable. Since it's not just doing (at this point) a standard
> matrix-based RMSD minimization operation (which is what you want to call
a
> superpositi
OK, so there are two things -- sequence alignment (which obviously this is
not) and then structural superposition based on some sort of selected
criteria. I'm having a bit of trouble seeing why that second stage is not
the "structural alignment" part -- you're sure of that? What other functions
are
On Mon, 15 Mar 2010 11:29:40 -0500, Robert Hanson
[snip]
>
> The operation Jmol is performing is definitely an alignment of sorts; I
can
> certainly be careful not to claim it is "structural" alignment if that
term
> is now synonymous with something more involved.
"of sorts"
It really is a su
If I am right, the Pymol align command does a sequence alignment followed by
a superposition of atoms.
http://www.pymolwiki.org/index.php/Align
I am not a big friend of naming discussions, just trying to help avoid
future questions ... ;-)
Andreas
On Mon, Mar 15, 2010 at 9:29 AM, Robert Hanson
Andreas,
Possibly. PyMol calls it structural alignment and uses the same command
name.
http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/
While I haven't implement that standard technique of minimization of
coordinate RMSD, the "align" command is set up to that if pe
Could you give the new command a different name? ALIGN is misleading since
you are not doing an alignment, but just a superposition.
http://en.wikipedia.org/wiki/Structural_alignment
Thanks,
Andreas
On Mon, Mar 15, 2010 at 6:05 AM, Robert Hanson wrote:
> Kersten,
>
> I have had some success in
Bob,
Thank you for setting up an alignment feature for Jmol. The preliminary
alignment looks good. I need to try it with some other RNA structures
that are a little more complicated to see if it continues to give good
results. I hope to have time by Wednesday to try it. To answer your
questions:
Kersten,
I have had some success in aligning your RNA fragments. Please get back to
me.
Jmol 11.9.34 will align proteins, RNA, and DNA based on quaternion frames
using a new ALIGN command.
See files in
http://chemapps.stolaf.edu/jmol/docs/examples-11/align
for examples.
This is a little diffe
I think I can do it with quaternions in about two lines of Jmol script. Is
there a good reference for Singular Value Decomposition?
Bob
On Wed, Mar 10, 2010 at 2:54 PM, Andreas Prlic wrote:
> For this you just need e.g. a Singular Value Decomposition ...
>
> Andreas
>
>
> On Wed, Mar 10, 2010
Bob,
Yes, I was thinking of something more simplistic. Pair_Fit in PyMol fits a set
of atom pairs between two models. I am aware that people use Xplor-NIH as well
to align models that contain nucleic acids. I am not sure if Xplor-NIH or
Pair_fit in Pymol is a better starting point.
I will be w
For this you just need e.g. a Singular Value Decomposition ...
Andreas
On Wed, Mar 10, 2010 at 11:57 AM, Robert Hanson wrote:
> I think what I'm thinking of is considerably more simplistic and less
> general -- just the ability to specify two sets of atoms and have Jmol align
> one set to the
I think what I'm thinking of is considerably more simplistic and less
general -- just the ability to specify two sets of atoms and have Jmol align
one set to the other via an optimized rotation and translation.
That's what you are interested in, right Kersten?
Bob
On Wed, Mar 10, 2010 at 12:47 P
no, protein only...
On Wed, Mar 10, 2010 at 10:43 AM, Robert Hanson wrote:
> Ah, that's useful information, Andreas. Does it also work with nucleic
> acids?
>
> On Wed, Mar 10, 2010 at 12:11 PM, Andreas Prlic wrote:
>
>> Hi,
>>
>> We are using Jmol to visualize protein structure alignments as p
Ah, that's useful information, Andreas. Does it also work with nucleic
acids?
On Wed, Mar 10, 2010 at 12:11 PM, Andreas Prlic wrote:
> Hi,
>
> We are using Jmol to visualize protein structure alignments as part of the
> RCSB PDB Protein Comparison Tool.
> http://www.rcsb.org/pdb/workbench/workbe
Hi,
We are using Jmol to visualize protein structure alignments as part of the
RCSB PDB Protein Comparison Tool.
http://www.rcsb.org/pdb/workbench/workbench.do
It contains the Combinatorial Extension (CE) algorithm (among others), which
is a frequently used algorithm for protein structure alignme
Kersten,
Let's talk more about this, can we? I've been thinking, and I suggest that
we might have the basis in Jmol for a very good and very simple model-model
alignment tool. It will take some experimentation, but if you would be
interested in working with me on it, we might have something VERY
i
A suggestion:
If that is all you have, I would suggest pre-aligning. It's easy enough with
those other programs --- just get the offsets necessary and then apply them
in Jmol using
translate {some atom list} {x.xxx y.yyy z.zzz}
if you don't want to create all new model files.
On Mon, Mar 8,
Dear Robert,
I really enjoy Jmol and am currently using it on a website I help create for
the kink-turn RNA motif
(http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_all.php).
Do you plan to develop a way to align model 1 onto model 2 in Jmol script?
Pairfit in PyMol does it, so there may be
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