I agree with Petr. For a rigid body displacement the RMSD is not much use as a
descriptor. Such
a displacement can be described by a translation along and rotation around a
direction, or
rotation-translation matrices. These will allow someone else to reproduce the
displacement,
but the RMSD wi
Sorry to come late to this discussion-
I think the actin and tubulin people already reverted "polymer"
to its etymological use- google "actin polymerization"
Another example of infinite polymers formed by domain swapping
(and the surprises you can get trying to engineer a molecular switch):
http
Thank you for your reply,
I am running Malphare through CCP4 GUI interface. I am giving mtz file and
Se.pdb file as input and running it. I do not know running Malphare through
script. Please help me with heavy atom refinement in Malphare.
On 20 June 2012 03:49, Pete Meyer wrote:
> It's not cle
Because sometimes it is important to know how much the structure moved
relative to the unit cell, such as before and after a round of
refinement.
-James Holton
MAD Scientist
On Tue, Jun 19, 2012 at 3:34 PM, Petr Leiman wrote:
> Would anyone be kind enough to explain what kind of information does
I am not sure I understood what you are asking. But let me explain my question
a little further.
If two structures are not identical, then the RMSD is a good enough parameter
to describe the superposition: this many atoms were used in the superposition
and they can be moved in such a way that t
Is part of your question based there being many ways to superimpose
structures, which there are?
JPK
On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman wrote:
> Would anyone be kind enough to explain what kind of information does the
> "RMSD" for two not-yet-superimposed structures transmit?
>
> If tw
Would anyone be kind enough to explain what kind of information does the "RMSD"
for two not-yet-superimposed structures transmit?
If two structures are indeed identical but are apart spatially, then it is more
appropriate to calculate the COM and the inertia tensor for both structures and
repor
Hi Herb,
yes, I know one:
phenix.pdb_interpretation model.pdb write_geo_files=true
Optionally you can give it ligand's cif files too:
phenix.pdb_interpretation model.pdb ligands.cif write_geo_files=true
Pavel
On Tue, Jun 19, 2012 at 11:11 AM, Axelrod, Herbert L. <
haxel...@slac.stanford.edu>
I echo with Nat and support depositing both structures. Despite the fact that
the 38 residues are disordered, these are 2 different proteins (chemically).
The disordered residues may not lead to a better model, but they do carry
information. They are there and still take up physical space, thus
Hi,
if I remember correctly Molprobity computes all that angles and put them in a
table for comparison to the ideal values.
Best Regards
Christian
Am Dienstag 19 Juni 2012 20:11:18 schrieben Sie:
> Hi,
> Does anyone know of a program that computes _all_ dihedral (phi/psi/chi)
> angles from crys
Hi,
Does anyone know of a program that computes _all_ dihedral (phi/psi/chi)
angles from crystal structures. That is, including angles from alternate
conformations?
Many Thanks,
Herb Axelrod
Staff Scientist
Stanford Synchrotron Radiation Lightsource
I have a jiffy script for just that here:
http://bl831.als.lbl.gov/~jamesh/pickup/rmsd
you run it like this:
./rmsd model1.pdb model2.pdb
output looks like this:
1156 atom pairs found
RMSD(CA )= 0.516368 (129 CA pairs)
RMSD(all)= 0.506422 (1156 atom pairs)
RMSD(Bfac)= 0.489973
MAXD(all)= 1.232
Hi,
Try modeling a zinc close to the histidine and then do one round of
refinement the density will improve close to that area, generally a zinc
ion coordinated to histidine also has a water molecule close to the zinc.
HTH,
Shya
On Tue, Jun 19, 2012 at 5:47 AM, Lianying Jiao wrote:
> Dear all,
>
Dear CCP4 user,
I am facing problem in running Mlphare
for *HEAVY
ATOM REFINEMENT and PHASE CALCULATO. It is running successfully but in
output log file i am not getting any FOM for acentric. Log file output of
one of the cycle is
** * *** Finished refinement cycl
On Tue, 2012-06-19 at 11:07 -0500, Jacob Keller wrote:
> What extra insight does the full-length protein give, i.e., why not
> just chuck it?
>
It proves that the N-terminus does not have a strong influence on the
rest of the structure. Other words, it's OK to draw conclusions about
the full-len
Hi everyone,
I have several protein-ligand crystal structures of different ligands bound to
a combination of mutants of the same enzyme.
I wanted to look at the energetics of these complexes based on the crystal
structures.
Is there a program or suite of programs that could calculate DeltaG of co
Hi,
Is there such a database that will allow me to search for particular structural
motifs involved in protein interactions. For example: search for any complex
in the PDB wherein interactions between the 2 proteins are at least partly
mediated by a 3(10) helix.
thanks,
Alan
On Tue, Jun 19, 2012 at 8:35 AM, RHYS GRINTER
wrote:
> There's no significant difference between the high res and low res proteins
> in the shared region (amino acid 38+) (r.m.s.d 0.46 A), and the while there
> is broken density for the first 38aa from the full length data it's too poor
> to mo
What extra insight does the full-length protein give, i.e., why not
just chuck it?
JPK
On Tue, Jun 19, 2012 at 10:35 AM, RHYS GRINTER
wrote:
> Dear All,
>
> I'm working out the finer details on a structural paper for submission to
> JBC. I'm having a slight problem with how to present my data.
This is a second announcement of a hands-on workshop on "Lipidic Cubic Phase
(LCP) Tools & Technologies" that will take place on the MIT campus in Boston on
August 2nd 2012 following the ACA 2012 Annual Meeting. Due to several
cancellations there is a limited number of spots became available on
On Tue, 2012-06-19 at 17:31 +0200, Robbie Joosten wrote:
> What if the displacement is a translation and a rotation?
Excellent point. A slight modification of this
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Print_the_shifts_in_individual_atom_positions
will do as follows
grep
Dear All,
I'm working out the finer details on a structural paper for submission to JBC.
I'm having a slight problem with how to present my data. I've got a high
resolution (1.46 A) truncated structure of the protein with the N-terminal 38aa
removed. I've also got data from lower resolution (2.
a Baltimorease flood of emails :-)
Hi from "across the street"
Jürgen
On Jun 19, 2012, at 11:25 AM, Ed Pozharski wrote:
just do this one-liner (assuming that your numbering is not messed up
and you have "the first atom")
grep 'ATOM 1' model1.pdb model2.pdb | cut -d: -f 2 | cut -c 31-54 |
a
just do this one-liner (assuming that your numbering is not messed up
and you have "the first atom")
grep 'ATOM 1' model1.pdb model2.pdb | cut -d: -f 2 | cut -c 31-54 |
awk '{printf "%s ",$0;}' | awk '{print sqrt(($1-$4)^2+($2-$5)^2
+($3-$6)^2);}'
On Tue, 2012-06-19 at 15:04 +, Claudia M
USF has something but beware it's not a GUI :-)
Moleman2
Jürgen
On Jun 19, 2012, at 11:04 AM, Claudia Millán Nebot wrote:
Hello everyone :)
I would like to know if it exist some tool that allows to calculate RMSD
between 2 pdbs that are identic, but just displaced in space. It should not
make
Hello everyone :)
I would like to know if it exist some tool that allows to calculate RMSD
between 2 pdbs that are identic, but just displaced in space. It should not
make a superposition, beause if this is the case it will just say that RMSD
is 0 .
I know is not such a difficult problem in terms
On Tue, 2012-06-19 at 16:43 +0800, LISA wrote:
> Hi all,
>
> does anyone solve their structure by molecular replacement with
> phaser with LLG < 0?
> Thanks
>
> lisa
AFAIU, this means that your estimate of the solvent content is too low.
If you increase that, eventually you should get positive
Check anomalous map. Likely a Zn
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1
Hi,
Without looking at your model/maps it is difficult to make a really educated
guess.
By looking at the single screen shot you attach, I would say it could be a
couple of different things, in order of likelihood based on a single screenshot
(at whatever level of confidence this assures):
1-Zn
Dear Lisa,
It is actually reasonably common that a clear solution (large TFZ) is found in
Phaser with a negative LLG. The negative LLG tells you that the model doesn't
agree with the data as well as one would expect, given what you have told
Phaser about the completeness of the model and its a
Hi all,
does anyone solve their structure by molecular replacement with phaser
with LLG < 0?
Thanks
lisa
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