Hi Monica,
A different option is they both bind but destabilize your protein (as you
suggested). This will likely not help much if you are trying to co-crystallize
them. But there are couple of examples out there in the literature that show
the contrary, despite destabilizing Tm they got struct
Hi Monica,
Your Tm results don't suggest any binding of your ligand to the protein. Your
ligand concentrations are quite high so I am not convinced of even weak
binding. The destabilization that you are seeing at the highest concentration
may be due to ligand precipitation causing protein denat
Hi Oarabile,
Coot allows you to align structures by selected atoms:
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/docs/coot-faq.html#How-do-I-do-a-superposition-on-just-a-part-of-my-structure_003f
I guess what you are trying to do can be accomplished by the “multi-range LSQ
superposition”
Dear Andrew,
Thank you very much for the detailed instructions. I am downloading it
Best Regards,
Oarabile M. Kgosisejo
o.kgosis...@usask.ca
From: Andrew Orry [a...@molsoft.com]
Sent: February 5, 2015 4:57 PM
To: Kgosisejo, Oarabile; CCP4BB@JISCMAIL.AC.UK
Subject
The free ICM-Browser from MolSoft can do this -
http://www.molsoft.com/icm_browser.html It will calculate the Ca-atom,
backbone and heavy atom differences between multiple structures and
superimpose.
To do this:
1. Download and install ICM-Browser here (Win, Mac or Linux)
http://www.molsoft.c
The program chimera will align homologous structures from which you can
generate a sequence alignment (based on the structural alignment)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
~JH
On 05.02.2015 14:41, Kgosisejo, Oarabile wrote:
Hi all,
Does anyo
Hi all,
Does anyone know of a program to use to superpose only selected protein
residues, e.g. enzyme active site residues. I solved my structure using
molecular replacement now I want to compare its active site to those of
homologous structures. I have used the DALI server before but I had to
Posted on behalf of the Organizing Committee: John Rose and Bi-Cheng Wang (University of Georgia, Athens, Georgia, U.S.A.) Manfred Weiss (Helmholtz-Zentrum Berlin für Materialien und Energie, Berlin, Germany) Christoph Mueller-Dieckmann (ESRF, Grenoble, France)2nd Announcement and New Additions to
Dear Jacob,
there was a nice small computation project by Anne Bochow published in the CCP4
Newsletters (2005),
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html, communication
9,
illustrating how strong and how confusing the ripples may be indeed; if you
want I may send it yo
> What about the bogey of Fourier truncation ripples--I have heard many have
> been fooled by the into thinking they were seeing orbitals. How does one
> tell the difference?
Indeed, there are such dangers. Hints are here:
On the possibility of observation of valence electron density for
individ
What about the bogey of Fourier truncation ripples--I have heard many have been
fooled by the into thinking they were seeing orbitals. How does one tell the
difference?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil
Jeffrey
Sent: Thurs
Mark,
In the small-molecule crystal structures I work with it's relatively
common to see localized difference electron density along covalent bonds
or in the places you'd expect to see lone pairs during refinement after
you've fit and modeled the atoms reasonably well and the phases are
prett
This may be useful reading on charge density crystallography:
http://journals.iucr.org/a/issues/1998/05/00/by0157/by0157.pdf
I like the phrase ‘gourmet crystallographers’
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark van
der Woerd
Sent: Thursday, Februa
Not very well. When you look in the originally quoted article, there is really
not much difference in the ED for H+ and H- (which are conveniently both shown
in Fig 2). You build a model that is consistent with 'book knowledge' (i.e.
normal hydrogen has only one bond) and take it from there.
Y
Hi Peter,
Try to think of it as a quantum chemist:
What you call H+ is not "H+ floating in space". They are hydrogens bound to the
rest of the structure by means of electrons. These electrons can be described
by wave functions, which relate to probabilities where they (electrons) might
be.
If
Hi Almudena,
Have a look in your PDB file in the second to last colum, if it looks something
like the example below then delete the As from the fine and it should connect
up. I've had this before, not sure where it came from but removing it fixed the
problem.
ATOM371 CA PRO A 48 -11
Did you try ShelxE autotrace? At that resolution it should work nicely, or at
least be able to distinguish between the two sequences.
D
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller,
Jacob
Sent: 05 February 2015 15:49
To: ccp4bb
Subject:
Sorry--should have included a bit more info:
A huge caveat: data is tetartohedrally twinned, which makes everything an
issue. But, I have managed to get Rfree down to ~32% in refmac with
intensity-based twin refinement. I know--R's with de-twinning are illusory, but
I still think it's solved, s
Hi Jacob,
I would superpose domain B onto each domain A in turn, and run
refinement in Phaser. If the LLG goes up, exchange that domain A for a
domain B, otherwise keep. This requires 14 refinement calculations.
This procedure may not give you what you are hoping for if your models
are dista
Dear Jacob,
Are you sure your MR solution is correct? What is your resolution?
Best,
D
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller,
Jacob
Sent: 05 February 2015 15:21
To: ccp4bb
Subject: [ccp4bb] Resolve Domain Sequence Ambiguities
H
Hi All,
I have 14 identical domains placed in my ASU with reasonable MR scores, but the
problem is that there should really be 7+7 or 8+8 of domains A and B (which are
structurally similar). Can anyone think of a great and easy way of resolving
the ambiguity?
I was thinking potentially:
-chan
Hi all,
I am working to crystallize a protein-ligand complex. I did a preliminary
melting curve analysis for the protein in the absence and presence of 2
ligands (dissolved in protein buffer). I kept the other controls as buffer
an a known standard to confirm instrument performance. All expts done
Hi, Bernhard,
ok, sure, you are right ! Nevertheless, I would not be so desperate and
categorical: you are right , at my knowledge also, there is currently NO known
algorithm to take into account the "flat mask bulk solvent contribution" at the
rotation step (maybe I am wrong?), however this do
Please see the recent job advert for a position with AstraZeneca in Cambridge.
http://jobs.astrazeneca.com/jobs/details/l1rRD1248-senior-scientist-crystallography
Chris Phillips
Associate Director, Protein Structure, UK
__
Dear all,
I do apologize for the slightly off-topic subject but, how could you
calculate ccp4 absolute-scale and noise maps in ccp4?. Basically I need e/A3
and noise maps to discard that some maps contoured at certain sigmas are not
just noise. I do know END/RAPID, but I have some proble
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