Dear John
you can try Promal3D..it will work hopefully..
bye and take care
On Sat, Apr 27, 2013 at 6:27 AM, Mike John wrote:
> Hello, Every one,
>
> I am preparing a ppt presentation in an emergency style. What I want is a
> graph of sequence alignment with secondary structure on the top. Usin
Respected Mam,
I used Cadmium at home source 1.54179Ang. For detecting the
anomalous peaks CAD and FFT was used. It has Se also. So while
refining the occupancies of Cd, Se, S and P are also refined.
Thanking you
Respectfully
Kavya
> Not sure I follow you completely.. You dont say what anom sca
Hello, Every one,
I am preparing a ppt presentation in an emergency style. What I want is a graph
of sequence alignment with secondary structure on the top. Using STRAP i can
got alignment nicely, but did not know the tips to add secondary structure on
top.
Anybody of experienced can give me a
Hi Patrick,
Did you try using a different refinement program (e.g. Refmac)? Which type
of NCS restraints did you use, global or local (torsion- or distance-based)?
Have you tried optimizing your restraint weights? Have you tried running a
huge number of refinement cycles? You can also try running
Hi Pat,
On top of Phil's suggestion for invoking TLS, what about the NCS? Is there
anything peculiar about them (tNCS or the like)? If there isn't, are you
imposing NCS during refinement? perhaps you should relax the NCS restraints or
not impose any at all and see what happens then?
My 2p thou
Responding to a couple of questions from Ethan, Charlie, and Phil:
Ethan: Using the default bulk solvent modeling in Phenix; no selenium, but I'll
double-check wavelengths as a sanity check for scattering factors (but several
other native data sets from the same synchrotron trip refined beautifu
Pat,
Try TLS - I usually don't invoke it at this type of resolution but in
one case I saw it make a surprisingly significant improvement.
I would also be tempted to put the structures through Arp/wArp and see
if it lowers the R-free any more - rightly or wrongly I view this as the
lowest rea
Hi all,
Here is a problem that's been annoying me, and demanding levels of thought all
out of proportion with the importance of the project:
I have two related crystal forms of the same small protein. In both cases, the
data look quite decent, and extend beyond 2 A, but the refinement stalls wi
Hi All:
I wish to identify and remove unstructured regions at the C-terminus of my
protein for crystallization and am considering using carboxypeptidase
digestions to achieve this.
1) I would like a protocol and your preferred source of commercial
carboxypeptidases as well their storage co
A postdoctoral position is available starting immediately to continue the
structural work on adenovirus capsids and associated proteins (Reddy et al.,
Crystal structure of human adenovirus at 3.5Å resolution. Science.
2010;329(5995):1071-5) at The Scripps Research Institute, La Jolla, California
Dear all, those of you working in the membrane protein and/or carbohydrate
field may be very interested in attending a 1 day workshop which will highlight
the unique capabilities of the CD beamline B23, at Diamond. The workshop is
focused on how the technique can aid your research in these key
Not sure I follow you completely.. You dont say what anom scatterer you
expect, or what the wavelength is.
1) How did you find the anomalous peaks? If from an anomalous difference
Fourier there will inevitably be noise.
In practice when there are S to check this can be very helpful in deciding
o
First for Paul and Eugene: I am using the version of coot labelled in brown
coot - 0.7 Clayton
COOT_PREFIX is /y/prog/linux/xtal/coot/coot-Linux-i386-fedora-12-gtk2-python
/y/programs/xtal/coot/coot-Linux-i386-fedora-12-gtk2-python//bin/coot-real
Acquiring application resources from
/y/prog/linux
Hi Eleanor,
The recent versions of Refmac work well with the records in PDB format.
According to the list of bug fixes on the website, Refmac should now take
the distance from the PDB file (it used to complain about the distance
record). Changing the 1.48 to 1.61 in the new LINK record should d
On 04/26/2013 12:29 PM, Eleanor Dodson wrote:
Is there any consensus about the accepted format for this?
I believe Garib uses LINKR to add a link name to the record, (cant
find a description in the documentation though???)
but also in the documentation REFMAC is said to provide a link
betwe
Is there any consensus about the accepted format for this?
I believe Garib uses LINKR to add a link name to the record, (cant find a
description in the documentation though???)
but also in the documentation REFMAC is said to provide a link between
symmetry related like this
with the target di
Input pdb and mtz should form a valid input for refmac, hence the same cell and
sym and merged mtz.
On 26 Apr 2013, at 09:17, Frank von Delft wrote:
> Hi -
>
> For Zanuda, the mtz input it wants: what spacegroup are the data meant to be
> merged to? The highest possible, potentially twinned
Yes I know all that; but where are the explicit instructions? (I
assume they're there, I just couldn't see them.)
On 26/04/2013 10:27, herman.schreu...@sanofi.com wrote:
Hi Frank,
I have not worked with Zanuda, but googled for the manual (first hit; <1sec).
It seems that there are 2 modes
Hi Frank,
I have not worked with Zanuda, but googled for the manual (first hit; <1sec).
It seems that there are 2 modes:
1) to restore the true (higher symmetry) space group after a structure had
intentionally been solved in a lower symmetry space group e.g. P1. In this case
the option to merg
Dear colleagues,
i hope every one doing well. i am trying to remove the 10x his tag , as i tried
to crystallize with the tag but i didn^t obtain crystals unless
some salt crystals , very small crystals and some precipitant. i want to use
factor 10a protease but i didn^t tried it before. this is
could this also be an alternative C-Terminus at lower occupancy?
Regards
Kornelius
On Fri, Apr 26, 2013 at 10:45 AM, Boaz Shaanan
wrote:
> Hi, it looks like gly-asp not asp-gly in this case, doesn'it?
> Cheers, Boaz
>
>
>
> הודעה מקורית
> מאת: Jonathan Cooper
> תאריך:
> אל
Hi, it looks like gly-asp not asp-gly in this case, doesn'it?
Cheers, Boaz
הודעה מקורית
מאת: Jonathan Cooper
תאריך:
אל: CCP4BB@JISCMAIL.AC.UK
נושא: Re: [ccp4bb] Curious electron density associated with Asp sidechain
Hello Tony
is that Asp-Gly? If so, it could
Hi -
For Zanuda, the mtz input it wants: what spacegroup are the data meant
to be merged to? The highest possible, potentially twinned? Or the
lowest possible?
I've looked reasonably hard (>10min on the manuals and The Google), and
the answer did not leap out at me at all. Even though it
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