Dear All,
Thanks a lot for your
replies. Glad to found so much help.
Clemens,
cell parameters are,
38.0020 78.0240
56.3800 90. 102.2770 90., in P21 spacegroup.
Raaij, Savvas,
we have checked for the
twining and no twining was detected.
Nat,
DEN is a good suggestion,
i will
If you install the .tcl update from the CCP4 site, you will find the clash
menu setting under advanced options, IIRC.
Roger Rowlett
On Jun 20, 2012 6:08 PM, "Santarsiero, Bernard D." wrote:
> The new CCP4I interface for PHASER removed the menu item where you could
> change the number of clashes.
Hi Sonali,
Did you use MBP as your purification tag? That's around 45-50kDa if I remember
right.
If not, I've had a decent amount of luck using in situ proteolysis to get
crystals of degraded fragments. Try a limited proteolysis first overnight at 4C
at varying concentrations of trypsin, see w
It seems to me that "concentration" is a statistical,
macroscopically-derived concept like temperature or pressure which
gets exceedingly weird when applied to microscopic phenomena. One
weirdness is, I guess, that the somewhat arbitrary size of the box you
mentioned makes a huge difference in the
On 06/20/12 00:36, Edward A. Berry wrote:
Sorry to come late to this discussion-
I think the actin and tubulin people already reverted "polymer"
to its etymological use- google "actin polymerization"
True. Objections withdrawn.
--
===
Dear crystallographers,
I have a question concerning effective concentration. Say you have a
crystal structure whereby two loops, each part of a different domain but
within the same molecule happen to be juxtaposed and can form an
interaction. The loops have some degree of flexibility, but are or
The new CCP4I interface for PHASER removed the menu item where you could
change the number of clashes. It's not set as a default to 5% of the
number of C-alpha atoms. Where is the default file?
I found the phaser_MR.def file in share/ccp4i/tasks, and changed the
parameter value, but it still used
*LANSCE Neutron Scattering School on Soft Matter*
*Neutron Techniques in Basic and Applied Science*
*lansce.lanl.gov/neutronschool*
*12-21 September 2012*
*Lujan Neutron Scattering Center, Los Alamos National Laboratory, Los
Alamos New Mexico*
The 2012 Lujan Neutron Scattering School will cove
Dear Sonali,
Following Michael's suggestion that you just might have
crystallized a contaminant (and all the signs point to that
I'm afraid - a small crystal growing after a long time that
diffracts surprisingly well), you might expect this crystal
form already to have been characterised and d
Dear Sonali
I would do the following things
1) Check your space group. Although rare it could be p2 or even p1
2) Run balbes server and check all space groups (in your case only p21 and p2)
If you want you can send data to me to see what might be going on
Regards
Garib
On 20 Jun 2012, at 19
Dear Sonali,
I think that first item on your possible to-do list is to verify that you have
indeed crystallized the protein you purified. We, too, got great crystals once
with protein X (100 kD) and noticed that 1) the lattice constants, space group
symmetry, and Matthew's coefficient were wit
Dear Sonali
have you run any diagnostics on your dataset e.g. via xtriage in PHENIX, or the
ccp4 programs to detect issues such as twinning and pseudotranslation.
You also did not provide any information regarding the data quality. Processing
your dataset via Xia2 from the ccp4 suite could also
Dear Sonali -
It seems very likely that your original protein (which did not
crystallize) was proteolytically degraded over the one year storage, and
you now have a fragment of the original protein which is capable of
crystallizing. You should analyze all of the homologous structures in
the
Sonali,
How did your MR search(es) fail?
1. Too many clashes? (allow more clashes or remove likely floppy bits
of the protein, e.g. N- and/or C-termini)
2. Could not place all molecules in the asymmetric unit? (Consider
searching for fewer molecules in asymmetric unit. A partial solution
On Wed, Jun 20, 2012 at 11:13 AM, sonali dhindwal <
sonali11dhind...@yahoo.co.in> wrote:
>
> I am working on a protein for last so many years and for which i have got
> crystal now in a tray which i kept 1 years ago. It diffracts well and
> resolution is 2.2A, which is good.
>
> I indexed in HKL20
Dear All,
I am working on a protein for last so many years and for which i have got
crystal now in a tray which i kept 1 years ago. It diffracts well and
resolution is 2.2A, which is good.
I indexed in HKL2000, mosflm and automar and it shows P21 space group in all
data reduction packages. But
Hell Sir,
I am using this input script to run the mlphare
#!/bin/sh
set -e
# bug # 3192 - run-all examples produce harvest files - well to counteract
# this here set HARVESTHOME to somewhere in $CCP4_SCR
HARVESTHOME=$CCP4_SCR
export HARVESTHOME
mlphare hklin /home/skumaran/Desktop
OK, I've added something to the coot wiki, basically wrapping the
rotamer name function and comparing strings. If different, rotamer info
is added to the list (adding a filter by residue type is an exercise for
reader) and a navigation dialog pops up with differences.
http://strucbio.biologie
> But I feel that this is a something of a proxy for the original question
> (which I took to be "show me NCS related residues that have side-chains in
> different rotamers").
Yes, a Kleywegt plot for side chain rotamers. Possibly with the option to look
just at hydrophobic or polar residues.
Hi Tony,
If you're happy to go outside of Coot, you can use ProSMART to do this for you.
You can view the results in a table, or coloured by residue using PyMOL or
CCP4mg. It will also account for any backbone flexibility between the
NCS-related copies, and tell you which side chains may be fli
That is exceedingly clever of James to have figured that out..
Programs like scalepack2mtz and truncate simply convert the input files and
preserve the same order and indices - for some people this seemed a GOOD
THING.
If you follow TRUNCATE by a FreeR assignment task, which I presumes is the
norm,
As one does if one examines the Valdiate -> NCS differences plot.
But I feel that this is a something of a proxy for the original question
(which I took to be "show me NCS related residues that have side-chains
in different rotamers").
The scripting function of interest in Coot is get-rotame
Try emailing ebi - they have some sophisticated search tools to do things
like this..
Eleanor
On 19 June 2012 17:26, stanley5101 wrote:
> Hi,
> Is there such a database that will allow me to search for particular
> structural motifs involved in protein interactions. For example: search
> for
You can View input command file, when working from the GUI.
Could you cut and paste this into your message - obviously some inmportant
parameter is not set, but I cant tell which without seeing that file.
Eleanor
On 20 June 2012 05:25, Appu kumar wrote:
> Thank you for your reply,
> I am run
Beware do ing this - you may just find the coordinates are on a different
origin or a different symmetry equivalent.
Eleanor
On 20 June 2012 09:20, Mark J van Raaij wrote:
> LSQKAB ("superpose" in CCP4i GUI) also outputs in its log-file the
> translation parameters and rotation matrix it used to
If you use the " superpose mo;lecules" task, using LSQKAB , and fit
molecule A over molecule B say, asking for all atoms to be fitted, you
will get a list of large deviations for main and side , which should
include all those residues with side chains in different rotamers.
Eleanor
On 20 June
Can I second that please? I am possibly in a similar situation -
2.8 Angstrom structure, 6 molecules in the asymmetric unit, refining with
ncs torsion restraint.
It would be very useful to identify which side-chains are in different
rotamers (without having to look at each and every side-chain).
LSQKAB ("superpose" in CCP4i GUI) also outputs in its log-file the translation
parameters and rotation matrix it used to superpose the structure.
On 20 Jun 2012, at 07:34, Jeremy Tame wrote:
> I agree with Petr. For a rigid body displacement the RMSD is not much use as
> a descriptor. Such
>
Hi Claudia,
this is very convenient with PyMOL:
http://pymolwiki.org/index.php/Rms_cur
Cheers,
Thomas
On 06/19/2012 05:04 PM, 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 dis
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