of an appropriate length.
If it is truly spurious density as I suspect it is, you'll see negative
density lighting up your screen despite using appropriately low occupancy.
Good luck!
Sangeetha.
On Sun, Nov 4, 2012 at 8:17 PM, Sangeetha Vedula sangeetha...@gmail.comwrote:
Could it be a fatty acid
Could it be a fatty acid? It looks like it has a (hydrophobic?) tail with a
(charged?) head. Partially occupied perhaps, as they're so close together.
On Sun, Nov 4, 2012 at 7:38 PM, yogesh khandokar yogesh.khando...@gmail.com
wrote:
Dear All
I am working on an enzyme which involved in fatty
Do you see the same MBP band (or corresponding to the same MW, in case it
isn't MBP) before cleavage, at the same total concentration of protein? If
not, your protein could be crashing out. Even so, if you use SDS and heat
up the sample, I am surprised that your protein just disappeared. TEV
Hello all,
I am working with a protein that is probably a hexamer based on homology
with other proteins but when I ran it on an analytical size gel filtration
column, I see multiple peaks. I would like to determine the exact
oligomerization state of the mixture and have considered blue native gel
Lucas, if your crystals diffract worse at room temp than cryoprotected, it
looks like there may be radiation damage at room temperature, so you may
need to cryoprotect. The change in osmotic pressure may be too much for
your crystals when you're cryoprotecting the crystals by a sudden dunk.
Also,
Dear bb users,
I am trying to crystallize a ~320 kDa protein that crashes out if
concentrated past about 3 mg/mL.
I would like to try to exchange it into various buffer-salt-additive
combinations to see which buffer works. For a starting point, I'd like to
use desalting colums.
Does anyone have
Dear all,
I am refining a crystal structure with two enantiomers of the ligand lying
on a two-fold crystallographic axis (making the density an average of 4
orientations/optical identity). The ligand fits pretty well over all in the
density, but some atoms stick out of density. While B-factors
Dear all,
My lab is looking into buying a protein purification system. The AKTA is
more versatile, but does anyone know if the Profinia is in any way superior
to the AKTA for purification of affinity-tagged proteins? If it is, I would
really appreciate if you can tell me in what way it is
Collins edward_coll...@med.unc.edu
wrote:
personally, I don't know why you would want to limit yourself to just using
affinity tags to purify your proteins. For my money the flexibility of the
AKTA is critical.
good luck
-ed
On Jan 28, 2010, at 11:08 AM, Sangeetha Vedula wrote:
Dear all
Clemens
On Thu, Jan 28, 2010 at 11:04:52AM -0500, Sangeetha Vedula wrote:
Dear all,
I am refining a crystal structure with two enantiomers of the ligand
lying
on a two-fold crystallographic axis (making the density an average of 4
orientations/optical identity). The ligand fits pretty
] *On Behalf Of
*Sangeetha
Vedula
*Sent:* Friday, November 20, 2009 8:03 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] hairpin formation in gene
Dear bb-ers,
I am trying to have a gene synthesized and found out that it forms an 11-bp
hairpin. Does that complicate expression? Would
Dear bb-ers,
I am trying to have a gene synthesized and found out that it forms an 11-bp
hairpin. Does that complicate expression? Would it be better to try and
disrupt it by altering codon usage to improve expression?
Thank you in advance,
Sangeetha.
number for finding spots
and instead define the spot range only in one line e.g. SPOT_RANGE=1 50
That should fix your problem I think.
Jürgen
On 11 Jun 2009, at 11:27, Sangeetha Vedula wrote:
I checked:
1. I did name it XDS.INP; no problem there.
2. The path along with file name
anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Thu, 11 Jun 2009, Sangeetha Vedula wrote:
I checked:
1. I did name it XDS.INP; no problem there.
2. The path along with file name template is only about 30 characters.
3. No. of files = 156 (DATA_RANGE=1 156
I moved the program to /Applications as well.
When I start XDSviewer giving it the whole path, it errors out, saying:
/Applications/XDS-Viewer.app/Contents/MacOS/XDS-Viewer: line 6: 818 Bus
error
$CURRENT_DIR/xds-viewer-bin
If I double-click on XDS-Viewer.app icon, it begins to
Hello all:
I am trying to merge library files for 2 molecules using libcheck dialogue.
But it only writes out the first library file that I read in.
FILE_L 1.cif
FILE_L2 2.cif
It writes out a file called libcheck.lib which contains only lines from
1.cif.
What am I doing wrong? Is there
Thank you, Sridhar.
For some reason, that gives an error, saying that it couldn't execute
libcheck. Instead, I tried using the keyworded input format. Do you know
what could be wrong with that?
I tried to install libcheck but apparently my computer can't figure out what
the make function is
Hi all,
I am trying to fit a ligand into density using ARP/wARP 7.0.1 in CCP4 suite
6.0.2 on CCP4interface 1.4.4.2.
I get an error message telling me to look for the error in a
##_warp_ligand_details.log.
_
Running Refmac5 to refine
Hi Manish,
But then volume is biased by the plot grid size one chooses and not the
converged volume. In short, one isn't even using the results of volume
refinement because one'd get the same answer from the same grid size for the
same orientation (given the same probe radius). Using the final
Hi Manish and everyone,
If one uses the volume on the plot grid size, volume is biased by the plot
grid size one chooses and not the converged volume. In short, one isn't even
using the results of volume refinement because one'd get the same answer
from the same grid size for the same orientation
Hello all
I am comparing the probe-occupied volumes of a protein cavity with and
without several ligands. Which cavity volume is used for the comparisons?
I found an FAQ link:
http://www.imsb.au.dk/~mok/o/ofaq/Q.507.htmlhttp://www.imsb.au.dk/%7Emok/o/ofaq/Q.507.html
Q.507 - Which VOIDOO cavity
, at 18:24, Sangeetha Vedula wrote:
Dear bb users,
I am refining a protein-ligand complex (at 1.68 A resolution) in which the
ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy
is, therefore, 0.5 in each asymmetric unit.
I am almost at the end of the refinement
:
You're probably better off trying to change the restraints in the
ligand .cif file. It sounds like you have some torsion angle or
chiral center set wrong.
-bob
On Tue, Jul 29, 2008 at 10:24 AM, Sangeetha Vedula
[EMAIL PROTECTED] wrote:
Dear bb users,
I am refining a protein-ligand complex
Dear bb users,
I am refining a protein-ligand complex (at 1.68 A resolution) in which the
ligand lies on a 2-fold crystallographic symmetry axis. The ligand occupancy
is, therefore, 0.5 in each asymmetric unit.
I am almost at the end of the refinement but one problem has me stumped.
Refmac keeps
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