Dear everyone,
I am using sfall in "MODE ATMMAP RESMOD" to compute a
tagged map with
which to score a model against a map. The input PDB is OK and regularly
read by all programs - but sfall seems to interpret the coordinates
wrongly (see the list of the firs
Hi All,
These days I found the model and the density map changed to dashed
lines
after typed something wrong in the keyboard, I donnot know what have been
typed
and couldnot change it back to the normal appearance until rerun coot. The
version
of my coot is 0.3.3 in fedora. Does anybody know a
Hi Pietro,
It looks as though SFALL thinks you have fractional coords and
has coverted them into orthog ones. Does the PDB have a CRYST1 and
SCALEi cards?
Adam
On Thu, 24 Apr 2008, Pietro Roversi wrote:
> Dear everyone,
>
> I am using sfall in "MODE ATMMAP RESMOD" to
Hi Peter,
Can you try to run xtriage and see what it tells you in terms of
possible twin laws and merging statistics in higher symmetry space
groups?
The log file is attached. xtriage does not find any clear signs of
pseudosymmetry or higher metric symmetry, but it does detect the
pseudo-t
Frankly when faced with these problems of generating symmetry
equivalents i revert to almn, where a) I can guarantee the
orthogonalisation is as I expect, and b) it generates an exhaustive set
of symmetry equivalent peaks.
But that is old technology..
If you have two dimers in the asymmetric
As far as I know SFALL reads PDB files - I dont think there is an option
to input fractional coordinates..
I suspect it thinks everything is displaced one space to the left or
right ..
Can you run pdbset xyzin now.pdb xyzout now+.pdb
end
and see if there is any difference?
When I run the map
Dear All,
I have a 50kDa protein that is soluble and monodisperse at up to approx
1mg/ml (after Ni-affinity and size-exclusion chromatography).
However, it aggregates (probably both via disulphides and via
'sticky/hydrophobic patches') when I concentrate it towards 2-3mg/ml,
even in the presence
I have a similar problem Matthew.
Just got some NVoy from Novexin in which some claim can help if
hydrophobic patches are the main problem. Will see.
Regards,
Roberto
On 24 Apr 2008, at 12:35, Bottomley, Matthew wrote:
Dear All,
I have a 50kDa protein that is soluble and monodisperse at up
can't you try different volumes: i.e. 360 nl protein solution in very little
buffer and salt + 40 nl precipitant. Should give roughly 10 mg/ml after
equilibration.
Best wishes
Kornelius
On Thu, 24 Apr 2008 12:42:42 +0100
Roberto Steiner <[EMAIL PROTECTED]> wrote:
> I have a similar problem Ma
we have NCS rotation (158.56, 180, 0) - rotation matrix [R]
and we have two CS operators (P21) - rotation matrix (0 0 0) [1]
and (90 90 180) [2].
So, all symmetry related (for [R]) rotations are
[1][R][1] = [R] - (158.56, 180, 0)
[1][R][2] = [R][2] - ( 111.44 0.0 180.0)
[2][R][1] = [2][R] - ( 11
Dear Matt,
make sure that you don't have slow or even fast formation of unspecific
intermolecular disulfides by simple checks at several time points on
SDS-PAGE using sample buffer without DTT. Check the content of free
thiols and disulfides of your protein over a period of time. If you need
Dear Matt,
In one of our project, the protein of interest used to elute from Ni-column
with
~20 other proteins. I also guessed it due to surface Cysteines.
Addition of 2mM free Cys in the protein sample helped, which competed with
free Cys on the protein surface and, ultimately, gave happy
Hi,
I've got a rather weird problem when trying to run arp/warp. When
trying to run arp/warp (latest version 7.0.1) it complains that I
should install a newer version of Refmac (5.4.0045). The version of
Refmac I have installed is 5.4.0066, and thats what is being used if I
run Refmac bot
On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote:
I've got a rather weird problem when trying to run arp/warp. When
trying to run arp/warp (latest version 7.0.1) it complains that I
should install a newer version of Refmac (5.4.0045). The version of
Refmac I have installed is 5.4.0066, an
in arp/warp classic the script does not call refmac5 (the first thing
in your path) but $CBIN/refmac5 (refmac from the CBIN place)
I suspect that you still kept refmac 5.2 in the official CBIN
directory and put refmac5 in another location but earlier in your
path, so its picked up first ...
Thanks for a very quick answer, it indeed solved the problem.
Cheers,
Ronnie
On Apr 24, 2008, at 4:55 PM, Chris Richardson wrote:
On 24 Apr 2008, at 3:38 PM, Ronnie Berntsson wrote:
I've got a rather weird problem when trying to run arp/warp. When
trying to run arp/warp (latest version 7.0.
BACKGROUND: Recently we acquired an Art Robbins Phoenix
crystallization robot. This instrument is in a shared environment,
accessible to labs with projects that range from small, well-behaved
soluble cytosolic proteins to large complexes and integral membrane
proteins. Many of our users ob
Hello everyone,
It seems that the reason I get "short summaries" in scala is because the
"Show Summary button" is affected by a possible intermitently appearing
change in scala log file formatting.
When I looked for the text "Summary" in the log file I did find the entire
table -intact.
SO just
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