Sorry for my boring response………
‘Short’ bit:
Has anyone here considered DOI’s onto data? Facility sites within Europe and
planning to make this available, I hope to do a proof of principle this year on
data from Diamond (volunteers?). But as an example the ISIS neutron site on the
same campus a
Also
http://www.guardian.co.uk/technology/2011/oct/13/dennis-ritchie
He was considered important enough to be highlighted in a general
interest newspaper.
Eleanor
On 10/18/2011 10:30 AM, Tim Gruene wrote:
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Dear Miguel,
There are a couple of wel
Has anyone raided the point that while archiving is good, it will only
be generally useful if the image HEADERS are informative and use a
comprehensible format - and the data base is documented...
Eleanor
On 10/19/2011 10:45 AM, Alun Ashton wrote:
‘Short’ bit:
Dear users, We have a structure which is a homodimer in the asymmetric unit.PISA predicts most probable assembly as a dimer but thisdimeric assembly is different from what is solved (offcoursewe can generate the symmetry equivalent molecule and get that).My question is - is it necessary that we dep
Hi,
What you must deposit is what is present in the asymmetric unit of the crystal.
The HEADER cards (and the publication) can describe the most likely biological
assembly.
Why is that: there is no reason why the crystal should conform to the
biological function (and associated quaternary stru
Hi Eleanor,
So far I have managed to "lurk" on this one - keeping an eye on things
but not getting involved. However this has prompted me to respond!
> Has anyone raided the point that while archiving is good, it will only be
> generally useful if the image HEADERS are informative and use a
> co
If you don't want to build Pointless yourself, there are binaries for Linux &
OSX (10.6) on our ftp site here (not Windows I'm afraid)
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.6.6.linux
.../pointless-1.6.6.osx10.6
You might also want to update the ccp4i task with .../pointless_ccp4i_1.4.t
Dear Kavya,
If I understand your question correctly, it is about the choice of asymmetric
unit for your deposition. In case of dimeric asymmetric unit (ASU), there are,
indeed, a few valid possibilities and you arrive to just one of them in the
course of structure solution. What you decide to d
Hi,
If I have two somewhat different overlayed models, is it possible in
COOT to replace part of one model by another?
Similarly to O command: merge_atoms residue_end> ?
That's a useful feature in O, but could not find it so far in COOT.
Thanks!
--
Dr. Leonid A. Sazanov
Research group leader
M
Many thanks to Alexander Schiffer, Petr Leiman and Stephen Cusack for drawing
our attention to this problem and supplying test cases to reproduce it. It was
an obscure problem in which a Phaser executable compiled on a 32-bit Linux
system would occasionally (but not reproducibly) crash when run
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Dear Leonid,
To merge part of molecule B into molecule A you do in in steps:
- - remove the part from A that you want to replace
- - remove from B everything you do not want to merge with A
- - merge B into A (Calculate->Merge...)
- - change the newly
You can also try
Extensions->Modelling->Replace fragment
(usage self-explanatory)
>
--
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number: 03674842 and a registered office at 2 King
Hello CCP4 user
I have collected a data set 2.1 for my complex. Actually after first run of
Rafmac i can see the density for my inhibitor but the problem is my inhibitor
is 6 KDa and i know the sequence of my inhibitor as well this inhibitor already
crystallize with other protein molecule pres
Dear Napoleão,
I will try to summarize our experience and give some suggestions.
Few reasons why MR with coiled coils can be very tricky, such as
their asymmetric shape and their ability to overlap onto themselves
upon a shift and rotation (for a heptad-based coiled coil, this would be a
shift b
3 ways:
cat mol1 mol2 > mol3
Use an editor such as nedit to cut and paste.
Coot merge molecules function.
Sent from Jack's iPad
On Oct 19, 2011, at 8:13 AM, "Afshan Begum"
mailto:afshan...@yahoo.com>> wrote:
Hello CCP4 user
I have collected a data set 2.1 for my complex. Actually after fir
On Wed, 2011-10-19 at 12:20 +0100, Leonid Sazanov wrote:
> Hi,
> If I have two somewhat different overlayed models, is it possible in
> COOT to replace part of one model by another?
> Similarly to O command: merge_atoms residue_end> ?
> That's a useful feature in O, but could not find it so far
Hello,
James Holton can probably tell more about this, but it is possible to create
a library of potential coiled coil structures with differences in number of
residues, superhelical radius, and residues per superhelical turn. A library
of 300 theoretical coiled coils was generated and, in conjunc
> My question is - is it necessary that we deposit a structure, which
> PISA predicted as most probable assembly in PDB as an
> asymmetric unit & biological assembly or can we deposit a dimer
> (asymmetric unit) and give explanation for the biological assembly
> according to what PISA predicted.
>
Dear all, thanks for replies!
Indeed, text editing or other combinations of manipulations will do the
trick of course, but I wanted to do it in one command, as I need to make
many substitutions in a very big model as I go along.
Suggested (replace-fragment) (or also (copy-residue-range)) do the
Why not do the molecular replacement - 6kDa is rather small but it most
likely will work
On Wed, 2011-10-19 at 06:13 -0700, Afshan Begum wrote:
> Hello CCP4 user
>
>
> I have collected a data set 2.1 for my complex. Actually after first
> run of Rafmac i can see the density for my inhibitor but
why don't you read in that chain in Coot and run the find ligand option with
flexible ligand turned on and select that 6kDa ligand ? You should also choose
Fo-Fc map to fit the ligand to maybe at 2.7 sigma. You might have to split up
the ligand into pieces, not sure what the limitations in Coot/
Dear Juergen
Many thank for your response yes you have excatly
understand my question we have a MR solution of the rest of our
protein and just asking how to make my life easier to not built de
novo 45-50 residues. so i could not find the option in coot find ligand
so, from where i get it?
B
Hi Afshan,
in Coot select calculate --> other modeling tools --> find ligands
In 0.6.2, there is a message that ligands are limited to 400 atoms or less.
Regards,
Mitch
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Afshan
Begum
Sent: Wednesday,
Dear users,Thank you all for the suggestions.With RegardsKavya--
This message has been scanned for viruses and
dangerous content by
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On Oct 19, 2011, at 4:36 AM, Kayashree M wrote:
> We have a structure which is a homodimer in the asymmetric unit.
> PISA predicts most probable assembly as a dimer but this
> dimeric assembly is different from what is solved (offcourse
> we can generate the symmetry equivalent molecule and get tha
Dear CCP4ers,
I am trying to run watertidy from the windows gui to add waters, but
get the error message below. Since the gui is so short, I don't think
I am missing anything, so what I am doing wrong? Is there an
alternative water-picker in the gui? I used to use watpick, but I
believe that was i
On Wed, 2011-10-19 at 12:45 -0500, Jacob Keller wrote:
> Is there an
> alternative water-picker in the gui?
watertidy is not a water-picker
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of Lemurs
Well, I see that it fixes/edits waters, but it seems to add them too,
according to the documentation
"Add/Tidy Waters - Watertidy
This task rationalises waters at the end of refinement.
See program documentation: Watertidy, Distang."
Is there a program in the gui that adds waters, if not this o
Dear users,
Are there any programs to calculate percentage of buried surface area that is
polar vs nonpolar?
Thanks in advance
Thanks!
Jyotica
Not sure where you quoting this from. I am looking at the official
documentation here
http://www.ccp4.ac.uk/html/watertidy.html
which clearly states
This program has two purposes.
1. It moves the H2O coordinates to the symmetry related position
nearest to the host molecule.
2
On Wed, 2011-10-19 at 20:17 +0100, Jyotica Batra wrote:
> Dear users,
>
> Are there any programs to calculate percentage of buried surface area that is
> polar vs nonpolar?
>
> Thanks in advance
>
> Thanks!
> Jyotica
Surface Racer includes breakdown by atom type (polar vs nonpolar) in the
outp
On 19/10/11 9:19 PM, "eugene.krissi...@stfc.ac.uk"
wrote:
>In case when ASU has the same multiplicity (number of chains) as the
>probable biological assembly, the latter is an ASU as well. In such a
>case, the PDB suggests to choose ASU in the form of that assembly, purely
>for simplicity. It see
Job opening for a crystallographer to join the Structural Motility team at the
Curie Institute Paris, France.
We are looking for a post-doctoral fellow to join the team Structural Motility
at the Curie Institute (Paris 5e) directed by Anne Houdusse. The position is
immediately available (prefer
Respected Sir, The space group is H3. if I generate the symmetry, it appears to be a dimer of trimers stacked one above the other with a rotation of 60 deg wrt each other, like this - A1, A2, A3 (in one trimer) stacked uponB1, B2, B3 (second trimer). So structure that is in the ASUis with A1-B1 wh
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