Re: [ccp4bb] IUCr committees, depositing images

[Alun Ashton]

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 as us have started to do this, as a random example you can go to 
http://doi.org  and put in the DOI reference 10.5286/ISIS.E.24079772 (catchy), 
but this takes you to a landing page where you can see some details of the data 
and an actual citable (I think) reference to the data for a publication. There 
is a link to the data but the data has not yet been made public by the author 
or facility, but at least its (should be) there and will eventually be public. 
The responsibility is now on the facility for looking after  and making the 
data available.

This wouldn’t suit everyone, and also there is the issue of home sources, but 
tools are under development to make this easy. I could easily imagine that 
within the UK STFC would probably host something like this for non facility 
data (it is actually them who host Diamond data for us)…. Maybe at a nominal 
cost of course….

Long bit:
Something similar at Diamond, /dls/$Beamline_name/data/$Year/$proposal-$visit 
and permissions are set accordingly so only the people on the visit or the PI’s 
of the proposal can see the data therein. What happens within that directory is 
still pretty much the users choice at the moment. Though once the data is 
collected its read only and its all recorded in ISPyB (beamline database with 
web pages developed at ESRF and Diamond). You can also record details of the 
sample and link the data collections to it.

There is an EU funded initiative that I have make the IUCr DDDwg aware of in 
Europe called PanData (http://www.pan-data.eu/) which includes most of Europe’s 
X-ray and neutron sites. Under this initiative the facilities are attempting to 
standardise on authorisation, data formats, some software, access policies 
(making data public) data retention and cataloguing.

Here we’ve been a bit lucky to get ahead on this and we have been able to keep 
a copy of all our data off all beamlines, raw and processed on tape (that’s 
just under 200Tb and 53 million catalogued files so far, lots of data including 
processed data its not yet catalogued but is on tape). We are currently beta 
testing a web page to the data that is catalogued, so anyone who has collected 
data at diamond should be able to get it from https://icat.diamond.ac.uk. The 
data will probably be coming off tape so can take a while, also it’s a little 
bit clumsy as an interface but it will get better. This is the same technology 
as is being proposed for PanData facilities, but the backend of the actual data 
archive is the choice of each facility, ours is hosted in a tape robot by STFC 
at the moment.

This is by no means the only solution out there but DOI’s could help unify the 
solutions?

Alun
___
Alun Ashton, alun.ash...@diamond.ac.uk Tel: +44 1235 778404
Scientific Software Team Leader,  http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tom Peat
Sent: 18 October 2011 23:29
To: ccp4bb
Subject: Re: [ccp4bb] IUCr committees, depositing images

If we are talking schemes, here is another one that we use that might be 
considered:

Date/person/project/barcode/well#/crystal#

At the Australian synchrotron, a directory is automatically made with the date, 
so that is our starting point.
We sometimes skip the person, but project-barcode-well are always there, as 
then it can correspond to our crystal database.
I imagine that most high throughput centres use barcodes, so barcodes and well 
numbers would be good things to have in the path.

Cheers, tom

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
mjvdwo...@netscape.net
Sent: Wednesday, 19 October 2011 6:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] IUCr committees, depositing images

Phoebe,

Just automate the archiving and come up with a reasonable scheme how to. Ours 
is that data sets are called:

userid_yearmonth_projectid_#

Userid is derived from the login into CrystalClear (oops, free advertizing), 
projectid is set by the PI (so she can remember 10 years from now what in the 
world these data are all about) and the users are asked (threatened) to call 
their data sets projectid_# (and not the ubiquitous test). We have a script 
that automatically archives everything away from our data collection computer 
into an archive - activated by an icon on the desktop - and it adds the userid 
and date to the filename. This has the nice added advantage that the data 
collection disk stays clean. This only breaks when we collect synchrotron data 
(which is all the time) because our synchrotron remote scientist who collects 
the 

Re: [ccp4bb] Dennis Ritchie

[Eleanor Dodson]

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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Hash: SHA1

Dear Miguel,

There are a couple of well-written obituaries:
http://www.wired.com/wiredenterprise/2011/10/dennis-ritchie/
http://edition.cnn.com/2011/10/14/tech/innovation/dennis-ritchie-obit-bell-labs/


To acknowledge his work, you might start you list counting from 0 rather
than 1 and swap the two items, because C was developed since Fortran did
not match the requirements to develop an OS like UNIX.

Tim

On 10/18/2011 10:58 AM, Miguel Ortiz Lombardía wrote:

Hi community,

I have been waiting for someone more knowledgeable to write about the
passing away of Dennis Ritchie (8 October) especially after the recent
obituaries posted in the list. I confess I know little about him, except:

1/ He created the C language ( and together with Brian Kernighan wrote
an extremely useful book about it )
2/ He and Ken Thompson were key in the development of something called
UNIX...

Undoubtedly, he made an impact in our field.




- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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Re: [ccp4bb] IUCr committees, depositing images

[Eleanor Dodson]

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:

[ccp4bb] Biological assembly

[Kayashree M]

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 deposit a structure, whichPISA 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 assemblyaccording to what PISA predicted.Other than such predictions what other criteria needs to be considered to say that one specific assembly is a biological assembly?Another question-In this case one of the chain has 3 MSE residues, while the otherchain has only 2 MSE (When we change MET to MSE, there will be a huge negetive density coming up).Are there any such instances in PDB, where two homodimer (or any mer)will have different percentage of MSE?Thanking youWith Regardskavya-- 
This message has been scanned for viruses and
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Re: [ccp4bb] Biological assembly

[Frederic VELLIEUX]

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 structure), there are examples 
of having the 
asymmetric unit different than the biological assembly. Such as a crystal 
asymmetric unit containing half a viral capsid.

So the PDB files contain what you see in the crystal, and there are places 
for the interpretation, such as these pictures appearing on the web page for 
the structure 
showing the most likely biological unit. Or if you (as a user) request the PDB 
to provide you with the coordinates for that most probable biological assembly.

Fred.

 Message du 19/10/11 12:36
 De : Kayashree M 
 A : CCP4BB@JISCMAIL.AC.UK
 Copie à : 
 Objet : [ccp4bb] Biological assembly
 
 Dear users, 

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 that).

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.

Other than such predictions what other criteria needs to be 
considered to say that one specific assembly is a biological assembly?


Another question-
In this case one of the chain has 3 MSE residues, while the other
chain has only 2 MSE (When we change MET to MSE, there will be a 

huge negetive density coming up).

Are there any such instances in PDB, where two homodimer (or any mer)
will have different percentage of MSE?


Thanking you
With Regards
kavya

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Re: [ccp4bb] IUCr committees, depositing images

[Graeme Winter]

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
 comprehensible format - and the data base is documented...

There are a number of issues here:

 - whether to publish data
 - how to publish data
 - how to make the published data useful
 - whether to centrally archive that data
 - whether to standardise the data, and if so how
 - who should pay
 - moving the data around

etc. The image headers issue is clearly one of these, however properly
resolving this has thus far proved to be if not intractable, at least
challenging. There is at least one standard comprehensible format
which is out there and has been for a while, but is thus far lacking
widespread adoption. However, and this is a huge however, we really
need to ask how much effort it is worth putting into (handling) each
data set. The more effort is needed to make the data available, the
less likely it is that it will ever become available. I know from
experience that even when people want you to have data the activation
energy is substantial. Making the process more complex will decrease
the likelihood of it occurring. If on the other hand we lower this
barrier (i.e. you make available the data you have on the hard disk
exactly how it is) you lower this barrier some way. We can make this
useful by also including the processing logs - i.e. your mosflm /
denzo / XDS log file - so that anyone who really wants to know can
look and figure it out.

This biases the effort in the right direction. Even if every data set
was perfectly published, it is pretty unlikely that any given data set
would be re-analysed - unless it is really interesting. If it is
really interesting, it is then worth the effort to figure out the
parameters, so make this possible if inconvenient. As I see it, a main
benefit of this is to allow that occasional questionable structure to
be looked at really hard - and simply the need to upload the original
data and processing results would help in reducing the possibility of
depositing anything fake.

Another factor I am painfully aware of is that disks die - certainly
mine do. This is all well and good - however the time it takes to move
4TB of data from one drive to another is surprisingly long, as even
with things like eSATA we have oceans of data connected by hosepipes.
Moving all of your raw data from a visit to the synchrotron (which
could easily be TB's) home is a challenge enough - subsequently moving
it to some central archive could be a real killer. Equally making the
data public from your own lab is also difficult for many. At least
facility sites are equipped to meet some of these challenges.

So - as I can see it we have much bigger fish to fry than getting the
headers for historical data standardised! Current and future data,
well that's a different pot of worms. And that's from someone who
really does care about image headers ;o)

Cheerio,

Graeme

Re: [ccp4bb] newbie question about data processing

[Phil Evans]

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.tar.gz

Phil

On 18 Oct 2011, at 22:18, Edward A. Berry wrote:

 I integrated data with mosflm using the lowest symmetry implied by
 the lattice- P4. Scaling with scala confirms that symmetry.
 Now I want to test P422, but scala doesn't seem to have a SYMM
 or SPACE GROUP keyword. I'm sure there is an obvious way to do
 this, which everyone else knows, but i don't see it.
 
 I understand that pointless can be inserted between mosflm
 and scala to decide and change space group. Unfortunately
 I built ccp4 without cctbx, phaser and pointless (phaser is
 installed separately) so I don't have pointless. I'm
 trying to get it installed now but if there is another way
 to rescale the batches with higher symmetry I would like
 to try it.
 
 Ed

Re: [ccp4bb] Biological assembly

[eugene . krissinel]

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 deposit, is your own choice, 
and I would think that the PDB can suggest an alternative but they would not 
really insist on it (hopefully).

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 
seems to me that this is not an unreasonable suggestion and it would be nice if 
that were a common practice. I do not want to imply here that PISA will always 
make a correct prediction, therefore, one should always be critical and use as 
much experimental evidence as possible. However, deposition of biological 
assembly as ASU, where possible, is always preferential irrespectively of 
whether the assembly agrees with PISA predictions or not. Preferential does not 
mean mandatory though :)

I hope this helps,

Eugene.


On 19 Oct 2011, at 11:36, Kayashree M wrote:

Dear users,

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 that).

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.

Other than such predictions what other criteria needs to be
considered to say that one specific assembly is a biological assembly?

Another question-
In this case one of the chain has 3 MSE residues, while the other
chain has only 2 MSE (When we change MET to MSE, there will be a
huge negetive density coming up).

Are there any such instances in PDB, where two homodimer (or any mer)
will have different percentage of MSE?

Thanking you
With Regards
kavya

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This message has been scanned for viruses and
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[ccp4bb] merging parts of models in COOT

[Leonid Sazanov]

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 from_molecule residue_start 
residue_end to_molecule residue_start ?

That's a useful feature in O, but could not find it so far in COOT.
Thanks!

--
Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge

[ccp4bb] Fixed! Intermittent floating point exception in Phaser-2.3 under 64-bit Linux

[Randy Read]

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 on a 64-bit 
Linux system.  Because the CCP4 binary distribution for Linux is compiled on a 
32-bit machine, this potentially affected anyone using that distribution on a 
64-bit machine.

David Waterman at CCP4 did some brilliant detective work and, with some help 
from Airlie McCoy, figured out how to make an executable that doesn't crash.  
David has now noted the issue on the CCP4 problems page 
(http://www.ccp4.ac.uk/problems.php#6.2.0-phaser), which has a link to where 
you can download the fixed executable.  The fixed executable is now also 
incorporated into the automated download.

We do pretty exhaustive tests, but they don't include compiling on one 
architecture and testing on another, so if everyone had suffered in silence we 
would never have been aware of this problem!  So we (and, I'm sure, other 
developers) really do appreciate bug reports.

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] merging parts of models in COOT

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

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 created chain ID (Calculate-Change Chain ID...)

Tim

On 10/19/2011 01:20 PM, 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 from_molecule residue_start
 residue_end to_molecule residue_start ?
 That's a useful feature in O, but could not find it so far in COOT.
 Thanks!
 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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zFjXn9JhwhZzIXUSOYcI50I=
=Ge9y
-END PGP SIGNATURE-

Re: [ccp4bb] merging parts of models in COOT

[Debreczeni, Judit]

You can also try
Extensions-Modelling-Replace fragment
(usage self-explanatory)




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-Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Tim Gruene
 Sent: 19 October 2011 13:17
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] merging parts of models in COOT

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1

 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 created chain ID (Calculate-Change Chain ID...)

 Tim

 On 10/19/2011 01:20 PM, 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 from_molecule residue_start
  residue_end to_molecule residue_start ?
  That's a useful feature in O, but could not find it so far in COOT.
  Thanks!
 

 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A

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 Version: GnuPG v1.4.10 (GNU/Linux)
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 zFjXn9JhwhZzIXUSOYcI50I=
 =Ge9y
 -END PGP SIGNATURE-

[ccp4bb] how can merge two PDB

[Afshan Begum]

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 present in PDB data bank so how can i 
put in to that electron density i mean are there any ways to combine two Pdb in 
one molecule? 


I would be thankful for your help

 



Best Regards

AFSHAN

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

[Sergei Strelkov]

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 by 7 residues) have been already mentioned.
And I can add two more.

First, we very often see that coiled coils get bent due to
crystal contacts. This means that the conformation may be
quite different compared to your search model.
Second, many coiled coil sequences were seen to
assemble into structures different to what
they were supposed to be. Examples I know include
a trimer when a dimer was expected, an antiparallel
coiled coil when a parallel one was expected,
a monomer when a a dimer was expected,
chains offset with respect to each other, etc etc

We were able to phase several short (40-60 residues)
coiled coils by MR in the past. The paper
Strelkov SV et al (2002) EMBO Journal describes
two such cases (please look at the Methods section
which provides a fairly detailed explanation of what
we did). Both were done with Molrep.

I do have to say that we also failed on MR
miserably in many other cases, whatever we tried.
One recent example of a coiled coil fragment
that assembled to something entirely different
than we expected it to, is in Nicolet S et al (2010)
J. Struct. Biol. There, we really had to use heavy atoms.




I collected
various data sets (home source, Brookhaven and Diamond), including some
at the resolution of 1.65 A, for which the space group appears to be
C222 or C2221.


You have collected many data sets and you are still not sure
about the space group - ? Have you looked at the systematic absences
carefully? If you are still missing the (00l) axis then you
probably could try collecting it again while considering the
orientation of your crystal.

Knowing the correct space group is a valuable
information. Yes there are cases when you can not
distinguish between two space groups from the diffraction pattern
(e.g. P61 and P65) and then you /have/ to run your MR search
twice in both groups. Yes modern programs will do
it almost by default for you. But if you do know your correct space
group (for instance C2221 and not C222) then when you
do the MR search in the two space groups you /may/ (with some
luck) see better results with the first than with the second.
This /may/ be a hint that your C2221 solution is correct.




  I have tried A LOT of Molecular Replacement using Phaser and Phenix
AutoMR.
As mentioned already, is really advisable to try other MR programs 
(MolRep, epmr etc),

as in fact they are all based on different algorithms.


I'm using a 80% identity coiled coil helix as search model.
  Regarding the search model, I already tried trimming some or all
side chains and removing 2, 3 or 5 residues on each/both sides.


From your description I am guessing that you use a monomeric helix
currently - ?

Indeed you really should try different models, anything you can
get your hands on. In fact this is a number one factor to
get MR to work.

On one hand, you should indeed try shortening your
model (even systematically trimming one residue at a time).
Do not hesitate to use much shorter models (less than
half of your full helix). You can trim the wrong side chains
but I would not advise chopping off all of them.

With a short helix, once you have the first candidate
solution, try searching for a second copy with the packing penalty
switched off. If you get another helix overlapping with your first
solution (with some offset) this may be a sign of success.
(see the EMBO J paper)

On the other hand, our experience shows that in many cases
you can only get a solution if you use a full coiled coil
(dimer, trimer,...) and not a monomeric helix.

If your real structure is a non-crystallographic dimer etc,
then you should definitely search with a dimer etc.
If your oligomer is due to a crystallographic axis, then
you may try this as well, after switching off the
packing penalty. But beware that the oligomer
will almost certainly land on the axis, even for a wrong solution.

Hope this will help, and best of luck with your MR
searches -- which are fun, since they still require
some thinking!
Sergei

--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven
ON2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium
Work phone: +32 16 330845  Fax: +32 16 323469 OR +32 16 323460
Mobile: +32 486 294132
Lab pages: http://pharm.kuleuven.be/anafar

Re: [ccp4bb] how can merge two PDB

[Tanner, John J.]

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 
afshan...@yahoo.commailto:afshan...@yahoo.com 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 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 present in PDB data bank so how can i 
put in to that electron density i mean are there any ways to combine two Pdb in 
one molecule?

I would be thankful for your help



Best Regards

AFSHAN

Re: [ccp4bb] merging parts of models in COOT

[Ed Pozharski]

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 from_molecule residue_start 
 residue_end to_molecule residue_start ?
 That's a useful feature in O, but could not find it so far in COOT.
 Thanks!
 

IIUC what you want to do, shouldn't this be a trivial operation in a
text editor?

-- 
Hurry up before we all come back to our senses!
   Julian, King of Lemurs

Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong

[Filip Van Petegem]

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 conjunction with EPMR,
was used successfully to solve the structure of a KCNQ tetrameric coiled
coil.

See: Howard et al (2007) Neuron 53(5),663-675.

And I second Sergei Strelkov's comment:  what should be an expected tetramer
could show up as a trimer, etc... so you may want to check via
ultracentrifugation that you have the expected stoichiometry.

Regards,

Filip


On Mon, Oct 17, 2011 at 10:09 AM, Napoleão Valadares n...@ifsc.usp.brwrote:

Hi there!
I got crystals from some synthetic peptides I bought, they are 30
 residues long and are supposed to form a coiled coil. I collected various
 data sets (home source, Brookhaven and Diamond), including some at the
 resolution of 1.65 A, for which the space group appears to be C222 or C2221.
 The unit cell is small, 22.67, 88.06, 26.13, and the Matheus Coefficient
 indicates that's there's only one helix in the asymmetric unit and a 25%
 solvent content.

I have tried A LOT of Molecular Replacement using Phaser and Phenix
 AutoMR. I'm using a 80% identity coiled coil helix as search model. The
 programs give me solutions with reasonable maps, but it is never possible
 to refine to achieve Rvalues below 0.40. Additionally, maps from different
 solutions look reasonable, so I'm thinking these are all bias.

I have 5 other synthetic 30 residues peptides (that crystallize in
 different space groups and diffract to lower resolutions), including a
 SelenoMethionine (SM) derivative (but it does not have enough anomalous
 signal, ASU is too big, it is possible that the SM are disordered). I'm
 stuck on this since March.

Regarding the search model, I already tried trimming some or all side
 chains and removing 2, 3 or 5 residues on each/both sides. I also tried
 other search models. Maybe some magic combination of parameters on Phaser
 or other programs can help me.

What is your advice regarding how to proceed with MR? Is there some
 program, procedure, parameter, pray or human sacrifice that could help me?
Thank you.
Regards,
  Napo




-- 
Filip Van Petegem, PhD
Assistant Professor
The University of British Columbia
Dept. of Biochemistry and Molecular Biology
2350 Health Sciences Mall - Rm 2.356
Vancouver, V6T 1Z3

phone: +1 604 827 4267
email: filip.vanpete...@gmail.com
http://crg.ubc.ca/VanPetegem/

Re: [ccp4bb] Biological assembly

[Ed Pozharski]

 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.
 
As others have said - you are free to deposit whatever model you believe
is consistent with your experimental data.  If we assume that you know
what the biological assembly is (see below), you still may (and people
do that) deposit a different arrangement - it's not wrong per se, but
think about non-structural folk (there should be a better word) that
will look at your deposited model and may not have the experience to
realize what they are looking at.


 Other than such predictions what other criteria needs to be 
 considered to say that one specific assembly is a biological assembly?
 
1. You need to show that your protein is a dimer in solution.
Gel-filtration (sometimes problematic), dynamic light scattering (often
problematic), analytical ultracentrifugation (less problematic but
instruments are not widely available) as well as methods I mention in 2
are useful here.

2. You need to show somehow that the dimer you see in crystal is the
same as dimer in solution.  Many approaches are available here - I am a
recent SAXS convert, and I wholeheartedly recommend that, but your
mileage may vary.  SAXS will also unequivocally determine the
oligomerization state. Cross-linking and HD exchange, both in line of
mass-spectrometry, are good ways to get it done too.  

With that said, you may be able to get away with just the crystal
structure assuming that the PISA results are convincing (e.g. you have
one heavily hydrophobic interface that is large enough and much larger
than any other more polar alternatives.

 Another question-
 In this case one of the chain has 3 MSE residues, while the other
 chain has only 2 MSE (When we change MET to MSE, there will be a 
 huge negetive density coming up).
 
This is rather curious.  While it's definitely possible that your
protein prep had variable incorporation ratio, the fact that you see it
in a specific spot seems to suggest that selenium slightly alters the
structure directing the crystallization.

 Are there any such instances in PDB, where two homodimer (or any mer)
 will have different percentage of MSE?
 
Hopefully someone knows the answer, but you can always just mine the
database.

Cheers,

Ed.

-- 
I'd jump in myself, if I weren't so good at whistling.
   Julian, King of Lemurs

Re: [ccp4bb] merging parts of models in COOT - SOLVED

[Leonid Sazanov]

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 
desired job.

Thanks!

Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Mitochondrial Biology Unit
Wellcome Trust / MRC Building
Hills Road
Cambridge


On 19/10/2011 14:41, Ed Pozharski wrote:

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_atomsfrom_molecule residue_start
residue_end  to_molecule residue_start  ?
That's a useful feature in O, but could not find it so far in COOT.
Thanks!


IIUC what you want to do, shouldn't this be a trivial operation in a
text editor?

Re: [ccp4bb] how can merge two PDB

[Ed Pozharski]

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 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
 present in PDB data bank so how can i put in to that electron density
 i mean are there any ways to combine two Pdb in one molecule? 
 
 
 
 I would be thankful for your help
 
  
 
 
 Best Regards
 
 AFSHAN
 
 
 
 
 
 
 

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] how can merge two PDB

[Bosch, Juergen]

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/Find Ligand are.

You already have a MR solution of the rest of your protein right ? So you are 
just asking how to make your life easier to not built de novo 45-50 residues ?

Jürgen

On Oct 19, 2011, at 10:00 AM, Ed Pozharski wrote:

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 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
present in PDB data bank so how can i put in to that electron density
i mean are there any ways to combine two Pdb in one molecule?



I would be thankful for your help




Best Regards

AFSHAN








--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
   Julian, King of Lemurs

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] how can merge two PDB

[Afshan Begum]

 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?

Best Regards

AFSHAN






From: Afshan Begum afshan...@yahoo.com
To: Bosch, Juergen jubo...@jhsph.edu
Sent: Wednesday, October 19, 2011 4:58 PM
Subject: Re: [ccp4bb] how can merge two PDB




 

H.EDU
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, October 19, 2011 4:29 PM
Subject: Re: [ccp4bb] how can merge two PDB


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/Find Ligand are.

You already have a MR solution of the rest of your protein right ? So you are 
just asking how to make your life easier to not built de novo 45-50 residues ?


Jürgen


On Oct 19, 2011, at 10:00 AM, Ed Pozharski wrote:

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 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

present in PDB data bank so how can i put in to that electron density

i mean are there any ways to combine two Pdb in one molecule? 







I would be thankful for your help









Best Regards



AFSHAN















-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
   Julian, King of
 Lemurs


..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:      +1-410-614-4894
Fax:      +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] how can merge two PDB

[Miller, Mitchell D.]

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, October 19, 2011 8:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how can merge two PDB



 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?

Best Regards

AFSHAN








From: Afshan Begum afshan...@yahoo.com
To: Bosch, Juergen jubo...@jhsph.edu
Sent: Wednesday, October 19, 2011 4:58 PM
Subject: Re: [ccp4bb] how can merge two PDB




 

H.EDU
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, October 19, 2011 4:29 PM
Subject: Re: [ccp4bb] how can merge two PDB


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/Find Ligand are.

You already have a MR solution of the rest of your protein right ? So you are 
just asking how to make your life easier to not built de novo 45-50 residues ?


Jürgen

On Oct 19, 2011, at 10:00 AM, Ed Pozharski wrote:


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 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


present in PDB data bank so how can i put in to that electron 
density


i mean are there any ways to combine two Pdb in one molecule? 





I would be thankful for your help






Best Regards



AFSHAN










-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
   Julian, King of Lemurs



..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://web.mac.com/bosch_lab/

Re: [ccp4bb] Biological assembly

[Kayashree M]

Dear users,Thank you all for the suggestions.With RegardsKavya-- 
This message has been scanned for viruses and
dangerous content by
MailScanner, and is
believed to be clean.

Re: [ccp4bb] Biological assembly

[James Stroud]

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 that).

This last sentence is a bit vague. Can you take the just dimer that PISA 
predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly in 
density but retaining the dimeric relationship predicted by PISA), and then 
generate the complete lattice using just this fitted dimer and crystallographic 
symmetries?

If so, that means that the PISA dimer is equivalent to the ASU you can deposit 
the PISA dimer as the ASU.

James

[ccp4bb] WaterTidy fails in windows ccp4i

[Jacob Keller]

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 in XPLOR...

Jacob


#CCP4I VERSION CCP4Interface 2.1.0#CCP4I SCRIPT LOG watertidy#CCP4I
DATE 19 Oct 2011  12:30:14#CCP4I USER 'UNKNOWN'#CCP4I PROJECT
Tues2bot#CCP4I JOB_ID 18#CCP4I SCRATCH C:/Ccp4Temp#CCP4I HOSTNAME
chloe#CCP4I PID 9820
html !-- CCP4 HTML LOGFILE --hrpre
###
###
### ###
CCP4 6.2: DISTANG                  version 6.2 : 02/04/08##
### User:
Jacob  Run date: 19/10/2011 Run time: 12:30:15

 Please reference: Collaborative Computational Project, Number 4.
1994. The CCP4 Suite: Programs for Protein Crystallography. Acta
Cryst. D50, 760-763. as well as any specific reference in the program
write-up.

  Logical name: XYZIN  File name:
C:/Users/Jacob/Desktop/Dallos_Lab/3MGL_Crystals/APS_10_10_2011/jacob/2botnr3/TuesProcessing/Tues2bot_4.1_buccaneer2_refmac1.pdb
 PDB file is being opened on unit 1 for INPUT.
  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE

             RF                                  RO
    0.012  -0.000  -0.000  -0.000       82.115   0.000   0.000  -0.000
  -0.000   0.012  -0.000   0.000        0.000  82.115   0.000   0.000
  0.000  -0.000   0.006  -0.000        0.000   0.000 159.320  -0.000
-0.000   0.000  -0.000   1.000       -0.000   0.000  -0.000   1.000
 ARSE  after CALL       RBSPGRP(SPGRP)P 43 21 2   Data line--- title
[No title given] Data line--- distance     vdw     intra Data line---
symmetry P43212
 Spacegroup information obtained from library file:  Logical Name:
SYMINFO   Filename: C:\CCP4-Packages\ccp4-6.2.0\lib\data\syminfo.lib
 Data line--- radii     CA 1.5     C 1.5     N 1.5     O 1.5     SG
1.5     OW 1.5 Data line--- from     atom 1 to 20 Data line--- to
   atom  to  DISTANG:   *** Two  limits required***Times: User:
0.0s System:    0.0s Elapsed:     0:00
/pre/html
Information from CCP4Interface
script***The
program run with command: distang XYZIN
C:/Users/Jacob/Desktop/Dallos_Lab/3MGL_Crystals/APS_10_10_2011/jacob/2botnr3/TuesProcessing/Tues2bot_4.1_buccaneer2_refmac1.pdb
DISTOUT C:/Ccp4Temp/Tues2bot_18_1_log_1.tmp has failed with error
message DISTANG:   *** Two  limits
required**

#CCP4I TERMINATION STATUS 0  DISTANG:   *** Two  limits
required***#CCP4I TERMINATION TIME 19 Oct 2011  12:30:15#CCP4I
MESSAGE Task failed


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] WaterTidy fails in windows ccp4i

[Ed Pozharski]

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

Re: [ccp4bb] WaterTidy fails in windows ccp4i

[Jacob Keller]

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 one? There
is of course arp/warp, but not in windows...

Jacob



On Wed, Oct 19, 2011 at 1:32 PM, Ed Pozharski epozh...@umaryland.edu wrote:
 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





-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

[ccp4bb] buried surface area

[Jyotica Batra]

Dear users,

Are there any programs to calculate percentage of buried surface area that is 
polar vs nonpolar?

Thanks in advance

Thanks!
Jyotica

Re: [ccp4bb] WaterTidy fails in windows ccp4i

[Ed Pozharski]

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. It attempts to design an H2O naming system which gives some
information about the residue which a particular H2O is hydrogen
bonded to. The user inputs chain IDs for host chains and assigns
an output ID for the H2Os bonded to this chain.

 Is there a program in the gui that adds waters, if not this one? There
 is of course arp/warp, but not in windows...
 

There is an option in refmac gui to use coot to add waters.  If you
don't want to do extra refinement, just set the number of steps to 0.

-- 
Hurry up before we all come back to our senses!
   Julian, King of Lemurs

Re: [ccp4bb] buried surface area

[Ed Pozharski]

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
output:

http://apps.phar.umich.edu/tsodikovlab/index_files/Page756.htm



-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs

Re: [ccp4bb] Biological assembly

[Bostjan Kobe]

On 19/10/11 9:19 PM, eugene.krissi...@stfc.ac.uk
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 seems to me that this is not an unreasonable
suggestion and it would be nice if that were a common practice.

Maybe I am misunderstanding what you are saying Eugene, but the ASU
interface may not necessarily be the biological interface. I think it is
perfectly possible that two subunits in a biological dimer, for example,
may be related by crystallographic axis, but the NCS may be a different
non-physiological crystal contact, therefore the ASU won't be the same as
the biological dimer. So I am not sure if the above applies in general.

Bostjan

Bostjan Kobe
NHMRC Research Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences

and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology) and Centre for Infectious Disease Research


Cooper Road
University of Queensland
Brisbane, Queensland 4072
Australia
Phone: +61 7 3365 2132
Fax: +61 7 3365 4699
E-mail: b.k...@uq.edu.au
URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe
Office: Building 76 Room 329
Notice: If you receive this e-mail by mistake, please notify me, and do
not make any use of its contents. I do not waive any privilege,
confidentiality or copyright associated with it. Unless stated otherwise,
this e-mail represents only the views of the Sender and not the views of
The University of Queensland.

[ccp4bb] Job opening for a crystallographer to join the Structural Motility team at the Curie Institute Paris, France.

[Houdusse-Juille Anne]

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 (preference for a start in January 2012).

The Structural Motility group at the Institut Curie uses X-ray crystallography 
to solve atomic structures that are essential for the understanding of how 
molecular motors produce force, how their activity is regulated and how they 
are recruited to their cellular targets. Many of these motors are also involved 
in human pathologies and they are thus good targets for new therapies which we 
are helping to develop.
The research project of the new candidate aims at a better understanding of how 
molecular motors coordinate their action in the cell and what adaptation 
acquired by some of these motors allow specific functions to be performed. It 
consists of a biochemical, crystallogenesis and structural determination study 
of several complexes that involve molecular motors. Coupled with functional and 
cellular studies, this project will elucidate how these motors are regulated 
and what role they play in the context of a cell.
A solid experience in crystallization and X-ray structural determination is 
absolutely required.
Experience in the production and purification of recombinant proteins is a plus 
but we are ready to train a dynamic and motivated candidate.

If you are interested, please send a CV and a letter of motivation as well as a 
letter of recommendation of your previous employer.

Contact : Anne Houdusse (anne.houdu...@curie.frmailto:anne.houdu...@curie.fr)
http://umr144.curie.fr/en/research-groups/structural-motility-anne-houdusse/structural-motility-00199

Some publications
1- Mukherjea M, Llinas P, Kim H-J, Travaglia M, Safer D, Zong AB, Ménétrey J, 
Franzini-Armstrong C, Selvin PR, Houdusse A and Sweeney HL. Myosin VI 
dimerization triggers an unfolding of a 3-helix bundle in order to extend its 
reach.  Molecular Cell, 35:305-15, 2009.
2- Houdusse A, Carter AP. Dynein swings into action. Cell, 136:395-6, 2009.
3- Ménétrey J*, Llinas P*, Mukherjea M, Sweeney HL and Houdusse A. The 
structural basis for the large powerstroke of myosin VI. Cell 131:300-308, 2007.
4- Ménétrey J, Bahloul A, Wells AL, Yengo CM, Morris CA, Sweeney HL, Houdusse 
A. The structure of the myosin VI motor reveals the mechanism of directionality 
reversal. Nature (London) 435, 779-85, 2005.
5- Sweeney HL and Houdusse A, Myosin VI rewrites the rules for myosin motors, 
Cell, 141:573-82, 2010.

Re: [ccp4bb] Biological assembly

[Kayashree M]

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 while PISA predicts A1-B2.Thank youWith ReagrdsKavya-CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote: -To: CCP4BB@JISCMAIL.AC.UKFrom: James Stroud Sent by: CCP4 bulletin board Date: 10/19/2011 10:41PMSubject: Re: [ccp4bb] Biological assemblyOn 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 thisdimeric assembly is different from what is solved (offcoursewe can generate the symmetry equivalent molecule and get that).This last sentence is a bit vague. Can you take the just dimer that PISA predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly in density but retaining the dimeric relationship predicted by PISA), and then generate the complete lattice using just this fitted dimer and crystallographic symmetries?If so, that means that the PISA dimer is equivalent to the ASU you can deposit the PISA dimer as the ASU.James-- 
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