Re: [ccp4bb] How to run UPPSALA-mapman in PBS?

[Hailiang Zhang]

Hi Tim:

Thanks a lot for suggeting "exec" in my shell script. It really works
under both shell and PBS; however, the running was just terminated right
after "exec ${DIR}/lx_mapman" was excutated. I am not sure why this
happens:-(

Hailiang

> Hello Hailiang,
>
> On Wed, Jun 23, 2010 at 10:01:04PM -0400, Hailiang Zhang wrote:
>> Hi there:
>>
>> I downloaded the binary files of UPPSALA-mapman and they run smoothly
>> under linux. However, when I write it into a shell script and run under
>> PBS queue, it cannot be excuated. A simple test turned out to be:
>>
>> (1)
>> ***
>> [Linux] ./lx_mapman  ->works
>>
>> (2)
>> ***
>> [Linux]source ${ABSDIR}/lx_mapman ->-bash:ELF: command not found
> I do not know the PBS syntax, but this line cannot work: the bash command
> 'source' instructs bash to read in the content of the next argument and
> execute
> it as though it were a shell-script. That's the reason for the error
> message:
> The first word in a linux-binary is 'ELF' and that's not a bash command
> (luckily, who knows what might have happened if the rest of the binary had
> been
> interpreted by bash).
>
> Try replacing 'source' with 'exec'. If PBS forces you to have the 'source'
> keyword there (which I would find odd) create a wrapper script 'mapman.sh'
> into
> which you write 'exec ${ABSDIR}/lx_mapman $*'.
>
> Tim
>
>>
>> It seems that only (2) can be directly implemented under PBS
>> environment.
>> I am wondering whether there is a way to circumstance this problem.
>>
>> Best Regards, Hailiang
>
> --
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>

Re: [ccp4bb] How to run UPPSALA-mapman in PBS?

[Tim Gruene]

Hello Hailiang,

On Wed, Jun 23, 2010 at 10:01:04PM -0400, Hailiang Zhang wrote:
> Hi there:
> 
> I downloaded the binary files of UPPSALA-mapman and they run smoothly
> under linux. However, when I write it into a shell script and run under
> PBS queue, it cannot be excuated. A simple test turned out to be:
> 
> (1)
> ***
> [Linux] ./lx_mapman  ->works
> 
> (2)
> ***
> [Linux]source ${ABSDIR}/lx_mapman ->-bash:ELF: command not found
I do not know the PBS syntax, but this line cannot work: the bash command
'source' instructs bash to read in the content of the next argument and execute
it as though it were a shell-script. That's the reason for the error message:
The first word in a linux-binary is 'ELF' and that's not a bash command
(luckily, who knows what might have happened if the rest of the binary had been
interpreted by bash).

Try replacing 'source' with 'exec'. If PBS forces you to have the 'source'
keyword there (which I would find odd) create a wrapper script 'mapman.sh' into
which you write 'exec ${ABSDIR}/lx_mapman $*'.

Tim

> 
> It seems that only (2) can be directly implemented under PBS environment.
> I am wondering whether there is a way to circumstance this problem.
> 
> Best Regards, Hailiang

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

GPG Key ID = A46BEE1A



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[ccp4bb] How to run UPPSALA-mapman in PBS?

[Hailiang Zhang]

Hi there:

I downloaded the binary files of UPPSALA-mapman and they run smoothly
under linux. However, when I write it into a shell script and run under
PBS queue, it cannot be excuated. A simple test turned out to be:

(1)
***
[Linux] ./lx_mapman  ->works

(2)
***
[Linux]source ${ABSDIR}/lx_mapman ->-bash:ELF: command not found

It seems that only (2) can be directly implemented under PBS environment.
I am wondering whether there is a way to circumstance this problem.

Best Regards, Hailiang

Re: [ccp4bb] Modified Arginine Coot and SHELX

[SIPPEL,KATHERINE H]

Since no one has answered the SHELX part of this question I'll 
jump in. The PRODRG restraints should work as is, assuming you've 
named the peptide atoms correctly (C, O, CA, N). But just in case 
they don't you can explicitly attach it to the main chain with the 
addition of a couple of spare restraints. The ones I've listed 
below are for a protein I work on whose numbering convention lacks 
residue 126 for some unfathomable reason. You'd need a set of 
these for both the preceding and following residues.


DFIX C_125 N_127 1.329
DANG O_125 N_127 2.250
DANG CA_125 N_127 2.425
DANG C_125 CA_127 2.435
FLAT 0.3 O_125 CA_125 N_127 C_125 CA_127
RTAB Omeg CA_125 C_125 N_127 CA_127
RTAB Phi C_125 N_127 CA_127 C_127
RTAB Psi N_125 CA_125 C_125 N_127

Hope this helps,

Katherine

On Wed Jun 23 12:10:33 EDT 2010, Paul Emsley 
 wrote:



On 23/06/10 14:40, Fatima wrote:

Dear all,

I'm finishing a refinement using SHELX and Coot (1.3A) and I 
have a modified Arginine. There???s a blob of positive density 
(9.04 and 7.01 sigma) binding NH2 in the 2 conformations. I 
think it could be a hydroxyl there.


1) How can I add that in Coot?



Centre on the residue you want to replace, then,

Extensions -> Modelling -> Replace Residue -> HAR -> Mutate

(that presumes that you have want an N-omega-hydroxyl-arginine)


2) Does SHELXL recognise modified residues?



Hmm... pass.


How can I get restraints then, by using PRODRG?



Libcheck (in this case). Coot runs libcheck for you.

Paul.






--
SIPPEL,KATHERINE H
Ph. D. candidate
McKenna Lab
Department of Biochemistry and Molecular Biology
College of Medicine
University of Florida

Re: [ccp4bb] Multiple NCS relations

[David Schuller]

I think you should be able to specify two different "NCSR" lines, one to 
cover chains A&A' and C&C', and another to cover chains B&B'.



On 06/23/10 18:51, Oganesyan, Vaheh wrote:

Dear bb contributors,

I would like to refer to your expertise and get advice regarding
multiple NCS relations between two macromolecular complexes in asu.
Resolution 2.5A, s.g. C2221, R-merge 6%, synchrotron data, 2 complexes
per a.s.u. Each complex consist of three polypeptide chains, let's say
A, B, C and A', B' and C'. A and A' have one NCS operator and B and B'
have another. C molecule follows A.
When I impose ncs in refinement my R-factors jump to ~30(35)% while
without they are around 21(27)%.
Does this mean that I can not use two different NCS operators or it
means I'm not applying ncs correctly?

I'm using refmac5 with TLS through GUI.

Thank you.

  Vaheh

P.S. I don't remember if such question have ever been discussed on bb.




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--
===
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===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] Multiple NCS relations

[Oganesyan, Vaheh]

Dear bb contributors,

I would like to refer to your expertise and get advice regarding
multiple NCS relations between two macromolecular complexes in asu. 
Resolution 2.5A, s.g. C2221, R-merge 6%, synchrotron data, 2 complexes
per a.s.u. Each complex consist of three polypeptide chains, let's say
A, B, C and A', B' and C'. A and A' have one NCS operator and B and B'
have another. C molecule follows A. 
When I impose ncs in refinement my R-factors jump to ~30(35)% while
without they are around 21(27)%. 
Does this mean that I can not use two different NCS operators or it
means I'm not applying ncs correctly?

I'm using refmac5 with TLS through GUI.

Thank you.  

 Vaheh 

P.S. I don't remember if such question have ever been discussed on bb. 




To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary.  This communication is expected 
to be read and/or used only by the individual(s) for whom it is intended.  If 
you have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose.  Thank you for your 
cooperation.

Re: [ccp4bb] Multiple ligand refinement

[xaravich ivan]

Thank you Tim and Partha,
The reason I do not have clear density of my ligands ( at 1.15 Angs) is that
I have a native-active enzyme complexed with substrate and product forming
at the active site. We have reason to believe from our enzyme kinetics data
that we would be able to capture both the states. The structure shows the
overall density of a substrate forming a product but the distinction is not
clear before any refinement of the individual ligands. I am sure that
correct refinement with partial occupation of substrate and product should
do it. Hence my question.

Thanks,
Ivan

On Tue, Jun 22, 2010 at 11:10 PM, Tim Gruene wrote:

> Dear Ivan,
>
>
>
> On Tue, Jun 22, 2010 at 11:06:08AM -0700, xaravich ivan wrote:
> > Hi all,
> > How can I refine multiple ligands( metall ions and other organic
> molecules)
> > and in the same structure? I guess Refmac automatically generates
> restraints
> > for common metal ions, but how could I put multiple pdbs and cif files of
> > molecules in my Refmac cycles other than just metal ions.
> you do not need multiple PDB-files. You can put all structures into one
> file.
> You help the programs distinguish them by using a separate chain ID for
> each
> molecule (waters can have all the same one, though).
> >
> > In my case even Arp ligand can only find one ligand in one of the sites
> > (1.15 Angs data). Is there a way to use the partially ligand fitted
> > structure to find the second ligand. Or is there a similar thing as
> > superpose that would give me the rough coordinates of the ligands in the
> > second site.
> At 1.15A you should see clear density for the ligand. If you do not, make
> sure
> that you do not fit something you only wish to be there.
>
> To answer you question: You could assign the same chain ID to the ligand
> and to
> the main molecule. Then, upon using this main molecule for superposition,
> the
> ligand is moved, too
>
> Tim
>
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.9 (GNU/Linux)
>
> iD8DBQFMIaVQUxlJ7aRr7hoRAmJnAJ9GJMVdDpq+6AjVCpcgEjC6SZVKKgCeN46X
> MbXcANyz66SLxlrC4PI4Ie0=
> =/Sa9
> -END PGP SIGNATURE-
>
>

[ccp4bb] SOLVED: Re: [ccp4bb] pymol python and cctbx

[Tim Gruene]

Dear all who answered,

the combination of 
- compiling cctbx from source
- modifying the pymol startup script to source the cctbx setpaths.sh AND use
  cctbx.python (instead of /usr/bin/python) eventually works.

Thanks to all the responses to make this work.

Tim

On Wed, Jun 23, 2010 at 01:02:03PM -0400, Robert Campbell wrote:
> On Wed, 23 Jun 2010 09:07:36 -0400 "Schubert, Carsten [PRDUS]"
>  wrote:
> 
> > Tim,
> > 
> > I'm shooting from the hip here, but I think the problem is that cctbx
> > comes with its own python, which you would need to run both pymol and
> > numpy under. According to Ralf it is at least not trivial to utilize the
> > system python to run cctbx. So I think you need to compile/install pymol
> > against cctbx.python and install it as a module under cctbx.python.
> > Similar deal for numpy, which may already be available in cctbx, if not
> > installation should be straightforward.
> > 
> > These broad steps may work (again shooting from the hip...)
> > -Install cctbx
> > -link cctbx.python to python and make sure its first in your path (may
> > be optional)
> > -install numpy under cctbx.python (if not already present)
> > -compile and install open.pymol against the cctbx.python, either via the
> > renaming trick 
> >  above or calling cctbx.python setup.py (build/install)
> > 
> > Good luck, let us know how it works...
> 
> I have no trouble running cctbx with pymol using the system python for both.
> I also use Debian testing and various Ubuntu versions.  To do so I
> install cctbx from the sources. I have a web page with instructions for using
> pymol and cctbx together at:
> 
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/cctbx/
> 
> In short, I install cctbx using the self-extracting *source* not a
> precompiled version.  Go to http://cci.lbl.gov/cctbx_build/ and scroll down to
> "Self-extracting cctbx sources for Unix".
> 
> Once that installation is done, I go to where the cctbx.python script is (in
> the /cctbx_build/bin directory). I then make a link to that called
> python:  (i.e. ln -s cctbx.python python).
> 
> Then to make sure that pymol "sees" the cctbx modules, I make sure
> that the command in the startup script for pymol has just "python", not
> "/usr/bin/python" in it so then it ends up running cctbx.python.  (The setup
> scripts for cctbx will place its directory and the *beginning* of the PATH
> environment variable).
> 
> I hope this helps,
> Rob
> -- 
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor 
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University, 
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821Fax: 613-533-2497
> http://pldserver1.biochem.queensu.ca/~rlc

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

GPG Key ID = A46BEE1A



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Re: [ccp4bb] pymol python and cctbx

[Robert Campbell]

On Wed, 23 Jun 2010 09:07:36 -0400 "Schubert, Carsten [PRDUS]"
 wrote:

> Tim,
> 
> I'm shooting from the hip here, but I think the problem is that cctbx
> comes with its own python, which you would need to run both pymol and
> numpy under. According to Ralf it is at least not trivial to utilize the
> system python to run cctbx. So I think you need to compile/install pymol
> against cctbx.python and install it as a module under cctbx.python.
> Similar deal for numpy, which may already be available in cctbx, if not
> installation should be straightforward.
> 
> These broad steps may work (again shooting from the hip...)
> -Install cctbx
> -link cctbx.python to python and make sure its first in your path (may
> be optional)
> -install numpy under cctbx.python (if not already present)
> -compile and install open.pymol against the cctbx.python, either via the
> renaming trick 
>  above or calling cctbx.python setup.py (build/install)
> 
> Good luck, let us know how it works...

I have no trouble running cctbx with pymol using the system python for both.
I also use Debian testing and various Ubuntu versions.  To do so I
install cctbx from the sources. I have a web page with instructions for using
pymol and cctbx together at:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/cctbx/

In short, I install cctbx using the self-extracting *source* not a
precompiled version.  Go to http://cci.lbl.gov/cctbx_build/ and scroll down to
"Self-extracting cctbx sources for Unix".

Once that installation is done, I go to where the cctbx.python script is (in
the /cctbx_build/bin directory). I then make a link to that called
python:  (i.e. ln -s cctbx.python python).

Then to make sure that pymol "sees" the cctbx modules, I make sure
that the command in the startup script for pymol has just "python", not
"/usr/bin/python" in it so then it ends up running cctbx.python.  (The setup
scripts for cctbx will place its directory and the *beginning* of the PATH
environment variable).

I hope this helps,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
http://pldserver1.biochem.queensu.ca/~rlc

Re: [ccp4bb] pymol python and cctbx

[Nat Echols]

On Wed, Jun 23, 2010 at 8:21 AM, Graeme Winter  wrote:

> There will be a cctbx.python dispatcher now which should set
> everything up - however if you source setpaths_debug I think this
> should make for a happy python as it includes everything from the
> dispatcher.
>

Don't use setpaths_debug - it pollutes the environment and is probably going
to be removed in the near future.  Otherwise, Graeme is correct, you need to
run cctbx.python to access the CCTBX modules.  You will still be able to
access any modules already available to the python interpreter that you used
to build CCTBX (i.e. /usr/bin/python in this case).  It is also possible to
modify the "pymol.com" script (created by setup2.py in the PyMOL
distribution) to use cctbx.python (it just needs to source setpaths.sh from
the CCTBX build directory).

Maybe we will incorporate this into the Phenix installer in the future - the
only drawback to this is that it will probably be missing the Tkinter
"external" GUI for PyMOL.

-Nat

Re: [ccp4bb] Modified Arginine Coot and SHELX

[Paul Emsley]

On 23/06/10 14:40, Fatima wrote:

Dear all,

I'm finishing a refinement using SHELX and Coot (1.3A) and I have a modified 
Arginine. There’s a blob of positive density (9.04 and 7.01 sigma) binding NH2 
in the 2 conformations. I think it could be a hydroxyl there.

1) How can I add that in Coot?
   


Centre on the residue you want to replace, then,

Extensions -> Modelling -> Replace Residue -> HAR -> Mutate

(that presumes that you have want an N-omega-hydroxyl-arginine)


2) Does SHELXL recognise modified residues?



Hmm... pass.


How can I get restraints then, by using PRODRG?
   


Libcheck (in this case). Coot runs libcheck for you.

Paul.

Re: [ccp4bb] pymol python and cctbx

[Graeme Winter]

Hi Tim,

There will be a cctbx.python dispatcher now which should set
everything up - however if you source setpaths_debug I think this
should make for a happy python as it includes everything from the
dispatcher.

At least, that was my understanding.

best wishes,

Graeme

On 23 June 2010 16:17, Tim Gruene  wrote:
> Ok, I just did that.
> After sourcing setpaths.sh, PYTHONHOME is set to /path/to/cctbx_build
>
> When I start python and enter
> from cctbx import sgtbx
>
> I get an error message about a missing __init__.py
>
> The whole cctbx_build does not contain a single __init__.py\*, but there are
> plenty in ../cctbx_sources.
>
> I don't think I missed a step as explained on the page given below. Did I miss
> anything else?
>
> The tests worked fine, I only noticed OK's.
>
> Since the page describes libtbx.scons to be similar to make, do I have to 
> issue
> something like 'libtbx.scons install' after everything was built?
>
> Cheers, Tim
>
> On Wed, Jun 23, 2010 at 03:27:32PM +0100, Graeme Winter wrote:
>> Dear Tim,
>>
>> There are instructions on how to build cctbx against your system
>> Python (which I assume is the one used by PyMol) here:
>>
>> http://cctbx.sourceforge.net/current/installation.html#manually-building-from-sources-under-unix
>>
>> >From there you can also install other Python modules e.g. Numpy in the
>> usual manner, assuming you do not already have these installed.
>>
>> Best wishes,
>>
>> Graeme
>>
>> On 23 June 2010 15:23, Tim Gruene  wrote:
>> > Dear Carsten,
>> >
>> > thank you for the instruction. The cctbx package seems to lack tkinter 
>> > which is
>> > required by pymol (and maybe numpy, too). How do I install a specific 
>> > python
>> > module (package? what's the correct term?) 'under' cctbx.python?
>> >
>> > Cheers, Tim
>> >
>> > On Wed, Jun 23, 2010 at 09:07:36AM -0400, Schubert, Carsten [PRDUS] wrote:
>> >> Tim,
>> >>
>> >> I'm shooting from the hip here, but I think the problem is that cctbx
>> >> comes with its own python, which you would need to run both pymol and
>> >> numpy under. According to Ralf it is at least not trivial to utilize the
>> >> system python to run cctbx. So I think you need to compile/install pymol
>> >> against cctbx.python and install it as a module under cctbx.python.
>> >> Similar deal for numpy, which may already be available in cctbx, if not
>> >> installation should be straightforward.
>> >>
>> >> These broad steps may work (again shooting from the hip...)
>> >> -Install cctbx
>> >> -link cctbx.python to python and make sure its first in your path (may
>> >> be optional)
>> >> -install numpy under cctbx.python (if not already present)
>> >> -compile and install open.pymol against the cctbx.python, either via the
>> >> renaming trick
>> >>  above or calling cctbx.python setup.py (build/install)
>> >>
>> >> Good luck, let us know how it works...
>> >>
>> >>       Carsten
>> >>
>> >>
>> >>
>> >> > -Original Message-
>> >> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
>> >> > Tim Gruene
>> >> > Sent: Wednesday, June 23, 2010 8:35 AM
>> >> > To: CCP4BB@JISCMAIL.AC.UK
>> >> > Subject: [ccp4bb] pymol python and cctbx
>> >> >
>> >> > Dear all,
>> >> >
>> >> > I've been trying to install the SuperSym module for pymol (svn trunk
>> >> > version of pymol as of today, 1.3.x). Upon restart the console says
>> >> > "Ooops!  SuperSym requires cctbx and numeric python to function.
>> >> Please
>> >> > install these."
>> >> >
>> >> > The system is i7 with Debian Testing 64bit with python2.5 (although
>> >> > python2.6 is also installed but not the default). cctbx was installed
>> >> > using cctbx_fedora8_x86_64_py265_inc.selfx and the installation output
>> >> > did not imply any issues, e.g. about the wrong python version (and I
>> >> > did only find cctbx packages for python 2.6.5 on their web site).
>> >> >
>> >> > python-numpy is install which I believe is the "numeric python" the
>> >> > module output complains about.
>> >> >
>> >> > Would anyone be so kind to direct someone who despises python (phyuuu,
>> >> > that
>> >> > helped...) to how to get the SuperSym module to work with pymol? A
>> >> > start would be if the module would tell me whether it complains about
>> >> > missing numeric python or cctbx or both.
>> >> >
>> >> > Do I have to compile pymol with python2.6? Just starting pymol with
>> >> > python2.6 did not change anything.
>> >> >
>> >> > Thanks a lot, Tim
>> >> >
>> >> >
>> >> > --
>> >> > Tim Gruene
>> >> > Institut fuer anorganische Chemie
>> >> > Tammannstr. 4
>> >> > D-37077 Goettingen
>> >> >
>> >> > GPG Key ID = A46BEE1A
>> >
>> > --
>> > --
>> > Tim Gruene
>> > Institut fuer anorganische Chemie
>> > Tammannstr. 4
>> > D-37077 Goettingen
>> >
>> > GPG Key ID = A46BEE1A
>> >
>> >
>> > -BEGIN PGP SIGNATURE-
>> > Version: GnuPG v1.4.9 (GNU/Linux)
>> >
>> > iD8DBQFMIhjbUxlJ7aRr7hoRAtF0AJoD+AosjYDnPShy5T4+rh/4xiABUQCg+Amu
>> > nmxBu9tMBneoDCfxsWxQyPc=
>> > =WL5a
>> > -END PGP SIGNATUR

Re: [ccp4bb] pymol python and cctbx

[Tim Gruene]

Ok, I just did that.
After sourcing setpaths.sh, PYTHONHOME is set to /path/to/cctbx_build

When I start python and enter
from cctbx import sgtbx

I get an error message about a missing __init__.py

The whole cctbx_build does not contain a single __init__.py\*, but there are
plenty in ../cctbx_sources.

I don't think I missed a step as explained on the page given below. Did I miss
anything else?

The tests worked fine, I only noticed OK's.

Since the page describes libtbx.scons to be similar to make, do I have to issue
something like 'libtbx.scons install' after everything was built?

Cheers, Tim

On Wed, Jun 23, 2010 at 03:27:32PM +0100, Graeme Winter wrote:
> Dear Tim,
> 
> There are instructions on how to build cctbx against your system
> Python (which I assume is the one used by PyMol) here:
> 
> http://cctbx.sourceforge.net/current/installation.html#manually-building-from-sources-under-unix
> 
> >From there you can also install other Python modules e.g. Numpy in the
> usual manner, assuming you do not already have these installed.
> 
> Best wishes,
> 
> Graeme
> 
> On 23 June 2010 15:23, Tim Gruene  wrote:
> > Dear Carsten,
> >
> > thank you for the instruction. The cctbx package seems to lack tkinter 
> > which is
> > required by pymol (and maybe numpy, too). How do I install a specific python
> > module (package? what's the correct term?) 'under' cctbx.python?
> >
> > Cheers, Tim
> >
> > On Wed, Jun 23, 2010 at 09:07:36AM -0400, Schubert, Carsten [PRDUS] wrote:
> >> Tim,
> >>
> >> I'm shooting from the hip here, but I think the problem is that cctbx
> >> comes with its own python, which you would need to run both pymol and
> >> numpy under. According to Ralf it is at least not trivial to utilize the
> >> system python to run cctbx. So I think you need to compile/install pymol
> >> against cctbx.python and install it as a module under cctbx.python.
> >> Similar deal for numpy, which may already be available in cctbx, if not
> >> installation should be straightforward.
> >>
> >> These broad steps may work (again shooting from the hip...)
> >> -Install cctbx
> >> -link cctbx.python to python and make sure its first in your path (may
> >> be optional)
> >> -install numpy under cctbx.python (if not already present)
> >> -compile and install open.pymol against the cctbx.python, either via the
> >> renaming trick
> >>  above or calling cctbx.python setup.py (build/install)
> >>
> >> Good luck, let us know how it works...
> >>
> >>       Carsten
> >>
> >>
> >>
> >> > -Original Message-
> >> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> >> > Tim Gruene
> >> > Sent: Wednesday, June 23, 2010 8:35 AM
> >> > To: CCP4BB@JISCMAIL.AC.UK
> >> > Subject: [ccp4bb] pymol python and cctbx
> >> >
> >> > Dear all,
> >> >
> >> > I've been trying to install the SuperSym module for pymol (svn trunk
> >> > version of pymol as of today, 1.3.x). Upon restart the console says
> >> > "Ooops!  SuperSym requires cctbx and numeric python to function.
> >> Please
> >> > install these."
> >> >
> >> > The system is i7 with Debian Testing 64bit with python2.5 (although
> >> > python2.6 is also installed but not the default). cctbx was installed
> >> > using cctbx_fedora8_x86_64_py265_inc.selfx and the installation output
> >> > did not imply any issues, e.g. about the wrong python version (and I
> >> > did only find cctbx packages for python 2.6.5 on their web site).
> >> >
> >> > python-numpy is install which I believe is the "numeric python" the
> >> > module output complains about.
> >> >
> >> > Would anyone be so kind to direct someone who despises python (phyuuu,
> >> > that
> >> > helped...) to how to get the SuperSym module to work with pymol? A
> >> > start would be if the module would tell me whether it complains about
> >> > missing numeric python or cctbx or both.
> >> >
> >> > Do I have to compile pymol with python2.6? Just starting pymol with
> >> > python2.6 did not change anything.
> >> >
> >> > Thanks a lot, Tim
> >> >
> >> >
> >> > --
> >> > Tim Gruene
> >> > Institut fuer anorganische Chemie
> >> > Tammannstr. 4
> >> > D-37077 Goettingen
> >> >
> >> > GPG Key ID = A46BEE1A
> >
> > --
> > --
> > Tim Gruene
> > Institut fuer anorganische Chemie
> > Tammannstr. 4
> > D-37077 Goettingen
> >
> > GPG Key ID = A46BEE1A
> >
> >
> > -BEGIN PGP SIGNATURE-
> > Version: GnuPG v1.4.9 (GNU/Linux)
> >
> > iD8DBQFMIhjbUxlJ7aRr7hoRAtF0AJoD+AosjYDnPShy5T4+rh/4xiABUQCg+Amu
> > nmxBu9tMBneoDCfxsWxQyPc=
> > =WL5a
> > -END PGP SIGNATURE-
> >
> >

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

GPG Key ID = A46BEE1A



signature.asc
Description: Digital signature

Re: [ccp4bb] Merohedral twining for P212121.

[John R Helliwell]

Dear Colleagues,
I hope the following detailed review will be of help both with terminology
as well as case studies of a wide variety of kinds, including possible
approaches for moving forward, regarding the various manifestations of
twinning, lattice disorders and multiple crystals.
Best wishes,
John
Prof John R Helliwell

J.R. Helliwell “Macromolecular crystal twinning, lattice disorders and
multiple crystals” Crystallography Reviews (2008) 14, 189-250.







On Tue, Jun 22, 2010 at 5:35 PM, Ian Tickle  wrote:

> On Tue, Jun 22, 2010 at 4:32 PM, Colin Nave 
> wrote:
> > Secondly, the difference in the cell dimensions (b=123.92 and c=128.89A)
> > appears to be quite large and should lead to split spots which (I think)
> > corresponds to non merohedral twinning. Did you observe these but
> integrated
> > them as one?
>
> The distinction between merohedry (incl. pseudo-merohedry) and
> non-merohedral twinning is not whether the spots are split: splitting
> to a greater or lesser degree is often observed in the
> pseudo-merohedral case since the pseudo-twin law is never perfect.
> Rather the defining feature is whether the overlap of the twin-related
> lattices occurs in 3 dimensions (i.e. exact overlap for merohedry, or
> approximate for pseudo-merohedry) or only 2 in the non-merohedral
> case.  In the latter case this means that there's no obvious
> relationship between the spot positions for the components of the twin
> (except possibly in the zone related to the plane of 2-D overlap).
>
> Cases where 3-D overlap occurs only for some integer fraction of the
> spots are often mistakenly termed 'non-merohedral' even though overlap
> occurs in 3-D and so there's a clear relationship for the fraction of
> spots that are twin-related.  The correct term for this case is
> 'reticular merohedry' (or 'reticular pseudo-merohedry').  A nice site
> where all the twinning terminology is clearly defined is:
>
> http://www.lcm3b.uhp-nancy.fr/mathcryst/twins.htm
>
> > (Regarding what to call the twinning I have some sympathies with Humpty
> > Dumpty's view "When I use a word... it means just what I choose it to
> > mean-neither more nor less" As important a philosopher as Wittgenstein.)
>
> But it helps a lot if everyone can agree on the terminology (e.g. on
> the precise definition of 'non-merohedral') - most of the arguments on
> the BB seem to stem from the use of conflicting definitions!
>
> Cheers
>
> -- Ian
>



-- 
Professor John R Helliwell DSc

Re: [ccp4bb] Impact Factor of Acta Crystallographica A is 49.9

[George M. Sheldrick]

Thankyou Tassos, Kay and others for the congratulations. Maybe I should 
put it in perspective:

Most of the people citing SHELX were small molecule crystallographers,
who do not feel obliged to cite the programs they used only in the 
supplementary material.

If you want to be cited you have to write the paper! I had been putting 
off writing this paper for the last 30 years until several Acta Editors 
succeeded in twisting my arm so hard that I wrote it. Speaking as a hobby 
programmer, it is much more fun to write programs than papers.

Fortunately the small molecule community are also helping to increase 
the impact factor of Acta Crystallographica Section D for 2010. The paper 
"Structure validation in chemical crystallography", 65 (2009) 148-155 by 
Ton Spek has already been cited 1751 times and is currently at position 
12 in http://www.info.scopus.com/topcited/ (it is a standard reference
for Ton's CIFCHECK program that is almost universally used for checking 
small molecule refinements before deposition).

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582


On Wed, 23 Jun 2010, Kay Diederichs wrote:

> Dear Tassos,
> 
> thanks for alerting us to this unexpected but welcome fact!
> I would like to take the opportunity to
> 
> a) congratulate George Sheldrick!
> 
> b) point out to the CCP4 community that we decide ourselves about the
> impact factors of journals that are important for our work:
> specifically, if we would cite Acta Cryst (and JAC) papers in our own
> articles, then this is what will raise (or rather, keep up) the impact
> factor of Acta Cryst in the next years. In other words, please _do_ cite
> the individual programs (separately!) that you use to solve and refine
> your structure, as suggested under "Referencing CCP4 etc" at
> http://www.ccp4.ac.uk/about.php . And cite these papers in the main
> article, not only in the "supporting material" (I surely will need to
> revise my own citing behaviour).
> Ultimately, those of us publishing in Acta Cryst and related journals
> will benefit from this, too. (whether it will suffice for tenure for
> methods-related work is still an open question)
> 
> c) point out that it is of little use to researchers if a review is
> cited instead of their original work.
> 
> thanks,
> 
> Kay
> 
> Anastassis Perrakis schrieb:
> > Dear all,
> > 
> > We are all used to the tyranny of impact factors: high impact
> > publication in "well esteemed" journals, as dictated by the Supreme
> > Authority - excuse me, I meant  Thomson Reuters - often substitutes the
> > judgement of interview panels, grant review panels and sometimes is a
> > decision-maker for lazy referees. A 'high impact' publication in your CV
> > often counts as much as consistent work done for years and is considered
> > the gateway for good jobs and careers. And, alas, your Acta Cryst
> > papers, would not count ...
> > 
> > Since yesterday though, a single person, no other than the ccp4bb
> > bulletin board subscriber and contributor, and an emblematic figure of
> > our community, George Sheldrick, has managed with one action to showcase
> > the flaws of this system. Since yesterday, officially, the top ranking
> > journal according to the official Thomson Reuters Impact factor is: Acta
> > Crystallographica Part A. How was that made possible? Simply by
> > publishing a 'short history about SHELX' and requesting users to cite
> > it. It took two years, but now Acta A has displaced Cell, Nature,
> > Science and even New England Journal of Medicine from the top ranks.
> > 
> > Well, good luck to all the methods-folk who are up for tenure, here is
> > your chance guys and girls ... it will not last long!!!
> > 
> > Best regards,
> > 
> > Tassos
> > 
> > Specifically, the publication with second highest impact factor in the
> > "science" category is/Acta Crystallographica - Section A/, knocking none
> > other than the/New England Journal of Medicine/from the runner's up
> > position. This title's impact factor rocketed up to 49.926 this year,
> > more than 20-fold higher than last year. A single article published in a
> > 2008 issue of the journal seems to be responsible for the meteoric rise
> > in the/Acta Crystallographica - Section A/'s impact factor."A short
> > history of SHELX,"
> > by
> > University of Göttingen crystallographerGeorge Sheldrick,
> > which reviewed the
> > development of the computer system SHELX, has been cited more than 6,600
> > times, according to ISI. This paper includes a sentence that essentially
> > instructs readers to cite the paper they're reading -- "This paper could
> > serve as a general literature citation when one or more of the
> > open-source SHELX programs (and the Bruker AXS version SHELXTL) are
> > employed 

Re: [ccp4bb] Stuck refinement

[Francis E Reyes]

Sorry a late comer to this thread but the OP mentioned "tweaking the  
error model" in HKL2000. I have heard this before.What's the validity  
in this? Does it actually help or does it only help the integration  
numbers but you'll pay for it during refinement?

FR

On Jun 23, 2010, at 8:25 AM, "Zhou, Tongqing (NIH/VRC) [E]" > wrote:



Hi All,

The problem has also been solved with a new 2.0A dataset collected  
over the last weekend. Same space group and dimensions, much less  
radiation damage. This time I used APS SER-CAT's weaker BM beamline.


Thanks,


Tongqing

Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
**
The information in this e-mail and any of its attachments is  
confidential and may contain sensitive information. It should not be  
used by anyone who is not the original intended recipient. If you  
have received this e-mail in error please inform the sender and  
delete it from your mailbox or any other storage devices. National  
Institute of Allergy and Infectious Diseases shall not accept  
liability for any statements made that are sender's own and not  
expressly made on behalf of the NIAID by one of its representatives.

**


-Original Message-
From: Zhou, Tongqing (NIH/VRC) [E]
Sent: Tuesday, June 15, 2010 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Stuck refinement

Hi, Everyone,

Thank you all very much  for the nice suggestions. I am trying to  
reply within this email.


I agree that the problem may be rooted from the crystal itself, we  
noticed during data collection that a wedge of the rotation was very  
mosaic, HKL2000 was able to pick up the right spots, but the scaling  
gives high chi^2, and when I used the rejection files, HKL2000  
complained "more than 5 rejections". Colleagues suggested  
tweaking the error model, the complaint of "more than 5  
rejections' went away and rejection dropped to below 300 spots. The  
new error model reduced the chi^2 as well as the I/sigI in the low  
resolution shells.


I run the P222 data set with Xtriage, the report says no twining,  
but the symmetry was too low. However, HKL2000 won't even pick up  
higher symmetry groups during indexing. I also rescaled the data  
omitting the bad wedge, xtriage gives "normal" report.



Refinement was done with combination of simulated annealing, TLS,  
ADP, individual sites in Phenix. The molecular replacement was done  
with CDR-loop-trimmed antibody Fab and antigen structures. The map  
quality was good and I was able to rebuild the new loops without any  
problem.


I will have beam time later this week, I think it will be better to  
put a better crystal on.


Best regards,


Tongqing

Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
**
The information in this e-mail and any of its attachments is  
confidential and may contain sensitive information. It should not be  
used by anyone who is not the original intended recipient. If you  
have received this e-mail in error please inform the sender and  
delete it from your mailbox or any other storage devices. National  
Institute of Allergy and Infectious Diseases shall not accept  
liability for any statements made that are sender's own and not  
expressly made on behalf of the NIAID by one of its representatives.

**


-Original Message-
From: Eleanor Dodson [mailto:c...@ysbl.york.ac.uk]
Sent: Tuesday, June 15, 2010 4:46 AM
To: Zhou, Tongqing (NIH/VRC) [E]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Stuck refinement

  When this happens, I firstly suspect that the spacegroup may be  
wrong.  We had a case where the symmetry was pseudo I4212 but was  
really
I222 (or was it really I212121) Anyway most of the structure obeyed  
the

I41212 symmetry but there was a tail which did not..)

Feed the unmerged reflections into pointless and see what it suggests

Eleanor

Zhou, Tongqing (NIH/VRC) [E] wrote:

Hi Everyone,

I have some problem in refining a structure. The data goes to 2.4A  
(with some 30% completeness at 2.15A), the structure was solved by  
MR with Phaser, refinement was done with Phenix, but the r and r- 
free are now staying at 26% and 32%, even with all possible waters  
and missing fragments added. Data was collected at APS at cryo  
condition. One thing I noticed during HKL2000 data processing was  
that the chi^2 were way too high at lower resolutions shells,  I  
had to adj

Re: [ccp4bb] pymol python and cctbx

[Graeme Winter]

Dear Tim,

There are instructions on how to build cctbx against your system
Python (which I assume is the one used by PyMol) here:

http://cctbx.sourceforge.net/current/installation.html#manually-building-from-sources-under-unix

>From there you can also install other Python modules e.g. Numpy in the
usual manner, assuming you do not already have these installed.

Best wishes,

Graeme

On 23 June 2010 15:23, Tim Gruene  wrote:
> Dear Carsten,
>
> thank you for the instruction. The cctbx package seems to lack tkinter which 
> is
> required by pymol (and maybe numpy, too). How do I install a specific python
> module (package? what's the correct term?) 'under' cctbx.python?
>
> Cheers, Tim
>
> On Wed, Jun 23, 2010 at 09:07:36AM -0400, Schubert, Carsten [PRDUS] wrote:
>> Tim,
>>
>> I'm shooting from the hip here, but I think the problem is that cctbx
>> comes with its own python, which you would need to run both pymol and
>> numpy under. According to Ralf it is at least not trivial to utilize the
>> system python to run cctbx. So I think you need to compile/install pymol
>> against cctbx.python and install it as a module under cctbx.python.
>> Similar deal for numpy, which may already be available in cctbx, if not
>> installation should be straightforward.
>>
>> These broad steps may work (again shooting from the hip...)
>> -Install cctbx
>> -link cctbx.python to python and make sure its first in your path (may
>> be optional)
>> -install numpy under cctbx.python (if not already present)
>> -compile and install open.pymol against the cctbx.python, either via the
>> renaming trick
>>  above or calling cctbx.python setup.py (build/install)
>>
>> Good luck, let us know how it works...
>>
>>       Carsten
>>
>>
>>
>> > -Original Message-
>> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
>> > Tim Gruene
>> > Sent: Wednesday, June 23, 2010 8:35 AM
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: [ccp4bb] pymol python and cctbx
>> >
>> > Dear all,
>> >
>> > I've been trying to install the SuperSym module for pymol (svn trunk
>> > version of pymol as of today, 1.3.x). Upon restart the console says
>> > "Ooops!  SuperSym requires cctbx and numeric python to function.
>> Please
>> > install these."
>> >
>> > The system is i7 with Debian Testing 64bit with python2.5 (although
>> > python2.6 is also installed but not the default). cctbx was installed
>> > using cctbx_fedora8_x86_64_py265_inc.selfx and the installation output
>> > did not imply any issues, e.g. about the wrong python version (and I
>> > did only find cctbx packages for python 2.6.5 on their web site).
>> >
>> > python-numpy is install which I believe is the "numeric python" the
>> > module output complains about.
>> >
>> > Would anyone be so kind to direct someone who despises python (phyuuu,
>> > that
>> > helped...) to how to get the SuperSym module to work with pymol? A
>> > start would be if the module would tell me whether it complains about
>> > missing numeric python or cctbx or both.
>> >
>> > Do I have to compile pymol with python2.6? Just starting pymol with
>> > python2.6 did not change anything.
>> >
>> > Thanks a lot, Tim
>> >
>> >
>> > --
>> > Tim Gruene
>> > Institut fuer anorganische Chemie
>> > Tammannstr. 4
>> > D-37077 Goettingen
>> >
>> > GPG Key ID = A46BEE1A
>
> --
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.9 (GNU/Linux)
>
> iD8DBQFMIhjbUxlJ7aRr7hoRAtF0AJoD+AosjYDnPShy5T4+rh/4xiABUQCg+Amu
> nmxBu9tMBneoDCfxsWxQyPc=
> =WL5a
> -END PGP SIGNATURE-
>
>

Re: [ccp4bb] Stuck refinement

[Zhou, Tongqing (NIH/VRC) [E]]

Hi All,

The problem has also been solved with a new 2.0A dataset collected over the 
last weekend. Same space group and dimensions, much less radiation damage. This 
time I used APS SER-CAT's weaker BM beamline.

Thanks,


Tongqing

Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
**
The information in this e-mail and any of its attachments is confidential and 
may contain sensitive information. It should not be used by anyone who is not 
the original intended recipient. If you have received this e-mail in error 
please inform the sender and delete it from your mailbox or any other storage 
devices. National Institute of Allergy and Infectious Diseases shall not accept 
liability for any statements made that are sender's own and not expressly made 
on behalf of the NIAID by one of its representatives.
**


-Original Message-
From: Zhou, Tongqing (NIH/VRC) [E]
Sent: Tuesday, June 15, 2010 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Stuck refinement

Hi, Everyone,

Thank you all very much  for the nice suggestions. I am trying to reply within 
this email.

I agree that the problem may be rooted from the crystal itself, we noticed 
during data collection that a wedge of the rotation was very mosaic, HKL2000 
was able to pick up the right spots, but the scaling gives high chi^2, and when 
I used the rejection files, HKL2000 complained "more than 5 rejections". 
Colleagues suggested tweaking the error model, the complaint of "more than 
5 rejections' went away and rejection dropped to below 300 spots. The new 
error model reduced the chi^2 as well as the I/sigI in the low resolution 
shells.

I run the P222 data set with Xtriage, the report says no twining, but the 
symmetry was too low. However, HKL2000 won't even pick up higher symmetry 
groups during indexing. I also rescaled the data omitting the bad wedge, 
xtriage gives "normal" report.


Refinement was done with combination of simulated annealing, TLS, ADP, 
individual sites in Phenix. The molecular replacement was done with 
CDR-loop-trimmed antibody Fab and antigen structures. The map quality was good 
and I was able to rebuild the new loops without any problem.

I will have beam time later this week, I think it will be better to put a 
better crystal on.

Best regards,


Tongqing

Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
**
The information in this e-mail and any of its attachments is confidential and 
may contain sensitive information. It should not be used by anyone who is not 
the original intended recipient. If you have received this e-mail in error 
please inform the sender and delete it from your mailbox or any other storage 
devices. National Institute of Allergy and Infectious Diseases shall not accept 
liability for any statements made that are sender's own and not expressly made 
on behalf of the NIAID by one of its representatives.
**


-Original Message-
From: Eleanor Dodson [mailto:c...@ysbl.york.ac.uk]
Sent: Tuesday, June 15, 2010 4:46 AM
To: Zhou, Tongqing (NIH/VRC) [E]
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Stuck refinement

   When this happens, I firstly suspect that the spacegroup may be wrong.  We 
had a case where the symmetry was pseudo I4212 but was really
I222 (or was it really I212121) Anyway most of the structure obeyed the
I41212 symmetry but there was a tail which did not..)

Feed the unmerged reflections into pointless and see what it suggests

Eleanor

Zhou, Tongqing (NIH/VRC) [E] wrote:
> Hi Everyone,
>
> I have some problem in refining a structure. The data goes to 2.4A (with some 
> 30% completeness at 2.15A), the structure was solved by MR with Phaser, 
> refinement was done with Phenix, but the r and r-free are now staying at 26% 
> and 32%, even with all possible waters and missing fragments added. Data was 
> collected at APS at cryo condition. One thing I noticed during HKL2000 data 
> processing was that the chi^2 were way too high at lower resolutions shells,  
> I had to adjust the default error model in HKL2000 to get the chi^2 to around 
> 1, but this adjustment reduced the overall I/sigI ratio a lot (from around 20 
> to 5).
>
> The quality of electron density maps looks fine to me for a 2.4 A data set 
> and I was able to build all the missing CDR loops for the antibody in the 
> complex. I am lost now, should I just re-collect a new data set?

Re: [ccp4bb] pymol python and cctbx

[Tim Gruene]

Dear Carsten,

thank you for the instruction. The cctbx package seems to lack tkinter which is
required by pymol (and maybe numpy, too). How do I install a specific python
module (package? what's the correct term?) 'under' cctbx.python?

Cheers, Tim

On Wed, Jun 23, 2010 at 09:07:36AM -0400, Schubert, Carsten [PRDUS] wrote:
> Tim,
> 
> I'm shooting from the hip here, but I think the problem is that cctbx
> comes with its own python, which you would need to run both pymol and
> numpy under. According to Ralf it is at least not trivial to utilize the
> system python to run cctbx. So I think you need to compile/install pymol
> against cctbx.python and install it as a module under cctbx.python.
> Similar deal for numpy, which may already be available in cctbx, if not
> installation should be straightforward.
> 
> These broad steps may work (again shooting from the hip...)
> -Install cctbx
> -link cctbx.python to python and make sure its first in your path (may
> be optional)
> -install numpy under cctbx.python (if not already present)
> -compile and install open.pymol against the cctbx.python, either via the
> renaming trick 
>  above or calling cctbx.python setup.py (build/install)
> 
> Good luck, let us know how it works...
> 
>   Carsten
> 
> 
> 
> > -Original Message-
> > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> > Tim Gruene
> > Sent: Wednesday, June 23, 2010 8:35 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] pymol python and cctbx
> > 
> > Dear all,
> > 
> > I've been trying to install the SuperSym module for pymol (svn trunk
> > version of pymol as of today, 1.3.x). Upon restart the console says
> > "Ooops!  SuperSym requires cctbx and numeric python to function.
> Please
> > install these."
> > 
> > The system is i7 with Debian Testing 64bit with python2.5 (although
> > python2.6 is also installed but not the default). cctbx was installed
> > using cctbx_fedora8_x86_64_py265_inc.selfx and the installation output
> > did not imply any issues, e.g. about the wrong python version (and I
> > did only find cctbx packages for python 2.6.5 on their web site).
> > 
> > python-numpy is install which I believe is the "numeric python" the
> > module output complains about.
> > 
> > Would anyone be so kind to direct someone who despises python (phyuuu,
> > that
> > helped...) to how to get the SuperSym module to work with pymol? A
> > start would be if the module would tell me whether it complains about
> > missing numeric python or cctbx or both.
> > 
> > Do I have to compile pymol with python2.6? Just starting pymol with
> > python2.6 did not change anything.
> > 
> > Thanks a lot, Tim
> > 
> > 
> > --
> > Tim Gruene
> > Institut fuer anorganische Chemie
> > Tammannstr. 4
> > D-37077 Goettingen
> > 
> > GPG Key ID = A46BEE1A

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

GPG Key ID = A46BEE1A



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Re: [ccp4bb] Dual boot--windows 7 and Linux

[Zhou, Tongqing (NIH/VRC) [E]]

Dear All,

The problem solved.

I have to remove one of the Dell factory partitions to install Linux. Here is 
what I did
1. Shrink the hard drive with Win 7 to give free space for Linux
2. Delete the READER partition (Did not touch the Dell Utility, OS and Recovery 
partitions)
3. Install from DVD using Free space.

Thanks for all the suggestions.


Tongqing

Tongqing Zhou, Ph.D.
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
**
The information in this e-mail and any of its attachments is confidential and 
may contain sensitive information. It should not be used by anyone who is not 
the original intended recipient. If you have received this e-mail in error 
please inform the sender and delete it from your mailbox or any other storage 
devices. National Institute of Allergy and Infectious Diseases shall not accept 
liability for any statements made that are sender's own and not expressly made 
on behalf of the NIAID by one of its representatives.
**



Zhou, Tongqing (NIH/VRC) [E] wrote:
> Dear All,
>
>
>
> I am trying to set up a dual boot system on a new Dell laptop factory
> installed with 64-bit Windows 7 professional.
>
>
>
> Model: Dell Latitude E6410
>
> OS: Windows 7 Professional
>
> MEM: 8G
>
> CPU: Corei7
>
> HD: 500GB
>
>
>
> I first shrank the HD with Win7 to give ~250GB space to the new OS, I
> then installed from DVD, so far, I tested Red Hat 5 workstation,
> Fedora 13, Ubantu 10, all of them complained that I don't have enough
> space to put partition.Further googling found out that DELL had put
> some hidden partitions (Dell Utility, Recovery, and a partition named
> READER) on the HD and there is a limit to 4 primary partitions.
>
>
>
> Did anyone have any success?
>
>
>
> Thanks,
>
>
>
>
>
> Tongqing
>
>
>
> *Tongqing Zhou, Ph.D. *
>
> Staff Scientist
>
> Structural Biology Section
>
> Vaccine Research Center, NIAID/NIH
>
> Building 40, Room 4607B
>
> 40 Convent Drive, MSC3027
>
> Bethesda, MD 20892
>
> (301) 594-8710 (Tel)
>
> (301) 793-0794 (Cell)
>
> (301) 480-2658 (Fax)
>
> */**/*
> //
>
> */The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be
> used by anyone who is not the original intended recipient. If you have
> received this e-mail in error please inform the sender and delete it
> from your mailbox or any other storage devices. National Institute of
> Allergy and Infectious Diseases shall not accept liability for any
> statements made that are sender's own and not expressly made on behalf
> of the NIAID by one of its representatives./*
>
> */**/*
>
>
>

--
___

Dr. Christian Biertümpfel
Laboratory of Molecular Biology

NIDDK/National Institutes of Health  phone: +1 301 402 4647
9000 Rockville Pike, Bldg. 5, Rm. B1-03  fax:   +1 301 496 0201
Bethesda, MD 20892-0580
USA   email: biertumpf...@niddk.nih.gov
___

[ccp4bb] Postdoc position EMBL

[Panne Daniel]

The Panne laboratory at the EMBL seeks to recruit an outstanding postdoctoral 
scientist in structural biology. Our research focus is directed towards the 
structure of macromolecular assemblies involved in the innate immune system and 
in epigenetic gene regulation (Panne et al., Cell 2007; Panne, Current Opinion 
Structural Biology, 2008; Shen et al. Structure 2009). The project focuses on 
the structural and biochemical characterization of regulatory complexes that 
are essential for the innate immune system. There are possibilities to 
participate in other ongoing exciting projects of high scientific impact.

Candidates must hold (or soon expect to hold) a PhD in biochemistry, molecular 
biology, biophysics or related fields. This position requires experience in 
xray structure determination projects including phasing and knowledge in 
expressing and purifying proteins and/or protein complexes. The candidate 
should be a highly motivated individual who enjoys working as part of a 
collaborative and multidisciplinary team.

The laboratory is located on an international research campus in Grenoble 
providing one of the best structural biology environments in Europe. We employ 
a wide range of techniques including molecular biology, biochemistry, 
single-molecule fluorescence, electron microscopy, light scattering, X-ray 
crystallography and computing. Access to techniques such as automated 
expression and crystallization of proteins and protein complexes and to modern 
biophysical instrumentation is provided. To apply please send your CV, a 
statement of research interests, and names (including email address) of at 
least two referees by email to Dr. Daniel Panne (pa...@embl.fr). For more 
information: http://www.embl.fr/research/unit/panne/index.html

Re: [ccp4bb] PEG 1000

[Oganesyan, Vaheh]

Actually it probably would be better ask the supplier of your screen
first how they got PEG 1K diluted to 12.5%. If they did hit it then you
have to do the same. But even better idea is to order that PEG 1K from
the same company that sells the screens. It will insure identical
treatment.

 

My 2 cents.

 

 

 Vaheh  



From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
R.Srinivasan
Sent: Wednesday, June 23, 2010 3:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PEG 1000

 

Dear All,

 I have got initial crystals in a condition with PEG 1000. The
PEG 1000 stock we had in our lab was rock solid and when i heated it to
about 50 degrees for 15 to 20 minutes it became a solution. We thought
the compound has got out dated or something like that and bought a brand
new bottle from Sigma and this is rock solid too.

Is this something characteristic of PEG1000? The hit condition
says its 12.5% w/v PEG 1000 but it apparently seems i could never get a
powder of it.

   So my question is, Can i go ahead using this melted solution form
of PEG1000 for setting up optimizations?

Thank you all in anticiaption,
Vasan

 




To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary.  This communication is expected 
to be read and/or used only by the individual(s) for whom it is intended.  If 
you have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose.  Thank you for your 
cooperation.

Re: [ccp4bb] PEG 1000

[Prince, D Bryan]

When the ACA meeting was in Hawaii (2006?), there was information about 
microwaving PEG solutions to artificially age new samples so that they would 
crystallize like the older PEG's. So I would infer that heat does have a 
significant effect on solid PEG's. All PEG's with MW >=600 are solids at room 
temperature. What I used to do was to make a large hot water bath (37-42C)  and 
put the container of PEG in the bath so that it was 2/3 covered by water and 
let it melt. It would take 3-4 hours to fully melt the sample, but then you can 
make a 50-70% (v/v) solution that will remain liquid at room temperature for 
your crystallization. 

Good Luck!
Bryan


--
Confidentiality Notice: This message is private and may contain confidential 
and proprietary information. If you have received this message in error, please 
notify us and remove it from your system and note that you must not copy, 
distribute or take any action in reliance on it. Any unauthorized use or 
disclosure of the contents of this message is not permitted and may be unlawful.
 
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Flip 
Hoedemaeker
Sent: Wednesday, June 23, 2010 6:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PEG 1000

The meting point of PEG 1000 is around 38C. Obviously, if Sigma has 
heated the batch to fill the bottles in the first place this is a futile 
exercise... I'd ask them first.

Flip



Vellieux Frederic wrote:
> R.Srinivasan wrote:
>> Dear All,
>>
>>  I have got initial crystals in a condition with PEG 1000. The 
>> PEG 1000 stock we had in our lab was rock solid and when i heated it 
>> to about 50 degrees for 15 to 20 minutes it became a solution. We 
>> thought the compound has got out dated or something like that and 
>> bought a brand new bottle from Sigma and this is rock solid too.
>>
>> Is this something characteristic of PEG1000? The hit condition 
>> says its 12.5% w/v PEG 1000 but it apparently seems i could never get 
>> a powder of it.
>>
>>So my question is, Can i go ahead using this melted solution 
>> form of PEG1000 for setting up optimizations?
>>
>> Thank you all in anticiaption,
>> Vasan
>>
> All higher molecular weight PEG's are solid. Some are stored as flakes, 
> but as you mention some are rock solid. And it's very difficult to get 
> them out of the container (breaking the bottle is sometimes necessary).
> 
> What I would go for personally would be mechanical grinding because I do 
> not know what happens to the PEG when it's heated to 50 deg or higher. 
> But perhaps you could take your bottle, cut the content in half, make a 
> powder out of the one half and use the other one with this heating 
> method and see if there are any differences. Or else if you happen to 
> have an analytical chemistry service at hand, provide them with a small 
> sample of each of the 2 and ask them to check if there is any difference.
> 
> Fred.
> 

[ccp4bb] Modified Arginine Coot and SHELX

[Fatima]

Dear all,

I'm finishing a refinement using SHELX and Coot (1.3A) and I have a modified 
Arginine. There’s a blob of positive density (9.04 and 7.01 sigma) binding NH2 
in the 2 conformations. I think it could be a hydroxyl there. 

1) How can I add that in Coot?

2) Does SHELXL recognise modified residues? How can I get restraints then, by 
using PRODRG?

Any suggestions will be welcome.

Cheers,
Fátima

Re: [ccp4bb] [COOT] Hardware stereo

[David Schuller]

1) Do you have a line:
Option "Stereo" "10"
in the "Screen" section of your xorg.conf?


2) Is the 3D Vision emitter hooked up both to a USB port _AND_ to the 
mini-DIN stereo socket on the Quadro card? AFAIK emitter sync with only 
USB connection is not supported under Linux.


http://http.download.nvidia.com/XFree86/Linux-x86/256.35/README/README.txt



On 06/22/10 21:37, Max Wang wrote:

I have just installed coot on a new machine. When I tried hardware stereo, it showed 
"Can't enable stereo visual - falling back".
Here is my set up:
Dell Precision T7500n Dual Processor
Red Hat Enterprise Linux WS V5.3 doe 64 bit system
1.5GB Nvidia Quadro FX 4800
Samsung SyncMaster 2233RZ

I have installed the new Nvidia driver NVIDIA-Linux-x86_64-256.35.run, 
currently using 120 refresh rate.
The stereo emmiter and glasses are NVIDIA GeForce 3D Vision from Nvidia.

Can anyone help me with this?

Thanks.

Max
   



--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

Re: [ccp4bb] pymol python and cctbx

[Schubert, Carsten [PRDUS]]

Tim,

I'm shooting from the hip here, but I think the problem is that cctbx
comes with its own python, which you would need to run both pymol and
numpy under. According to Ralf it is at least not trivial to utilize the
system python to run cctbx. So I think you need to compile/install pymol
against cctbx.python and install it as a module under cctbx.python.
Similar deal for numpy, which may already be available in cctbx, if not
installation should be straightforward.

These broad steps may work (again shooting from the hip...)
-Install cctbx
-link cctbx.python to python and make sure its first in your path (may
be optional)
-install numpy under cctbx.python (if not already present)
-compile and install open.pymol against the cctbx.python, either via the
renaming trick 
 above or calling cctbx.python setup.py (build/install)

Good luck, let us know how it works...

Carsten



> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Tim Gruene
> Sent: Wednesday, June 23, 2010 8:35 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] pymol python and cctbx
> 
> Dear all,
> 
> I've been trying to install the SuperSym module for pymol (svn trunk
> version of pymol as of today, 1.3.x). Upon restart the console says
> "Ooops!  SuperSym requires cctbx and numeric python to function.
Please
> install these."
> 
> The system is i7 with Debian Testing 64bit with python2.5 (although
> python2.6 is also installed but not the default). cctbx was installed
> using cctbx_fedora8_x86_64_py265_inc.selfx and the installation output
> did not imply any issues, e.g. about the wrong python version (and I
> did only find cctbx packages for python 2.6.5 on their web site).
> 
> python-numpy is install which I believe is the "numeric python" the
> module output complains about.
> 
> Would anyone be so kind to direct someone who despises python (phyuuu,
> that
> helped...) to how to get the SuperSym module to work with pymol? A
> start would be if the module would tell me whether it complains about
> missing numeric python or cctbx or both.
> 
> Do I have to compile pymol with python2.6? Just starting pymol with
> python2.6 did not change anything.
> 
> Thanks a lot, Tim
> 
> 
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A

[ccp4bb] pymol python and cctbx

[Tim Gruene]

Dear all,

I've been trying to install the SuperSym module for pymol (svn trunk version of
pymol as of today, 1.3.x). Upon restart the console says "Ooops!  SuperSym
requires cctbx and numeric python to function. Please install these."

The system is i7 with Debian Testing 64bit with python2.5 (although python2.6 is
also installed but not the default). cctbx was installed using
cctbx_fedora8_x86_64_py265_inc.selfx and the installation output did not imply
any issues, e.g. about the wrong python version (and I did only find cctbx
packages for python 2.6.5 on their web site).

python-numpy is install which I believe is the "numeric python" the module
output complains about.

Would anyone be so kind to direct someone who despises python (phyuuu, that
helped...) to how to get the SuperSym module to work with pymol? A start would
be if the module would tell me whether it complains about missing numeric python
or cctbx or both.

Do I have to compile pymol with python2.6? Just starting pymol with python2.6
did not change anything.

Thanks a lot, Tim


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

GPG Key ID = A46BEE1A



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Description: Digital signature

Re: [ccp4bb] Merohedral twining for P212121. -

[Jonathan Elegheert]

I recently ran into a similar case where the SG was P2(1)2(1)2(1) with a 
~ b (within a few angstroms), thus emulating a P422 metric symmetry.


Full details here: Pubmed ID: 20057079

As Ian says, sometimes the spot splitting was particularly visible, 
sometimes it was not. SAINT was not able to integrate the split spots 
separately (it works great for non-merohedral twins though, followed by 
TWINABS for scaling). In the end, I ended up using XDS and even the most 
severely split spots were nicely integrated in the same integration box. 
Putting the pseudo-merohedral twin operator in to SHELXL dropped 
R/R-free and improved the GooF and least-squares refinement convergence, 
even though the twin fraction was rather low (~ 5%).


HTH,

Jonathan

--
Jonathan Elegheert
Ph.D. Student

Unit for Structural Biology&  Biophysics
http://www.lprobe.ugent.be/xray.html

Lab for Protein Biochemistry and Biomolecular Engineering
Department of Biochemistry&  Microbiology
Ghent University, Belgium

e-mail: jonathan.eleghe...@ugent.be


Op 6/23/2010 11:46 AM, Frank von Delft schreef:

My experience with pseudo-merohedral twinning (it was actually the
reticular case with half the spots overlapped and the other
non-overlapped half on a pseudo C-centred lattice) is that the degree
of splitting varies widely over the diffraction pattern.  In some
places there was complete overlap, in others you see elongation of the
spots, in others partial separation, and in others complete separation
(and of course all shades in-between), with around 50-50 intensity
split.  In this situation the mosaicity becomes meaningless!  I'm not
aware of any software that can handle this kind of thing successfully
(and certainly the data we did manage to get turned out to be
garbage!).

Both DIRAX or SAINT should be able to handle it, you'll need SADABS to 
scale it.  (The latter two are in the Bruker software.)


phx.
<>

Re: [ccp4bb] PEG 1000

[Flip Hoedemaeker]

The meting point of PEG 1000 is around 38C. Obviously, if Sigma has 
heated the batch to fill the bottles in the first place this is a futile 
exercise... I'd ask them first.


Flip



Vellieux Frederic wrote:

R.Srinivasan wrote:

Dear All,

 I have got initial crystals in a condition with PEG 1000. The 
PEG 1000 stock we had in our lab was rock solid and when i heated it 
to about 50 degrees for 15 to 20 minutes it became a solution. We 
thought the compound has got out dated or something like that and 
bought a brand new bottle from Sigma and this is rock solid too.


Is this something characteristic of PEG1000? The hit condition 
says its 12.5% w/v PEG 1000 but it apparently seems i could never get 
a powder of it.


   So my question is, Can i go ahead using this melted solution 
form of PEG1000 for setting up optimizations?


Thank you all in anticiaption,
Vasan

All higher molecular weight PEG's are solid. Some are stored as flakes, 
but as you mention some are rock solid. And it's very difficult to get 
them out of the container (breaking the bottle is sometimes necessary).


What I would go for personally would be mechanical grinding because I do 
not know what happens to the PEG when it's heated to 50 deg or higher. 
But perhaps you could take your bottle, cut the content in half, make a 
powder out of the one half and use the other one with this heating 
method and see if there are any differences. Or else if you happen to 
have an analytical chemistry service at hand, provide them with a small 
sample of each of the 2 and ask them to check if there is any difference.


Fred.

Re: [ccp4bb] Merohedral twining for P212121. -

[Frank von Delft]

My experience with pseudo-merohedral twinning (it was actually the
reticular case with half the spots overlapped and the other
non-overlapped half on a pseudo C-centred lattice) is that the degree
of splitting varies widely over the diffraction pattern.  In some
places there was complete overlap, in others you see elongation of the
spots, in others partial separation, and in others complete separation
(and of course all shades in-between), with around 50-50 intensity
split.  In this situation the mosaicity becomes meaningless!  I'm not
aware of any software that can handle this kind of thing successfully
(and certainly the data we did manage to get turned out to be
garbage!).

   
Both DIRAX or SAINT should be able to handle it, you'll need SADABS to 
scale it.  (The latter two are in the Bruker software.)


phx.

Re: [ccp4bb] Merohedral twining for P212121. -

[Ian Tickle]

On Tue, Jun 22, 2010 at 11:09 PM,   wrote:

> My interest was really what happened in the observed diffraction
> pattern. With the large difference in the orthorhombic cell dimensions,
> the spots will gradually separate for the higher orders. The point I
> really wanted to discuss was whether there would be an advantage if one
> could distinguish the spots and measure the intensity of each component.
> I am sure one could do this - the question I had was whether it would be
> useful.

My experience with pseudo-merohedral twinning (it was actually the
reticular case with half the spots overlapped and the other
non-overlapped half on a pseudo C-centred lattice) is that the degree
of splitting varies widely over the diffraction pattern.  In some
places there was complete overlap, in others you see elongation of the
spots, in others partial separation, and in others complete separation
(and of course all shades in-between), with around 50-50 intensity
split.  In this situation the mosaicity becomes meaningless!  I'm not
aware of any software that can handle this kind of thing successfully
(and certainly the data we did manage to get turned out to be
garbage!).

Cheers

-- Ian

Re: [ccp4bb] PEG 1000

[Tim Gruene]

On Wed, Jun 23, 2010 at 12:40:35PM +0530, R.Srinivasan wrote:
> Dear All,
> 
>  I have got initial crystals in a condition with PEG 1000. The PEG
>  1000 stock we had in our lab was rock solid and when i heated it to
>  about 50 degrees for 15 to 20 minutes it became a solution. We
>  thought the compound has got out dated or something like that and
>  bought a brand new bottle from Sigma and this is rock solid too.
> 
> Is this something characteristic of PEG1000? The hit condition says
> its 12.5% w/v PEG 1000 but it apparently seems i could never get a
> powder of it.
> 
>So my question is, Can i go ahead using this melted solution form of
>PEG1000 for setting up optimizations?
Since mass is temperature independent you can use the PEG1000 solution to weight
50mg and dissolve it in 50-80ml water, let it cool down to room temperature and
top it up to 100ml (with water). I think this way you created a 50% w/v stock
solution of PEG1000 which you can further dilute to set up the desired
concentration.

Tim

> 
> Thank you all in anticiaption,
> Vasan
> 
> 

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

GPG Key ID = A46BEE1A



signature.asc
Description: Digital signature

Re: [ccp4bb] PEG 1000

[Vellieux Frederic]

R.Srinivasan wrote:

Dear All,

 I have got initial crystals in a condition with PEG 1000. The 
PEG 1000 stock we had in our lab was rock solid and when i heated it 
to about 50 degrees for 15 to 20 minutes it became a solution. We 
thought the compound has got out dated or something like that and 
bought a brand new bottle from Sigma and this is rock solid too.


Is this something characteristic of PEG1000? The hit condition 
says its 12.5% w/v PEG 1000 but it apparently seems i could never get 
a powder of it.


   So my question is, Can i go ahead using this melted solution 
form of PEG1000 for setting up optimizations?


Thank you all in anticiaption,
Vasan

All higher molecular weight PEG's are solid. Some are stored as flakes, 
but as you mention some are rock solid. And it's very difficult to get 
them out of the container (breaking the bottle is sometimes necessary).


What I would go for personally would be mechanical grinding because I do 
not know what happens to the PEG when it's heated to 50 deg or higher. 
But perhaps you could take your bottle, cut the content in half, make a 
powder out of the one half and use the other one with this heating 
method and see if there are any differences. Or else if you happen to 
have an analytical chemistry service at hand, provide them with a small 
sample of each of the 2 and ask them to check if there is any difference.


Fred.

Re: [ccp4bb] Impact Factors

[Kay Diederichs]

Dear Tassos,

thanks for alerting us to this unexpected but welcome fact!
I would like to take the opportunity to

a) congratulate George Sheldrick!

b) point out to the CCP4 community that we decide ourselves about the
impact factors of journals that are important for our work:
specifically, if we would cite Acta Cryst (and JAC) papers in our own
articles, then this is what will raise (or rather, keep up) the impact
factor of Acta Cryst in the next years. In other words, please _do_ cite
the individual programs (separately!) that you use to solve and refine
your structure, as suggested under "Referencing CCP4 etc" at
http://www.ccp4.ac.uk/about.php . And cite these papers in the main
article, not only in the "supporting material" (I surely will need to
revise my own citing behaviour).
Ultimately, those of us publishing in Acta Cryst and related journals
will benefit from this, too. (whether it will suffice for tenure for
methods-related work is still an open question)

c) point out that it is of little use to researchers if a review is
cited instead of their original work.

thanks,

Kay

Anastassis Perrakis schrieb:
> Dear all,
> 
> We are all used to the tyranny of impact factors: high impact
> publication in "well esteemed" journals, as dictated by the Supreme
> Authority - excuse me, I meant  Thomson Reuters - often substitutes the
> judgement of interview panels, grant review panels and sometimes is a
> decision-maker for lazy referees. A 'high impact' publication in your CV
> often counts as much as consistent work done for years and is considered
> the gateway for good jobs and careers. And, alas, your Acta Cryst
> papers, would not count ...
> 
> Since yesterday though, a single person, no other than the ccp4bb
> bulletin board subscriber and contributor, and an emblematic figure of
> our community, George Sheldrick, has managed with one action to showcase
> the flaws of this system. Since yesterday, officially, the top ranking
> journal according to the official Thomson Reuters Impact factor is: Acta
> Crystallographica Part A. How was that made possible? Simply by
> publishing a 'short history about SHELX' and requesting users to cite
> it. It took two years, but now Acta A has displaced Cell, Nature,
> Science and even New England Journal of Medicine from the top ranks.
> 
> Well, good luck to all the methods-folk who are up for tenure, here is
> your chance guys and girls ... it will not last long!!!
> 
> Best regards,
> 
> Tassos
> 
> Specifically, the publication with second highest impact factor in the
> "science" category is/Acta Crystallographica - Section A/, knocking none
> other than the/New England Journal of Medicine/from the runner's up
> position. This title's impact factor rocketed up to 49.926 this year,
> more than 20-fold higher than last year. A single article published in a
> 2008 issue of the journal seems to be responsible for the meteoric rise
> in the/Acta Crystallographica - Section A/'s impact factor."A short
> history of SHELX,"
> by
> University of Göttingen crystallographerGeorge Sheldrick,
> which reviewed the
> development of the computer system SHELX, has been cited more than 6,600
> times, according to ISI. This paper includes a sentence that essentially
> instructs readers to cite the paper they're reading -- "This paper could
> serve as a general literature citation when one or more of the
> open-source SHELX programs (and the Bruker AXS version SHELXTL) are
> employed in the course of a crystal-structure determination." (Note:
> This may be a good way to boost your citations.)


-- 
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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[ccp4bb] PEG 1000

[R.Srinivasan]

Dear All,

 I have got initial crystals in a condition with PEG 1000. The PEG 1000 
stock we had in our lab was rock solid and when i heated it to about 50 degrees 
for 15 to 20 minutes it became a solution. We thought the compound has got out 
dated or something like that and bought a brand new bottle from Sigma and this 
is rock solid too.

Is this something characteristic of PEG1000? The hit condition says its 
12.5% w/v PEG 1000 but it apparently seems i could never get a powder of it.

   So my question is, Can i go ahead using this melted solution form of 
PEG1000 for setting up optimizations?

Thank you all in anticiaption,
Vasan