[ccp4bb] ligand refinemnet

[peter hudson]

Hello all

I have refined and built model a dataset of 3.0A resolution dataset. This
model is assocaied with a ligand. After final refinement and model building
i found  a big blob of  Fo-Fc density of around 4sigma level at the
N-terminal of the fianl model. My protein doesnot carry any tag at the
N-terminal. But, the template i have used for the molecular replacement
carrying a tag at the N-termianl, which can occupy only 1/4th of this
positive density after superpostion. My crystallisation conditions component
cannot occupy such higher level of positive density. Since my protein binds
to a ligand, i looked carefully to the positive density and it seems very
similar to the ligand density but its obscure. Refinement after fitting the
ligand leads to very high B-factor of  the ligan, which vary for various
atoms from 50-90 and simultaneously positive density goes off. I also tried
to change the occupancy of the ligand but as i reduce the occupancy the B
factor comes down at the noraml expected average B factor value but again
Fo-Fc density appears in the map over ligand. If i leave to refine the
occupancy to the programme automatically, this lead to the zero occupancy of
the few atoms in the ligand and avearge B factor remains normal.
suggestions  would be appreciated.

Thanks in advance
Peter

Re: [ccp4bb] Acrylamide in RNA crystallization

[Pascal Egea]

Hi Vanessa
It is better to get rid of traces of residual acrylamide that may
contaminate your final purified and refolded RNA.
It is usual to have contaminations with monomeric acrylamide. NMR
spectroscopists studying RNA can usually detect its presence on their
spectra.
If you can dialyze your purified product to try to get rid of it it would be
the best. Traces (sometimes it is not a negligible amount) are  not good
because you may not be able to reproduce your results and optimize eventual
crystals. And for RNA this can be an excruciating pain.
When we transcribe RNA, we usually run the preparative acrylamide-urea gels
and elute the RNA out of the gel (most of the time by electroelution). The
RNA usually contains urea and acrylamide so I either precipitate using the
salt/ethanol technique and then resuspend the pellet and dialyze/refold or I
further purifiy on an ion exchange (Q type column) to try to clean it up.

If you have an NMR spectroscopist friend around, try to look at the presence
of acrylamide before and after these steps and see what works the best for
you.

Hope this helps

Pascal Egea, PhD
University of California San Francisco
Department of Biochemistry and Biophysics

[ccp4bb] RIP SGI

[William G. Scott]

Sadly, it is no joke:

Silicon Graphics timeline - San Jose Mercury News:

http://www.mercurynews.com/businessheadlines/ci_12049125

[ccp4bb] Glycerol for crystal screens

[Matthew Alan Bratkowski]

Hi.

I am trying to optimize a commercial crystallization condition that
contains glycerol.  So far, I have not been able to even reproduce the
results from the initial screen, and I thought that this may be due to
poor quality glycerol (among other possibilities).  I believe that the
glycerol that I'm using is reagent grade and am not sure what company it
is manufactored by.  Can anyone recommend a supplier and grade of glycerol
suitable for making crystallization screens?

Thanks,
Matt

Re: [ccp4bb] Acrylamide in RNA crystallization

[Francis E Reyes]

Are you talking about chunks of acrylamide? Or perhaps trace molecules?

As for chunks, we normally pass it through a  0.2 um filter before  
setting up trays.


FR

On Apr 1, 2009, at 4:48 PM, vanessa delfosse wrote:


Dear all,

I'm currently trying to crystallize a 70 nt RNA and I would like to  
know if the presence of acrylamide, some traces from the  
purification step, may interfere with crystallization of nucleic  
acids ?


Thanks in advance,

Vanessa.


--

Vanessa Delfosse - PhD

Universite de Montreal
Departement de Biochimie
CP 6128 Succ. Centre Ville
Montreal QC H3C 3J7
CANADA

tel : 514 343-6111 3780
@ : v.delfo...@umontreal.ca



-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

[ccp4bb] Acrylamide in RNA crystallization

[vanessa delfosse]

Dear all,

I'm currently trying to crystallize a 70 nt RNA and I would like to know if
the presence of acrylamide, some traces from the purification step, may
interfere with crystallization of nucleic acids ?

Thanks in advance,

Vanessa.


-- 

Vanessa Delfosse - PhD

Universite de Montreal
Departement de Biochimie
CP 6128 Succ. Centre Ville
Montreal QC H3C 3J7
CANADA

tel : 514 343-6111 3780
@ : v.delfo...@umontreal.ca

[ccp4bb] GLRF and interpreting self rotation functions...

[Francis E Reyes]

I am experimenting with GLRF and am having trouble calculating the  
locked self  rotation function for a protein of known structure. The  
protein has a 3 fold NCS axis that is not parallel to a  
crystallographic axis. I'm at the step of specifying the local  
symmetry elements for the locked self rotation function.


I guess the goal here is to search for 'one general rotation which  
will bring the non crystallographic symmetry point group in a  
"standard" orientation. What does this mean? How do I write the  
LOCSymmetry instruction for the input file?


My s.g. is P 21 21 21 and the following solutions are found for the  
normal self rotation function.




Fine searches around peaks with the slow rotation function --

  The large-term cut-off is  1.50

 Listing of the fitted angles of the top5 peaks --

  No. Old Angles S A N G L  
E   O A N G L EOld Ht.New Ht.
 (polar,  
XYK)  (polar, XZK)
 phi  psi   
kap phi  psi  kap


1  52.000   50.000  120.000  52.000   50.500   
120.000  53.246  127.449  120.000417.36420.74
2 128.000  130.000  120.000 128.000  129.500   
120.000 233.246  127.449  120.000417.36420.74
3 128.000   50.000  120.000 129.000   50.000   
120.000 126.870  126.536  120.000400.32407.69
4  52.000  130.000  120.000  51.000  130.000   
120.000 306.870  126.536  120.000400.32407.68
5  44.000   60.000  120.000  42.000   61.000   
120.000  36.719  125.820  120.000385.56391.96


The goal of all this is to use GLRF to explore NCS in cases where  
structures are not known and molecular replacement


Thanks

FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] Eleven plausible phasing elements remain unused

[Ethan Merritt]

On Wednesday 01 April 2009 07:21:16 Thomas Womack wrote:
> A perusal of the PDB reveals that the game of Periodic Table bingo still
> has eleven rounds to run:
> 
> scandium, titanium, germanium, zirconium, niobium, neodymium,
> dysprosium, thulium, hafnium, bismuth and thorium remain absent from PDB
> entries.

Does this imply that there is a PDB entry containing Radon?

I can't find any such entry, but then again I have never had much
luck with the search tools on www.pdb.org

Ethan

> OK, many of these are elements that would rather be refractory oxides or
> jet-engine components than hexammines, and niobium chloride clusters
> don't seem to be as water-stable as Ta6Br14, but why have neodymium,
> dysprosium and thulium so consistently been left out there in the cold
> rather than admitted to the warmish embrace of carboxyl groups?  There
> must somewhere be a protein with a site that cries out for ThCl2(2+), an
> unexpectedly water-stable cation.
> 
> Tom
> 



-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

Re: [ccp4bb] curvature of a helix

[Sergei Strelkov]

Dear Peter,

some time ago I have written the program Twister
to analyze the geometry of coiled coils (Strelkov SV and Burkhard P 
(2002) J. Struct. Biol.)
It will calculate the curvature of each individual a-helix in a coiled 
coil,
among other things. But in fact you can ask it to analyze an isolated 
a-helix as well.


I gladly send the program executables by e-mail to anyone interested.

Best wishes,
Sergei


Hello all
 
I would like to calculate the curvature  of a curved helix. Is any 
method or program exists, which can calculate the cuvature of  a 
curved helix? I would appreciate the suggestions.
 
Thanks in advance
 
 


--
Prof. Sergei V. Strelkov
Laboratory for Biocrystallography
Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven
O&N2, Campus Gasthuisberg, Herestraat 49 bus 822, 3000 Leuven, Belgium


Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Re: [ccp4bb] NCBHT: severe warning

[Michael Matho]

Sorry 'bout that. I don't know if this one is black, but it's definitely an 
A-hole...

LOL

Cheers,
Michael


- Original Message - 
From: "Marius Schmidt" 

To: 
Sent: Wednesday, April 01, 2009 1:48 PM
Subject: Re: [ccp4bb] NCBHT: severe warning



Interesting, isn't it? :-), nice person.



F*** Off.. it might be 1st April but most people are not interested
about
your shit sense of humour.. send them to your friends..

MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pcha...@nimr.mrc.ac.uk
Phone: + 44 208 816 251

On Wed, Apr 1, 2009 at 5:19 PM, Marius Schmidt
wrote:


   SEVERE BLACK HOLE WARNING ***


The National Center for Black Hole Tracking (NCBHT) is issuing
a black hole warning. During the night shift from March 31st
to April 1st, a black hole formed in the Atlas Detector at the
Large Hadron Collider, Cern/Geneva, Switzerland, although the
machine was off line. The black hole escaped from the Atlas
Detector and took course North. Being only a mini-black hole, it
started to absorb material from the suburbs of Geneva and part
of the French alps. On its way north it crossed the French/
German border changing course to the west gaining strength.
It is now a category 2 black hole. The northern part of
France has disappeared completely. The German town of Merzig,
once located at the scenic river Saar, now is on the edge of
a 2.5 mile deep gorge flanked by vertical walls. It appears
that most of England and Ireland is gone. Presently, the black
hole is heading towards Greenland and Newfoundland/Canada and
the northern part of the U.S.. Funded by a multinational rescue
fund, the NCBHT acquired newest technology to predict courses
of all black holes from CERN in the past, presence and future.
Using superconducting cosmic strings the NCBHT is now able to
reliably model black hole formation and black hole dynamics.
A simulation performed with the data of the present black hole
suggest within a 99.5 % reliability bracket that the black hole
will reach a full category 5 status before it will reach the
cost of the U.S. and Canada. Most likely, when it makes landfall,
it will be upgraded to a cosmic black hole. In this case, it will
start to move out of the earth's gravitational field heading
towards the B42 galaxy. There is a slight change that Uranus
and Pluto will be absorbed on the path out of our solar system.

The NCBHT




--
MRC National Institute for Medical Research
Division of Molecular Structure
The Ridgeway, NW7 1AA, UK
Email: pcha...@nimr.mrc.ac.uk
Phone: + 44 208 816 251

Re: [ccp4bb] NCBHT: severe warning

[Miguel Ortiz Lombardia]

Not nice either to air the address of someone who wrote you privately.


Miguel

Le 1 avr. 09 à 22:48, Marius Schmidt a écrit :


Interesting, isn't it? :-), nice person.



F*** Off.. it might be 1st April but most people are not interested
about
your shit sense of humour.. send them to your friends..



--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2


--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [ccp4bb] NCBHT: severe warning

[Phil Jeffrey]

Posting private emails on a public email list is rarely considered good 
form, in fact on some email lists it would get you thrown off fairly 
quickly, especially considering your intended purpose.


(Who is the list admin here ?)

If you're going to post semi-humorous way off-topic posts, you should 
consider tolerating a few ill-humored replies - at least that particular 
responder didn't post to the entire list.


Phil Jeffrey

Marius Schmidt wrote:

Interesting, isn't it? :-), nice person.


[rest of content removed]

Re: [ccp4bb] NCBHT: severe warning

[Marius Schmidt]

Interesting, isn't it? :-), nice person.


> F*** Off.. it might be 1st April but most people are not interested
> about
> your shit sense of humour.. send them to your friends..
> 
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: pcha...@nimr.mrc.ac.uk
> Phone: + 44 208 816 251
> 
> On Wed, Apr 1, 2009 at 5:19 PM, Marius Schmidt
> wrote:
> 
>>    SEVERE BLACK HOLE WARNING ***
>>
>>
>> The National Center for Black Hole Tracking (NCBHT) is issuing
>> a black hole warning. During the night shift from March 31st
>> to April 1st, a black hole formed in the Atlas Detector at the
>> Large Hadron Collider, Cern/Geneva, Switzerland, although the
>> machine was off line. The black hole escaped from the Atlas
>> Detector and took course North. Being only a mini-black hole, it
>> started to absorb material from the suburbs of Geneva and part
>> of the French alps. On its way north it crossed the French/
>> German border changing course to the west gaining strength.
>> It is now a category 2 black hole. The northern part of
>> France has disappeared completely. The German town of Merzig,
>> once located at the scenic river Saar, now is on the edge of
>> a 2.5 mile deep gorge flanked by vertical walls. It appears
>> that most of England and Ireland is gone. Presently, the black
>> hole is heading towards Greenland and Newfoundland/Canada and
>> the northern part of the U.S.. Funded by a multinational rescue
>> fund, the NCBHT acquired newest technology to predict courses
>> of all black holes from CERN in the past, presence and future.
>> Using superconducting cosmic strings the NCBHT is now able to
>> reliably model black hole formation and black hole dynamics.
>> A simulation performed with the data of the present black hole
>> suggest within a 99.5 % reliability bracket that the black hole
>> will reach a full category 5 status before it will reach the
>> cost of the U.S. and Canada. Most likely, when it makes landfall,
>> it will be upgraded to a cosmic black hole. In this case, it will
>> start to move out of the earth's gravitational field heading
>> towards the B42 galaxy. There is a slight change that Uranus
>> and Pluto will be absorbed on the path out of our solar system.
>>
>> The NCBHT
>>
> 
> 
> -- 
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: pcha...@nimr.mrc.ac.uk
> Phone: + 44 208 816 251

Re: [ccp4bb] Fix for MIFit8 compatibility issue with CCP4 6.1.1

[Donnie Berkholz]

On 21:12 Wed 01 Apr , John Badger wrote:
> We are examining alternatives for water-picking that workable in the 
> context of automated refinement and are not aware of any other 
> incompatibilities at this time.

No doubt you're already aware of findwaters, which comes with coot and 
looks like it can be run in an automated fashion:

Usage: /usr/bin/findwaters-real --pdbin pdb-in-filename --hklin mtz-filename 
--f f_col_label --phi phi_col_label --pdbout waters-filename --sigma 
sigma-level --flood --chop
--mapin ccp4-map-name can be used instead of --hklin --f --phi
where pdbin is the protein (typically)
and pdbout is file for the waters.
The default sigma level is 2.0
Use --chop to remove waters below given sigma-level
In this case, pdbout is the modified input coordinates
Use ---flood to fill everything with waters (not just water peaks)


-- 
Thanks,
Donnie

Donnie Berkholz
P. Andrew Karplus lab
Oregon State University


pgpXoh69TK36J.pgp
Description: PGP signature

[ccp4bb] Fix for MIFit8 compatibility issue with CCP4 6.1.1

[John Badger]

The automated cocrystal solution pipeline and refinement applications in 
MIFit8  ( http://code.google.com/p/mifit/ ) employs arp_waters for water-
picking and some automated error detection. However, arp_waters is 
deprecated in CCP4 6.1.1.

For now, one solution (Linux or Windows) is simply to copy the arp_waters 
binary from /bin in CCP4 6.0.* to /bin in CCP4 6.1.1.

Thanks to Martyn Winn for also reminding that on Linux the source code for 
arp_waters is still available and may still be built 

>Actually, it has not gone entirely, but was moved to the deprecated
> folder:
>
> $CCP4/deprecated/src/arp_waters_
>
> If you type "make" in $CCP4/deprecated/src you should get it back.

We are examining alternatives for water-picking that workable in the context 
of automated refinement and are not aware of any other incompatibilities at 
this time.

Thanks
John Badger

[ccp4bb] curvature of a helix

[peter hudson]

Hello all

I would like to calculate the curvature  of a curved helix. Is any method or
program exists, which can calculate the cuvature of  a curved helix? I would
appreciate the suggestions.

Thanks in advance

Re: [ccp4bb] Lowest resolution you can do MR with

[Christian Biertuempfel]

Hi,
I cannot really answer what the lowest resolution for MR is but I have
been successful with 4 A data for a protein-DNA complex and so I
encourage you to try your 3.6 A data set. Of course, it also depends on
the quality of your data, in particular how well/how many low resolution
reflections were measured, solvent content and your search model.

In my case, I have used only protein as the search model (45% of the
molar mass was missing) to reduce model bias and to avoid trouble with
different DNA conformations (deviating from ideal B-DNA).
The obtained MR solution gave a correct packing (for protein) with a lot
of space for DNA. The resulting electron density map showed clear
density for protein but it was very noisy apart from that. I have used
density modification (solvent flipping) in CNS to increase the contrast
of the map and it brought out a signal for DNA (solvent content was
65%). As Raji pointed out, have a look for the phosphate backbone or
some density in a helical arrangement. Most probably, you will not be
able to resolve individual bases.

Good luck,
christian



Muthiah wrote:
> What is the lowest resolution one can try to do molecular replacement
> with? I have a 3.6 angstroms resolution data for a protein-DNA complex
> and wondering whether I can try MR to see the density for DNA.


___

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
___

Re: [ccp4bb] Eleven plausible phasing elements remain unused

[James Holton]

Just because it is not in the PDB does not mean that noone has ever 
tried it.  I think I can attest to seeing pretty much all the 
Lanthanides tried at my beamline.  Indeed, Hampton sells a Lanthanide 
kit, and I recommend using it as every Lanthanide has a slightly 
different ionic radius.  For example, Holmium appears to be able to 
substitute for Mg (Ku, Smith & Howell. 2007).


As for Sc, Ti, Zr, Nb and Th, all these have edges outside the 
"normally" useful wavelength range between 2 A and ~0.8 A.  I imagine 
this probably reduces the frequency of their use, as does the 
radioactivity of Th.  Nevertheless, until today there was no place to 
publish most of the heavy atom soaks I have seen.  In fact, I have ~50 
TeraBytes of diffraction data to upload to the new JFCE, but I have been 
unable to find their submission site.  Any help?



As for the other "missing" heavy atoms, I just found that a hafnium 
cluster can be seen in 1o7t and a Zr cluster in 1xc1, so perhaps parsing 
is to blame for missing those?  Also, how can you tell if a particular 
metal was used to solve a structure, but the authors only deposited 
their native?  For example, there was a Dy derivative used to solve 
insulin (Blundell & Johnson, 1976), but apparently that atom never made 
it into the PDB.  Thulium was used to solve 1b79 (Fass et al. 1999), but 
that is not apparent from the PDB entry either.  Indeed, it is a very 
common practice to neglect depositing derivative data and derivative 
structures, and the original MAD/MIR data do tend to be lost to history 
(which is bad news for the beamline used to collect them).


I will add that I have never seen a Germanium derivative, and I also 
think that it would be cool to solve the first structure using 
Pepto-Bismol (Bismuth subsalicylate) as the heavy ion reagent.  Then 
Proctor & Gamble can add "poor electron density" to their list of things 
that Pepto can cure.


-James Holton
MAD Scientist

Thomas Womack wrote:

A perusal of the PDB reveals that the game of Periodic Table bingo still
has eleven rounds to run:

scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium, thulium, hafnium, bismuth and thorium remain absent from PDB
entries.

OK, many of these are elements that would rather be refractory oxides or
jet-engine components than hexammines, and niobium chloride clusters
don't seem to be as water-stable as Ta6Br14, but why have neodymium,
dysprosium and thulium so consistently been left out there in the cold
rather than admitted to the warmish embrace of carboxyl groups?  There
must somewhere be a protein with a site that cries out for ThCl2(2+), an
unexpectedly water-stable cation.

Tom
  

Re: [ccp4bb] protein-progesterone or estrogen complexes

[Kendall Nettles]

 
Are you talking about the respective ligand with progesterone or estrogen
receptor ligand binding domains? That has been done many times. Larger
pieces of the receptor have proven more difficult.

Adding 10uM compound in the fermentation media is the traditional route,
because a significant portion of the receptor misfolds in bacteria
otherwise. If you do want to add compounds to concentrated protein, don't
worry about compound solubility. We have solved over 20 ER LBD structures
with different compounds by diluting 100mM stocks in 100% ethanol or DMSO to
1mM. Most of the compound crashes out, but gets soaked up by the protein.
The next day we microcentrifuge and set up trials with supernatant.

We used to carbamylate free cysteines with iodoacetic acid, but switched to
high MBE (10-50mM), which gives adducts.  You'll also want the LxxLL peptide
at 3-5 fold excess. With ER LBD, almost all our agonist conformation
structures are in PEG3350. Also, we never did get a structure with
estradiol; the receptor crystallized readily with genistein.

See this paper for purification details.
 http://www.nature.com/nchembio/journal/v4/n4/abs/nchembio.76.html
Regards, Kendall. 


On 4/1/09 12:59 PM, "KUMARASWAMI MUTHIAH"  wrote:

> Anybody tried to cocrystallize the protein-progesterone or estrogen complexes,
> if so how do you go about the solubility of these compounds? Progesterone is
> only soluble in 50% chloroform or 100% DMSO and the dilution of this stock is
> not possible as chloroform falls out of solution. Lots of papers out there
> used soaking with progesterone or expressed the protein in the presence of
> progesterone. Any suggestions would be appreciated.
> Thanks
> 
> 
> 
> 
> Rediscover Hotmail®: Now available on your iPhone or BlackBerry Check it out.
>  le1_042009> 

[ccp4bb]

[Kornelius Zeth]

Unless you want a ligand free molecule it might be a good idea to add the 
substance already to the growing Ecoli (?) culture. That has proven to be 
successful for such molecules.

Best wishes

Kornelius

On Wed, 1 Apr 2009 16:59:05 +
 KUMARASWAMI MUTHIAH  wrote:
> 
> Anybody tried to cocrystallize the protein-progesterone or estrogen 
> complexes, if so how do you go about the solubility of these compounds? 
> Progesterone is only soluble in 50% chloroform or 100% DMSO and the dilution 
> of this stock is not possible as chloroform falls out of solution. Lots of 
> papers out there used soaking with progesterone or expressed the protein in 
> the presence of progesterone. Any suggestions would be appreciated.Thanks
> 
> 
> 
> _
> Rediscover Hotmail®: Now available on your iPhone or BlackBerry
> http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Mobile1_042009

 --
 Kornelius Zeth
 Max Planck Institute for Developmental Biology
 Dept. Protein Evolution
 Spemannstr. 35
 72076 Tuebingen, Germany
 kornelius.z...@tuebingen.mpg.de
 Tel -49 7071 601 323
 Fax -49 7071 601 349

[ccp4bb]

[KUMARASWAMI MUTHIAH]

Anybody tried to cocrystallize the protein-progesterone or estrogen complexes, 
if so how do you go about the solubility of these compounds? Progesterone is 
only soluble in 50% chloroform or 100% DMSO and the dilution of this stock is 
not possible as chloroform falls out of solution. Lots of papers out there used 
soaking with progesterone or expressed the protein in the presence of 
progesterone. Any suggestions would be appreciated.Thanks



_
Rediscover Hotmail®: Now available on your iPhone or BlackBerry
http://windowslive.com/RediscoverHotmail?ocid=TXT_TAGLM_WL_HM_Rediscover_Mobile1_042009

Re: [ccp4bb] New human genome policy - please read.

[Warren DeLano]

You know Kevin,

April fools notwithstanding, you idea actually makes good sense in a
tiny-url sort of way.  There would of course be collisions, and thus,
need for a global disambiguation registry, but society could do a whole
lot worse than something like:

http://prot.seq.db/3fc28e91d74b39ec/a6

(translated: protein sequence hash #afc28e91274739ec, registry index
#a6) 

as a way of unambiguously storing, referring to, and retrieving known
sequences.  

The URL, when requested, would of course simply return the registered
sequence.  Keeping the scope extremely narrow like that would be the key
to the registry's success: just "natural 20" sequences with no
annotations.

Optimal details might differ of course (CRC64 is suboptimal for ASCII
sequences), but as a general concept, I do think you're on to something
powerful here...

Cheers,
Warren

> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Kevin Cowtan
> Sent: Wednesday, April 01, 2009 5:02 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] New human genome policy - please read.
> 
> Why molecular weight? That's just arbitrary.
> 
> There is a simple way of referring to proteins which avoids any
> ambiguity - by it's sequence. When referring to a protein, we should
use
> its sequence as an identifier. No ambiguity.
> 
> Now, I understand that some smart people in America are now solving
> proteins of more than a dozen aa in length. For these, quoting the
whole
> sequence could be a bit long. Fortunately this is a solved problem:
all
> we need to do is quote a CRC64 hash of the ascii representation of the
> protein sequence. This gives a name space big enough that we can name
> about 4 billion proteins before the probability of a name clash
becomes
> significant.
> 
> 
> James Stroud wrote:
> > I think actually *naming* the proteins would be too extreme. Even
the
> > current alpha-numeric system is overwrought. I liked it better when
we
> > just called proteins "p75" or "p105". For instance, how many
proteins in
> > the human genome are 75 kD, anyway? My guess is not enough to make
the
> > situation ambiguous in any catastrophic way.
> 
> 
> 

[ccp4bb] NCBHT: severe warning

[Marius Schmidt]

    SEVERE BLACK HOLE WARNING ***


The National Center for Black Hole Tracking (NCBHT) is issuing
a black hole warning. During the night shift from March 31st 
to April 1st, a black hole formed in the Atlas Detector at the
Large Hadron Collider, Cern/Geneva, Switzerland, although the
machine was off line. The black hole escaped from the Atlas
Detector and took course North. Being only a mini-black hole, it
started to absorb material from the suburbs of Geneva and part
of the French alps. On its way north it crossed the French/
German border changing course to the west gaining strength.
It is now a category 2 black hole. The northern part of 
France has disappeared completely. The German town of Merzig,
once located at the scenic river Saar, now is on the edge of
a 2.5 mile deep gorge flanked by vertical walls. It appears
that most of England and Ireland is gone. Presently, the black
hole is heading towards Greenland and Newfoundland/Canada and
the northern part of the U.S.. Funded by a multinational rescue
fund, the NCBHT acquired newest technology to predict courses
of all black holes from CERN in the past, presence and future.
Using superconducting cosmic strings the NCBHT is now able to
reliably model black hole formation and black hole dynamics.
A simulation performed with the data of the present black hole
suggest within a 99.5 % reliability bracket that the black hole
will reach a full category 5 status before it will reach the 
cost of the U.S. and Canada. Most likely, when it makes landfall,
it will be upgraded to a cosmic black hole. In this case, it will
start to move out of the earth's gravitational field heading 
towards the B42 galaxy. There is a slight change that Uranus
and Pluto will be absorbed on the path out of our solar system.

The NCBHT

Re: [ccp4bb] Eleven plausible phasing elements remain unused

[Mischa Machius]

Huber's empire in Martinsried had a cabinet with ~500 compounds, many  
of them synthesized by himself (occasionally blowing up a lab in the  
process...) that in fact contained thorium, hafnium, etc. compounds.  
Radioactive compounds were kept in a little lead box. I am not aware  
of any successful derivatization with the heavy atoms you mention, but  
it certainly wasn't for lack of trying... Some of us went through  
hundreds of trials to get phases. That was in the early to mid 90's. I  
just checked my own dissertation and found that I had indeed used  
dysprosium and hafnium. Since these were not successful I should  
probably write them up and publish in the Journal of Failed  
Crystallization Experiments. Cheers - MM



Mischa Machius, PhD
Associate Professor
Department of Biochemistry
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353



On Apr 1, 2009, at 9:21 AM, Thomas Womack wrote:

A perusal of the PDB reveals that the game of Periodic Table bingo  
still

has eleven rounds to run:

scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium, thulium, hafnium, bismuth and thorium remain absent from  
PDB

entries.

OK, many of these are elements that would rather be refractory  
oxides or

jet-engine components than hexammines, and niobium chloride clusters
don't seem to be as water-stable as Ta6Br14, but why have neodymium,
dysprosium and thulium so consistently been left out there in the cold
rather than admitted to the warmish embrace of carboxyl groups?  There
must somewhere be a protein with a site that cries out for  
ThCl2(2+), an

unexpectedly water-stable cation.

Tom

[ccp4bb] ECM25 in Istanbul - August 16-20 - New Abstract Deadline - April 3

[Wolf-Dieter Schubert]

Dear Colleague,

in case you haven't yet submitted an abstract for the
European Crystallography Meeting (ECM25) scheduled
for August 16 (Sunday) to August 20 (Thursday) in
Istanbul, Turkey, you can still do so until this Friday,
April 3, 2009.

The link to the conference site is:
http://www.ecm25.org/

Apart from taking place in the fascinating city of
Istanbul - where Europe meets Asia - a wide range
of scientific topics should ensure a memorable
stay.

Looking forward to seeing you there.

Best regards,
Wolf-Dieter Schubert

(Secretary of SIG1 - Macromolecular Crystallography)



--
Wolf-Dieter Schubert, Dr.rer.nat.
Molecular Host-Pathogen Interactions (MHPI)
Division of Structural Biology (SB)
Helmholtz-Centre for Infection Research (HZI)
Inhoffenstr. 7
38124 Braunschweig
Germany

phone: +49-531-61817043
fax: +49-531-61817099
wolf-dieter.schub...@helmholtz-hzi.de
www.helmholtz-hzi.de

[ccp4bb] MedImmune - Summer Intern CCP4

[Heather Farrar]

Title: Intern - CCP4
Location: Gaithersburg, MD
Req: 01497

Position Summary: 
Perform testing, data analysis, and computer based structural modeling
in a biophysical characterization group. Correlate model predictions to
data collected by analytical ultracentrifugation, light scattering, and
other techniques. Investigate the biophysical properties, hydrodynamic
properties, and structure of biopharmaceutical products such as
humanized monoclonal antibodies, recombinant antibody derived proteins,
and viral vaccines. 

Major Duties and Responsibilities (including supervising others):
Perform hydrodynamic modeling using the computer programs HYDROPRO and
SOMO. Collect or generate model input data from experiments, previous
data records, and existing protein structure files. Read, understand,
train on, and follow relevant SOP's. Conduct experiments and calculate
simple hydrodynamic parameters or tables. Maintain and calibrate
instruments. Maintain general orderliness of lab and order supplies as
needed. Maintain accurate lab notebook and update lab notes and data
binders. Summarize data at department and group meetings.

 

Experience: 0-2 years lab experience 

Special Skills/Abilities: Ability to generate hypothetical protein
structures (pdb) files from existing protein structure files. General
knowledge of protein biochemistry and analytical laboratory skills. 

 

Education: Enrollment in a Bachelors or Masters program in a scientific
discipline 

 

If you are interested in this position, please visit
www.medimmune.com/careers and type in 01497 to "Search by Req Number".

 

MedImmune, LLC. is an Equal Opportunity Employer and does not
discriminate on the basis of race, color, religion, gender, age,
national origin, disability, veteran status, or any other characteristic
protected by federal, state or local law. 

 

 

 

 

[ccp4bb] Eleven plausible phasing elements remain unused

[Thomas Womack]

A perusal of the PDB reveals that the game of Periodic Table bingo still
has eleven rounds to run:

scandium, titanium, germanium, zirconium, niobium, neodymium,
dysprosium, thulium, hafnium, bismuth and thorium remain absent from PDB
entries.

OK, many of these are elements that would rather be refractory oxides or
jet-engine components than hexammines, and niobium chloride clusters
don't seem to be as water-stable as Ta6Br14, but why have neodymium,
dysprosium and thulium so consistently been left out there in the cold
rather than admitted to the warmish embrace of carboxyl groups?  There
must somewhere be a protein with a site that cries out for ThCl2(2+), an
unexpectedly water-stable cation.

Tom

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[artem]

The impact factor of UAt4 has recently been upgraded from 'huge' to 'all
over the place' after the unfortunate accident at the Miscatonic
university labs which left half the building as glowing multi-colored
glass puddle.

Artem

> What  is the impact factor for that? 100 or 1000?
>
> leo
>
> ar...@xtals.org wrote:
>> Hey,
>>
>> This is *the* place to report my experiments with Uranium (IV) Astatide
>> (UAt4) and Radon for phasing!
>>
>> Artem
>>
>>
>>> Dear Crystallography Community:
>>>
>>>
>> ... good stuff ...
>>
>>> Sehl Oediter
>>> Chief Guy in Charge
>>> Journal of Failed Crystallization Trials
>>> Sell Press
>>> Boston, MA
>>>
>>>
>>
>>
>

Re: [ccp4bb] New human genome policy - please read.

[artem]

In a powerful counter-proposal I recommend that human genes be named after
actual people. I think many of us have heard of the star catalogue - for
fifty bucks you can have a star named after you (not sure if they still do
this). So, the same deal applies - only a bit more expensive because
there's considerably fewer human proteins than theer are stars.

Imagine weary crystallographer coming home:

Darling, we finally solved the structure of Edgar Allan Poe!
What, full-length?
No, unfortunately we had to chop the head off - it was wobbling all over
the  place.

Artem

> H... just saw this.  !!!?!??!
>
>
> 
> The International Human Genome Organization (HUGO) has announced its
> intention to commercialize the naming of human genes. They put it out for
> public consultation, and are asking for responses on their web site (
> http://www.internationalhugo.org/). If you have strong opinions on this,
> please do respond.
> 
>

Re: [ccp4bb] Choosing weighing term

[Ian Tickle]

Hi Hongnan

The standard criterion for choosing the optimum weight(s) is to choose the 
value(s) that minimise Rfree at convergence of the refinement, i.e. at the 
local or global maximum of the likelihood function.  Axel Brunger and his group 
have published a lot of nice work in this area.  Alternatively maximising the 
free likelihood (or equivalently minimising the free negative log likelihood) 
at convergence seems to have a somewhat better statistical justification (see 
Bricogne, G., Methods Enzymol. 1997, 276, 361-423).

So it's not possible to say whether particular value of the weights are 
appropriate for your problem, you have adjust them for each individual case.  
Personally I always use the 'weight auto x' option in Refmac for the X-ray 
weighting since then the weighting term x seems to stay within a reasonable 
range (typically between 1 and 4), and is also incidentally the same term used 
in CNS & (I believe) phenix-refine.

I note you are quoting Rfree only to the nearest 0.01 whereas smaller 
variations than this are probably significant.  If you round Rfree like this 
you won't see the small differences.  The big problem with Rfree is that 
there's no way of knowing what differences are significant, whereas there do 
exist significance tests for the free likelihood.

Hope this helps!

Cheers

-- Ian

> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On
> Behalf Of conancao
> Sent: 01 April 2009 06:13
> To: ccp4 mailing list
> Subject: Choosing weighing term
> 
> Dear All:
> 
>Hi. I have a question about selecting weighing term during
> restrained refinement using Refmac5 of CCP4 packages.
> 
>For a 300kDa homodimer protein structure at 2.5A, 91% complete. I
> obtain optimal R and Rfree by using NCS tight restraints of the peptides
> of the two monomers. Weighing term 0.15 gives (R=0.22, Rfree=0.28) and
> weighing term 0.1 gives(R=0.23, Rfree=0.28). Higher weighing term gives
> larger difference between R and Rfree.
> 
>Is there a criteria or special range of choosing weighing term? Is
> weighing term 0.1 too small? I read the references by Ian Tickle (Acta
> Cryst D, 1998 and 2000)on R and Rfree ratio, those helped a lot but I
> still do not know the key of weighing term.
> 
> Thanks so much.
> 
> Best,
> Hongnan Cao
> Biochemistry Department
> UC Riverside
> 
> 
> 
> 
> 把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！ 


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Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[junfeng liu]

What  is the impact factor for that? 100 or 1000?

leo 


ar...@xtals.org wrote:

Hey,

This is *the* place to report my experiments with Uranium (IV) Astatide
(UAt4) and Radon for phasing!

Artem

  

Dear Crystallography Community:



... good stuff ...
  

Sehl Oediter
Chief Guy in Charge
Journal of Failed Crystallization Trials
Sell Press
Boston, MA




  

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[Boaz Shaanan]

Dear Sehl Oediter,

I am not sure this is the right forum but I cannot resist. While I welcome the 
announcement of this new and important journal, as I'm sure all other members 
of the community do, I'd like to urge you reconsider  for publication the paper 
which I submitted to your journal this morning: "Failures in Crystallization of 
Hen Egg Lysozyme - A Systematic Study". As far as I can see, it meets all the 
criteria advertised in your call for papers, let alone the fact that much human 
effort and resources have been invested in this research in my lab. We also 
prepared a cover picture, which I'm sure you'll find attractive. Please reply 
in private (i.e. not to the list) as this is a too serious issue.

Kind regards,

  Boaz Shaanan
           

- Original Message -
From: Sehl Oediter 
Date: Wednesday, April 1, 2009 12:11
Subject: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments
To: CCP4BB@JISCMAIL.AC.UK

> Dear Crystallography Community:
> 
> I am happy to announce the Journal of Failed Crystallization 
> Experiments, a
> bimonthly publication that highlights the exciting field of failed
> crystallography projects and trials.
> 
> As you are all well aware, most scientific journals have been 
> publishingcrystal structures for quite some time. While crystal 
> structures of
> biologically relevant proteins and protein complexes might be 
> important,they really don't evoke the kind of broader interest 
> as stuff like these
> massive sequencing efforts we have to read about in just about 
> every other
> friggin' article in the big journals. [Ed.: I mean, what could 
> be more
> exciting than shotgun sequencing of the lint that collects in 
> one's belly
> button?] Moreover, solving crystal structures is getting so easy 
> even grad
> students can do it. It's all point-and-click these days. All the 
> real skill
> is in finding some way to clone homologs from every species that 
> ever lived
> and getting those damn things expressed before the grant runs 
> out--maybe one
> of them will diffract and then we'll have a shot at a postdoc, faculty
> position, or even tenure--if the global financial system doesn't 
> collapsefirst, thanks to those crooks on Wall Street.
> 
> To respond to this broader interest (which I only parenthetically
> wholeheartedly share), the owners, editors, and janitorial staff 
> at Sell
> Press have decided that the crystallography community has been 
> sitting on a
> mountain of tedious data since about time immemorial--or maybe a 
> littleafter that, but not much. Moreover, we recognize that all 
> of the easy
> structures have been solved and only the hard ones remain and 
> these hard
> ones are going to take a lot of crystallization trials that will 
> serve as
> fodder for hundreds of pages of supplementary information--which 
> we will be
> sure to include only as jpeg attachments with the hopes that optical
> character recognition will catch up some day, making this 
> supplementaryinformation actually useful. But until then, good 
> luck sifting through it
> because it would have been just as easy to include it as an excel
> spreadsheet or even a tab delimited text file. Don't make the 
> mistake of
> thinking that we can actually use bzip or tar or could even 
> grasp that a pdf
> is fundamentally different from a flat file database. You're 
> lucky we are
> even competent enough to know how to download attachments from 
> our web mail.
> 
> For our first issue, we invite you to submit your most agonizing 
> failures.A4 or letter scoring sheets, scanned at 600 dpi, will 
> suffice for original
> data.  We will also accept pictures of wells with oil or 
> heavy precipitant.
> We have decided that clear wells represent hope for crystals 
> some time in
> the future, so we can't accept pictures of clear wells except 
> when the wells
> have obviously dried completely. (We relish dried wells, let me tell
> you--nothing screams "FAIL!" like a dry well.)  We will 
> accept pictures of
> crystals only if they show no diffraction or at least display 
> irremediablediffraction pathology. Clean diffraction images will 
> be accepted only when
> the author can demonstrate that their project was being scooped 
> concomitantwith data collection.
> 
> Please be aware that the Journal of Failed Crystallization 
> Experiments has a
> strict policy regarding data deposition. All data must be 
> deposited in a
> publicly accessible database and any journal submissions must include
> acquisition identifiers. Moreover, despite the fact that any of 
> dozens of
> software programs might serve as a reference implementation for 
> a data
> format, we have decided to form a committee of mostly clueless 
> computerspecialists to design a confusing and unintelligible 
> data standard for
> failed crystallization trials. Moreover, we will randomly change 
> the format
> approximately once or twice per year. The deposition process 
> will require

Re: [ccp4bb] New human genome policy - please read.

[Kevin Cowtan]

Why molecular weight? That's just arbitrary.

There is a simple way of referring to proteins which avoids any 
ambiguity - by it's sequence. When referring to a protein, we should use 
its sequence as an identifier. No ambiguity.


Now, I understand that some smart people in America are now solving 
proteins of more than a dozen aa in length. For these, quoting the whole 
sequence could be a bit long. Fortunately this is a solved problem: all 
we need to do is quote a CRC64 hash of the ascii representation of the 
protein sequence. This gives a name space big enough that we can name 
about 4 billion proteins before the probability of a name clash becomes 
significant.



James Stroud wrote:
I think actually *naming* the proteins would be too extreme. Even the 
current alpha-numeric system is overwrought. I liked it better when we 
just called proteins "p75" or "p105". For instance, how many proteins in 
the human genome are 75 kD, anyway? My guess is not enough to make the 
situation ambiguous in any catastrophic way.

Re: [ccp4bb] New human genome policy - please read.

[James Stroud]

I think actually *naming* the proteins would be too extreme. Even the  
current alpha-numeric system is overwrought. I liked it better when we  
just called proteins "p75" or "p105". For instance, how many proteins  
in the human genome are 75 kD, anyway? My guess is not enough to make  
the situation ambiguous in any catastrophic way.



On Apr 1, 2009, at 3:16 AM, Frank von Delft wrote:


H... just saw this.  !!!?!??!



The International Human Genome Organization (HUGO) has announced its  
intention to commercialize the naming of human genes. They put it  
out for public consultation, and are asking for responses on their  
web site ( http://www.internationalhugo.org/). If you have strong  
opinions on this, please do respond.

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[artem]

Hey,

This is *the* place to report my experiments with Uranium (IV) Astatide
(UAt4) and Radon for phasing!

Artem

> Dear Crystallography Community:
>
... good stuff ...
> Sehl Oediter
> Chief Guy in Charge
> Journal of Failed Crystallization Trials
> Sell Press
> Boston, MA
>

Re: [ccp4bb] New human genome policy - please read.

[jane . wibley]

April Fools Day? I hope so!!

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Frank von Delft
Sent: 01 April 2009 11:16
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] New human genome policy - please read.

H... just saw this.  !!!?!??!




The International Human Genome Organization (HUGO) has announced its
intention to commercialize the naming of human genes. They put it out
for public consultation, and are asking for responses on their web site
( http://www.internationalhugo.org/). If you have strong opinions on
this, please do respond.

 
 
Syngenta Limited, Registered in England No 2710846
Registered Office : Syngenta Limited, European Regional Centre, Priestley Road, 
Surrey Research Park, Guildford, Surrey, GU2 7YH, United Kingdom 


This message may contain confidential information. If you are not the 
designated recipient, please notify the sender immediately, and delete the 
original and any copies. Any use of the message by you is prohibited.

Re: [ccp4bb] Building structure in COOT

[Anastassis Perrakis]

On Apr 1, 2009, at 4:35, Liew Chong Wai wrote:


Hi,

Good day
I am currently building my structure by using COOT. My protein is a  
tetramer protein and I have fit my protein sequence into one of the  
monomer of the homologous model. May I know how can I replace other  
monomer with the amended monomer??

Thanks



I admit that a trick I found useful, is after building one chain do a  
molecular replacement with this as a model and lookign for four  
copies. Then go back to Coot ... avoids thinking about rotations  
matrixes which is always a challenge (for me that is).


Tassos



Chong-wai



P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

Re: [ccp4bb] Choosing weighing term

[Anastassis Perrakis]

On Apr 1, 2009, at 7:12, conancao wrote:


Dear All:

   Hi. I have a question about selecting weighing term during  
restrained refinement using Refmac5 of CCP4 packages.


   For a 300kDa homodimer protein structure at 2.5A, 91%  
complete. I obtain optimal R and Rfree by using NCS tight restraints  
of the peptides of the two monomers. Weighing term 0.15 gives  
(R=0.22, Rfree=0.28) and weighing term 0.1 gives(R=0.23,  
Rfree=0.28). Higher weighing term gives larger difference between R  
and Rfree.


   Is there a criteria or special range of choosing weighing  
term? Is weighing term 0.1 too small? I read the references by Ian  
Tickle (Acta Cryst D, 1998 and 2000)on R and Rfree ratio, those  
helped a lot but I still do not know the key of weighing term.


The absolute value of the weighing term is rather irrelevant - it has  
no physical meaning.
A term of 0.1 for 2.5 A data sounds about right in my experience, and  
from what you say.


What you could try to do is to play a bit with the Bweight as well  
(look at ccp4i under the Restraints panel).


At 2.5 you might want to try and relaxing NCS restraints (use medium  
or exclude some regions that have a reason to be different, if they  
are eg in a different crystal contact environment in each copy) and  
see if they lower the Rfree. I also presume you use TLS.


Tassos





Thanks so much.

Best,
Hongnan Cao
Biochemistry Department
UC Riverside

把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！


P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

[ccp4bb] New human genome policy - please read.

[Frank von Delft]

H... just saw this.  !!!?!??!



The International Human Genome Organization (HUGO) has announced its intention 
to commercialize the naming of human genes. They put it out for public 
consultation, and are asking for responses on their web site ( 
http://www.internationalhugo.org/). If you have strong opinions on this, please 
do respond.

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[Adam Ralph]

What's the date today? It must be Christmas I have lots of stuff to
publish. A

Re: [ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[Rajesh Ponnusamy]

Ha ha ha  Good Try..Better luck next time !!!... Mr. Sehl Oediter !!!



Sehl Oediter wrote:

Dear Crystallography Community:

I am happy to announce the Journal of Failed Crystallization 
Experiments, a bimonthly publication that highlights the exciting 
field of failed crystallography projects and trials.


As you are all well aware, most scientific journals have been 
publishing crystal structures for quite some time. While crystal 
structures of biologically relevant proteins and protein complexes 
might be important, they really don't evoke the kind of broader 
interest as stuff like these massive sequencing efforts we have to 
read about in just about every other friggin' article in the big 
journals. [Ed.: I mean, what could be more exciting than shotgun 
sequencing of the lint that collects in one's belly button?] Moreover, 
solving crystal structures is getting so easy even grad students can 
do it. It's all point-and-click these days. All the real skill is in 
finding some way to clone homologs from every species that ever lived 
and getting those damn things expressed before the grant runs 
out--maybe one of them will diffract and then we'll have a shot at a 
postdoc, faculty position, or even tenure--if the global financial 
system doesn't collapse first, thanks to those crooks on Wall Street.


To respond to this broader interest (which I only parenthetically 
wholeheartedly share), the owners, editors, and janitorial staff at 
Sell Press have decided that the crystallography community has been 
sitting on a mountain of tedious data since about time immemorial--or 
maybe a little after that, but not much. Moreover, we recognize that 
all of the easy structures have been solved and only the hard ones 
remain and these hard ones are going to take a lot of crystallization 
trials that will serve as fodder for hundreds of pages of 
supplementary information--which we will be sure to include only as 
jpeg attachments with the hopes that optical character recognition 
will catch up some day, making this supplementary information actually 
useful. But until then, good luck sifting through it because it would 
have been just as easy to include it as an excel spreadsheet or even a 
tab delimited text file. Don't make the mistake of thinking that we 
can actually use bzip or tar or could even grasp that a pdf is 
fundamentally different from a flat file database. You're lucky we are 
even competent enough to know how to download attachments from our web 
mail.


For our first issue, we invite you to submit your most agonizing 
failures. A4 or letter scoring sheets, scanned at 600 dpi, will 
suffice for original data.  We will also accept pictures of wells with 
oil or heavy precipitant. We have decided that clear wells represent 
hope for crystals some time in the future, so we can't accept pictures 
of clear wells except when the wells have obviously dried completely. 
(We relish dried wells, let me tell you--nothing screams "FAIL!" like 
a dry well.)  We will accept pictures of crystals only if they show no 
diffraction or at least display irremediable diffraction pathology. 
Clean diffraction images will be accepted only when the author can 
demonstrate that their project was being scooped concomitant with data 
collection.


Please be aware that the Journal of Failed Crystallization Experiments 
has a strict policy regarding data deposition. All data must be 
deposited in a publicly accessible database and any journal 
submissions must include acquisition identifiers. Moreover, despite 
the fact that any of dozens of software programs might serve as a 
reference implementation for a data format, we have decided to form a 
committee of mostly clueless computer specialists to design a 
confusing and unintelligible data standard for failed crystallization 
trials. Moreover, we will randomly change the format approximately 
once or twice per year. The deposition process will require that your 
data conform to our obscure standard. If it doesn't, we will advise 
you with senseless error messages or perhaps our servers will crash. 
We may even drop your connection so your browser will sit there 
indefinitely just not refreshing and you forgot to note the session ID 
before you uploaded your data. Tough luck. Start again. Oh but wait, 
the page isn't coming up. Restart your browser. Tough luck again. Try 
rebooting. Nothing. Must be our server. Try again tomorrow.


To entice the community into submitting their reports, we offer the 
following tantalizing abstract (to be published in our first issue 
along with the corresponding article):


=
/The 5-HT serotonin receptor serves as the receptor for the serotonin 
neurotransmitter and is also the target of many pharmaceutical and 
psychotropic compounds. Here we show that this receptor just can't be 
crystallized, no matter what we do. We chopped off the N-terminus, the 
C-terminus, the transmembrane region, and even fused different parts 
together 

[ccp4bb] [ANNOUNCE] Journal of Failed Crystallization Experiments

[Sehl Oediter]

Dear Crystallography Community:

I am happy to announce the Journal of Failed Crystallization Experiments, a
bimonthly publication that highlights the exciting field of failed
crystallography projects and trials.

As you are all well aware, most scientific journals have been publishing
crystal structures for quite some time. While crystal structures of
biologically relevant proteins and protein complexes might be important,
they really don't evoke the kind of broader interest as stuff like these
massive sequencing efforts we have to read about in just about every other
friggin' article in the big journals. [Ed.: I mean, what could be more
exciting than shotgun sequencing of the lint that collects in one's belly
button?] Moreover, solving crystal structures is getting so easy even grad
students can do it. It's all point-and-click these days. All the real skill
is in finding some way to clone homologs from every species that ever lived
and getting those damn things expressed before the grant runs out--maybe one
of them will diffract and then we'll have a shot at a postdoc, faculty
position, or even tenure--if the global financial system doesn't collapse
first, thanks to those crooks on Wall Street.

To respond to this broader interest (which I only parenthetically
wholeheartedly share), the owners, editors, and janitorial staff at Sell
Press have decided that the crystallography community has been sitting on a
mountain of tedious data since about time immemorial--or maybe a little
after that, but not much. Moreover, we recognize that all of the easy
structures have been solved and only the hard ones remain and these hard
ones are going to take a lot of crystallization trials that will serve as
fodder for hundreds of pages of supplementary information--which we will be
sure to include only as jpeg attachments with the hopes that optical
character recognition will catch up some day, making this supplementary
information actually useful. But until then, good luck sifting through it
because it would have been just as easy to include it as an excel
spreadsheet or even a tab delimited text file. Don't make the mistake of
thinking that we can actually use bzip or tar or could even grasp that a pdf
is fundamentally different from a flat file database. You're lucky we are
even competent enough to know how to download attachments from our web mail.

For our first issue, we invite you to submit your most agonizing failures.
A4 or letter scoring sheets, scanned at 600 dpi, will suffice for original
data.  We will also accept pictures of wells with oil or heavy precipitant.
We have decided that clear wells represent hope for crystals some time in
the future, so we can't accept pictures of clear wells except when the wells
have obviously dried completely. (We relish dried wells, let me tell
you--nothing screams "FAIL!" like a dry well.)  We will accept pictures of
crystals only if they show no diffraction or at least display irremediable
diffraction pathology. Clean diffraction images will be accepted only when
the author can demonstrate that their project was being scooped concomitant
with data collection.

Please be aware that the Journal of Failed Crystallization Experiments has a
strict policy regarding data deposition. All data must be deposited in a
publicly accessible database and any journal submissions must include
acquisition identifiers. Moreover, despite the fact that any of dozens of
software programs might serve as a reference implementation for a data
format, we have decided to form a committee of mostly clueless computer
specialists to design a confusing and unintelligible data standard for
failed crystallization trials. Moreover, we will randomly change the format
approximately once or twice per year. The deposition process will require
that your data conform to our obscure standard. If it doesn't, we will
advise you with senseless error messages or perhaps our servers will crash.
We may even drop your connection so your browser will sit there indefinitely
just not refreshing and you forgot to note the session ID before you
uploaded your data. Tough luck. Start again. Oh but wait, the page isn't
coming up. Restart your browser. Tough luck again. Try rebooting. Nothing.
Must be our server. Try again tomorrow.

To entice the community into submitting their reports, we offer the
following tantalizing abstract (to be published in our first issue along
with the corresponding article):

=
*The 5-HT serotonin receptor serves as the receptor for the serotonin
neurotransmitter and is also the target of many pharmaceutical and
psychotropic compounds. Here we show that this receptor just can't be
crystallized, no matter what we do. We chopped off the N-terminus, the
C-terminus, the transmembrane region, and even fused different parts
together that had no business being together. Moreover, we tried just about
every crystallization reagent in the book. We used PEG, lipids, salts, and
extreme pH conditions. We trie

Re: [ccp4bb] Building structure in COOT

[Paul Emsley]

David Cobessi wrote:

Liew Chong Wai wrote:

Hi,
 
Good day
I am currently building my structure by using COOT. My protein is a 
tetramer protein and I have fit my protein sequence into one of the 
monomer of the homologous model. May I know how can I replace other 
monomer with the amended monomer??

Thanks
 
*Chong-wai*
 

Hi Chong-wai,
Several possibilities to generate the tetramer from the monomer, let 
say A.
You can calculate the RT matrices ( in CCP4 or using LSQMAN and 
MOLEMAN2 or using O for example) to superpose the monomer A onto B, C 
and D and then apply these matrices to the amended monomer (A) in 
order to generate the tetramer.
You can also superpose the monomer A onto B in COOT by using SSM or 
LSQ and save the new position as monomer B in COOT etc... and then 
you can generate 4 monomers and the tetramer. Do not forget to change 
the chain ID before refinement.




Blimey.

Extensions -> NCS -> Copy NCS Chain...

See Section 5.27 of the user manual for more information.

http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC137

Paul