Re: [ccp4bb] delete subject

2013-03-27 Thread VAN RAAIJ , MARK JOHAN

Dear Tom,
don't feel too bad about it - everyone can make a mistake.
Some of the replies give crystallographic tips that may be useful to  
other beginning and not-so-beginning crystallographers. Although I  
agree the attachments to the first mail would perhaps better be  
deleted from the records.

Greetings,
Mark


Quoting Tom Van den Bergh tom.vandenbe...@student.kuleuven.be:

Is it possible to delete my post: refinement protein structure from  
ccp4 bb, i get too many bad reactions. I think its bettter to just  
delete the whole topic.


Greetings,

Tom


Re: [ccp4bb] Strange density

2012-11-28 Thread VAN RAAIJ , MARK JOHAN

could it be a PEG molecule?

Quoting Read, Jon:


Anyone see anything like this before? The data is 1.7Angstrom data with
good statistics. The picture shows the solid FoFc density contoured at 3
Sigma in light brown and -3 Sigma in purple. The density is odd as it
appears to be bound to a peptide carbonyl with no other obvious
interactions with the protein. There is a characteristic tail at one
end.










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Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] ccp4mg question

2012-11-15 Thread VAN RAAIJ , MARK JOHAN
possible ugly workaround: renumber the pdb file so where ccp4mg thinks  
the N and C-termini are is hidden in the image you are making (if  
possible)
if you want to make different views you may need to make differently  
renumbered pdb files.

(but probably other people have a smarter way)
as an aside, PyMol I think does not have these problems, at least we  
make images of cyclic peptides with it and I haven't run into it.


Quoting SANCHEZ BARRENA, MARIA JOSE:


Dear all,
I am working with a cyclic protein and I am trying to make a figure  
with ccp4mg. I would like to know how to say to ccp4mg that the N  
and C-terminus are bound Although atoms are at a covalent bond  
distance, the chain is broken by ccp4mg...

Many thanks in advance for your suggestions and help!
Maria




Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] side chain density

2012-11-10 Thread VAN RAAIJ , MARK JOHAN
before modelling a long side-chain in non-existing or dubious density,  
also make sure it is really there in the protein by sequencing your  
expression plasmid. Your arginine (for example) may in fact be a  
serine or glycine...databases are not 100% accurate and neither is PCR  
if it was used in the cloning.


Quoting Ed Pozharski:


OK, here we go again.

This has been argued ad nauseam, see for example

http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19738.html
or
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20268.html

(hard to believe we have gone more than a year without another  
version of what to do with disordered side chains 250-post long  
discussion :)


I do not have much to add to the above, however

On 11/09/2012 05:22 PM, Matthew Franklin wrote:
I think we can all agree that virtually every structure in the PDB  
will have a few residues where some of the atoms are not visible in  
the density.  So the trim the side chains crowd is a  
well-represented minority at 30%, but 70% of depositors chose  
another option.
This maybe the historical average, I suspect that currently the  
trim the side chains crowd may be at least at 50% (but what about  
Ohio? :).  Majority, however, is not always right (don't get me  
started on I-over-sigma ratios).


I personally like to leave all atoms on the side chains; they look  
wrong to me when beheaded.  I just try to put the invisible atoms  
in a stereochemically plausible conformation, leave the occupancy  
set to 1, and let the refinement program deal with them.


With all due respect, to model something where there is no density  
(aka experimental evidence) cannot be justified by aesthetics.  On  
the contrary, there is some evidence suggesting that modelling  
disordered side chains in the way you describe adds small, but  
detectable error to the rest of the model.


Cheers,

Ed.

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





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] protein cleavage

2012-11-04 Thread VAN RAAIJ , MARK JOHAN
We once had a more-or-less MBP-sized fragment before cleavage, but  
this turned to be a spontaneous mutation. This expression experiment  
had been started from a glycerol stock with an unknown number of  
growth cycles prior to expression.
Starting from a fresh transformation with the purified and sequenced  
plasmid solved the problem.
Since then, I insist everybody does a fresh transformation before  
every expression experiment and not generate extra growth/dilution  
cycles beyond the normal transformation, growth on plate, overnight  
culture, dilution into large-scale expression culture.



Quoting Bosch, Juergen:


@Cynthia,
On Nov 4, 2012, at 10:58 AM, Cynthia Kinsland wrote:

Since you're seeing the MBP band, it sounds as if you're getting  
some cleavage.  If there were no cleave you would only see the  
fusion and TEV bands on the gel.


I think that is a wrong assumption.
He did not specify if he sees the MBP band also just before TEV  
addition - it might also be truncation products which we happen to  
see all the time. The ratio varies depending on the construct but it  
can be as bad as a 1:1 ratio. You can really only tell if TEV  
cleaves if you do a time course experiment at RT with a defined  
amount of your protein and see if the fusion construct decreases. An  
alternative for the lack of your 17kDa desired band is simply your  
fusion construct is cleaved but your cleaved product might a) not be  
soluble at that pH or b) aggregates and precipitates.
You might be able to perform the cleavage on the Amylose column  
keeping a constant flow cycling.


Jürgen


..
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Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry  Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
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Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] Plate crystals

2012-10-16 Thread VAN RAAIJ , MARK JOHAN
apart from optimising the crystallisation conditions, it might be  
worth optimising the protein preparation or do some limited  
proteolysis - or even express short N-terminal and/or C-terminal  
deletions.

Mark

Quoting Patrick Shaw Stewart:


Jahan

It sounds as though the protein crystallizes well, so microseeding (done
the right way) is very likely to solve the problem.  Make a strong seed
stock with as much crystalline material as possible from several wells,
including different hits if possible.  Just mix them all together, but keep
PEG conditions separate from salt conditions (or you will get two layers).
 Make a set of serial dilutions from neat up to 1 in 100,000 and freeze
them at -80.  You need to seed into *random screens*, so that you can pick
up new conditions.  Then you should optimize two or three new conditions by
using the diluted seed stock.  For example, if you estimate that there are
1000 crystals in the drop, you use the 1:1000 dilution.

For info and references see http://www.douglas.co.uk/mms.htm


On 15 October 2012 23:01, Jahan Alikhajeh ja...@graduate.org wrote:



Dear Friends,

I am trying to crystalize a 70 kDa nasty protein but I got plate shape
crystals with high mosaicity and useless diffraction (up to 4A).
I tried to improve/optimize crystallization but either I got the same or
nothing. I tried seeding but I had so many crystals without any
improvement. Does anyone have better idea than routine optimization method
in the lab? Thanks in advance.

Jahan





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Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] how to interpret DALI search results

2012-06-12 Thread VAN RAAIJ , MARK JOHAN
if this is the first (or second, or third) time you do a DALI search,  
take the list output from DALI, start from the top and superpose each  
structure with yours and look at the superpositions with your  
favourite superposition software.
This is very educational and the only way you get a feeling for what  
numbers mean.



Quoting Jerry McCully:



Dear ALL;

After we solved our structure by anomalous scattering, we  
did a DALI search. Here are the results but it is not easy to draw  
meaningful conclusions whether our structure represents a novel fold  
or is homologous to others.


   Basically the Z-score is between 2 and 6.4 since our  
structure only contains 130 residues. Sequence identity is between 5  
to 15%.


   The RMSD of structural alignment is between 2.5 to 6 angstrom.

   Any suggests to interpret the DALI results? Many thanks,

Jerry McCully







Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] how to interpret DALI search results

2012-06-12 Thread VAN RAAIJ , MARK JOHAN

...I meant visualisation software of course...

Quoting VAN RAAIJ , MARK JOHAN:

if this is the first (or second, or third) time you do a DALI  
search, take the list output from DALI, start from the top and  
superpose each structure with yours and look at the superpositions  
with your favourite superposition software.
This is very educational and the only way you get a feeling for what  
numbers mean.



Quoting Jerry McCully:



Dear ALL;

   After we solved our structure by anomalous scattering, we  
did a DALI search. Here are the results but it is not easy to draw  
meaningful conclusions whether our structure represents a novel  
fold or is homologous to others.


  Basically the Z-score is between 2 and 6.4 since our  
structure only contains 130 residues. Sequence identity is between  
5 to 15%.


  The RMSD of structural alignment is between 2.5 to 6 angstrom.

  Any suggests to interpret the DALI results? Many thanks,

Jerry McCully







Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] Off-topic: PDB deposition of multiple structure factor files

2012-04-27 Thread VAN RAAIJ , MARK JOHAN
so perhaps the problem indeed is sending different wavelengths as one  
file...in our case there is only one crystal, one wavelength, i.e. one  
loop, while I clearly submitted all three wavelengths.




Quoting Miller, Mitchell D.:


We (JCSG) too have been depositing multiple data sets (including unmerged
original index intensities for each wavelength and even for multiple crystals
when one was used for phasing and another for refinement, and MAD phases
and DM modified map coefficients) since 2004 without problems. These
are all in separate data loops of a single structure factor file.
Regards,
Mitch

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf  
Of Jens Kaiser

Sent: Friday, April 27, 2012 11:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: PDB deposition of multiple  
structure factor files


It might be a portal issue. But the pdb staff is very helpful in getting
this deposited. We deposited data of I think 4 crystals and 3
wavelengths with different phase sets in 2008. (The data was
anisotropic, 3.5/4.2 A resolution, model building was not straight
forward, so we wanted to preserve as much information as possible. If
memory serves right, we have experimental fobs, anisotropy corrected
fobs, a derivative and a semet dataset; if you're interested, pdb code
is 3dhw, have a look at the sf-file)
hth,

Jens

On Fri, 2012-04-27 at 20:35 +0200, Mark J van Raaij wrote:

again, it looks like this is particular to the US portal.
We submit via the European www.pdbe.org and can submit multiple datasets.
See 2XGF for an example.
Note: I think from www.rcsb.org only one file can be downloaded,  
but www.pdbe.org clearly shows both.
Although you are in the US, you can use the pdbe deposition tool  
AUTODEP - or the Japanese one, if you like.


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote:

 Dear All,

 With my most recent PDBe deposition, in addition to the native  
data, I had intended to deposit the anomalous data, used for  
structure determination, and make it available for download. This  
turned out to be less straightforward than I had anticipated,  
because the current PDB convention is to only allow a single  
structure factor file for experimental data (usually the native  
dataset), available for download from the PDB. In my case, the  
anomalous data were concatenated with the native data into a single  
cif file (this worked and made sense, because both for both  
datasets the unit cell dimensions are virtually identical).


 I imagine it would be beneficial to be able to make available  
more than a single structure factor file, including the ones  
derived from experimental phasing, in the PDB, along with the final  
coordinates, without concatenating the data into a single file  
(which may lead to confusion to users when downloaded). Is this  
anything the PDB is already working to implement in the near future  
(perhaps via the coming PDBx format)?


 Best regards,

 Florian


















Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] negative difference density around sulphur and oxygen atoms

2012-04-04 Thread VAN RAAIJ , MARK JOHAN
apart from radation damage it could be a combination of: 
- too tight restraints on the B-factors 
- 9 sigma not being that much on a the e/A3 scale, i.e. your difference map is 
very flat (which is good) and the few peaks that remain stand out a lot, even 
if their absolute height is low... 

Quoting Chris Meier:

Message

Dear all,

I am refining the X-ray structure of a protein:
Data to ~2A were collected at a latest-generation synchrotron.
The 2fo-Fc maps are crisp, the model of the protein is complete and I
am reasonably happy with the stats (R below 20%, Rfree below 25% in
Refmac 5.5).

However, I am seeing a lot of negative difference density,
especially around sulphur atoms (negative density around -9 sigma)
and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues
with negative density around -6 sigma).

Has anyone observed this before?

I have found CCP4bb postings discussing radiation damange of suplphur
atoms
(e.g.
http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html
).
Can this also happen with oxygen atoms?

What would be an appropriate way to deal with this issue during
refinement?

Suggestions greatly appreciated.

Thanks,
Chris

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

[ccp4bb] PEG MME 2000 in powder form?

2012-04-04 Thread VAN RAAIJ , MARK JOHAN


Dear All, 

is PEG MME 2000 still available in powder form? I think Fluka used to sell it, 
but Fluka is no more and Sigma-Aldrich don't sell it. 

Hampton Research and Molecular Dimensions (and perhaps others) do sell 50% 
(w/v) solutions. 

Mark 

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] PEG MME 2000 in powder form?

2012-04-04 Thread VAN RAAIJ , MARK JOHAN

ok, I stand corrected, Sigma DOES sell it, but under a slightly different name: 

81321 FLUKA 
Poly(ethylene glycol) methyl ether average Mw 2,000 

81321-250G, 23.60 euros 

81321-1KG, 71.80 euros   

(prices given for Spain) 

thanks! 

Quoting VAN RAAIJ , MARK JOHAN:



 Dear All,

 is PEG MME 2000 still available in powder form? I think Fluka used to 
 sell it, but Fluka is no more and Sigma-Aldrich don't sell it.

 Hampton Research and Molecular Dimensions (and perhaps others) do 
 sell 50% (w/v) solutions.

 Mark

 Mark J van Raaij
 Laboratorio M-4
 Dpto de Estructura de Macromoléculas
 Centro Nacional de Biotecnología - CSIC
 c/Darwin 3, Campus Cantoblanco
 28049 Madrid
 tel. 91 585 4616
 email: mjvanra...@cnb.csic.es

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

2012-04-01 Thread VAN RAAIJ , MARK JOHAN

another singular/plural grump:
Recently we can read: phage are.
Phage is singular, the plural is phages (and this does not have that  
much to do with latin or greek).

more reading:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109450/

Quoting Paul Emsley:


The PDBe page for 3k78 says:

The experimental data has been deposited

the data cif file says:

data is under question

Grump.

Is it to late to refer to data as if there were more than one of them?

Anyway, the data mtz file is here if you want to refine with it:

http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz

Paul.





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] one datum many data?

2012-04-01 Thread VAN RAAIJ , MARK JOHAN

and using dice for the singular die

Quoting Robert Blessing:


How can spectrum and spectra have been overlooked in this thread?

Síocháin!  Sláinte!
  In Irish:  Peace!  Health!
  Pronounced roughly Shee'-kahn, Slawn'-tche.

Bob

Robert H. Blessing, Ph.D.
Senior Research Scientist
  Hauptman-Woodward Medical Research Institute, Inc.
Professor of Structural Biology and Research Professor of Chemistry
Director of Graduate Studies in Structural Biology
Interim Chairman of the Department of Structural Biology
  State University of New York at Buffalo

Hauptman-Woodward Institute
700 Ellicott Street
Buffalo, New York 14203, USA
  Phone  716-898-8613
  Fax716-898-8660
  eMail  bless...@hwi.buffalo.edu
  Internet   http://www.hwi.buffalo.edu





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] How to reduce no. of overlaps

2012-03-06 Thread VAN RAAIJ , MARK JOHAN
typo correction, you'll want the long axis parallel to the rotation  
axis, not to the beam.

Mark

Quoting Frank von Delft:

You probably have to tilt your crystal, so that the long axis is  
parallel to the beam.  We do this routinely:  cut a plastic pipette  
tip to have a sharp point, then push the loop where it attaches to  
the pin, to bend the crystal itself.


You have to identify from your diffraction whether the long axis is  
pointing through the face or the edge of the loop.  As it's P6,  
chances are it's through the face, because long-axis P6 tends to  
make flat hexagons which lie flush with the face.  So you have to  
bend so the face of the loop upwards.


You'll have to practice this first, though, so put up an empty loop.  
 Top tips:

* Don't breathe!  You'll blow the cryostream away.
* Bend the loop towards (rather than away from) the rim edge of  
the pin to which it's glued.

* Don't breathe!
* Practise practise practise.


Another thing:  most in-house sources allow you to reduce divergence  
of the beam.  You lose intensity, but no matter, just expose longer.  
 That also improves overlap.


Cheers
phx



On 07/03/2012 04:56, Dipankar Manna wrote:


Dear Crystallographers,

I am working on a protein having SG P6, the cell parameters are a=  
79, b= 79, c= 325. The crystals are forming in big size and with  
very good shape. It also diffracting very well in Home source  
facility both in terms of resolution and intensity. But the only  
problem is the number of overlaps. Its showing much more than the  
good spots. As a result the completeness is showing maximum up to  
65% even after collecting 180 degrees. I am unable to get a  
complete data. I tried with reducing the oscillation angel to 0.3  
degree/0.5 degree but it did not improve that much. Please give me  
some suggestions.


Regards,

Dipankar

/Dipankar Manna/

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Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] pH optimisation for crystallisation

2012-02-07 Thread VAN RAAIJ , MARK JOHAN

Dear Sreetama,
First of all, there are no hard-and-fast rules for successful  
crystallisation, try changing as many different variables as possible  
and go with what works.
Having said that, yes, next I would go for a grid optimisation varying  
the pH in 0.2 or 0.5 units over as wide a range as the buffer can  
reasonable tolerate at the same molarity, and try different  
precipitant concentrations on the other axis.
If you have enough protein, try plates at different temperatures as  
well, and different protein concentrations (in multidrop wells you can  
do this in the same experiment).
A very important variable is the protein preparation itself, prepare  
more protein regularly and try to improve on purity and concentration.

Mark

Quoting sreetama das:


Dear all,
   I have a 17 KDa protein that gives crystals in a  
condition that has 0.1M bis-tris pH 6.5. The crystals are thin  
needle clusters and do not diffract. I have tried additives, but  
they haven't improved the crystals. I intend to vary the pH of the  
condition.

   My questions are-
1. should the buffer be kept the same or can it also be changed (as  
long as the desired pH is within the range of both the buffers)?
2. in case of a different buffer, should its molarity be the same as  
that of the original one in the crystallization condition?


regards,
sreetama





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] symmetry for ages 6 and up

2011-12-13 Thread VAN RAAIJ , MARK JOHAN

reminds me of these symmetric 2D P3 lizards:
http://www.worldofescher.com/store/Z51.html
I bought the RGB-coloured set/puzzle after visiting an Escher  
exhibition and sometimes use them in crystallography/symmetry teaching.
Nice to make the students assemble them and then decide on the  
symmetry operator, unit cell and asymmetric unit.


Quoting Phoebe Rice:


Hi all,
  For those who teach xtallography - we found some plastic turtles  
that can be snapped together in an amazing variety of space groups.   
Worked well in a workshop for our students, so I thought I'd share  
the shopping tip.  They're called Reptangles, and we got them from  
Amazon.


http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4

Have fun!

  Phoebe

=
Phoebe A. Rice
Dept. of Biochemistry  Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] symmetry for ages 6 and up

2011-12-13 Thread VAN RAAIJ , MARK JOHAN

(oops, previous mail got sent before I wanted)

the turtles would be really nice to extend things into 3D.
great find,
Mark

Quoting Phoebe Rice:


Hi all,
  For those who teach xtallography - we found some plastic turtles  
that can be snapped together in an amazing variety of space groups.   
Worked well in a workshop for our students, so I thought I'd share  
the shopping tip.  They're called Reptangles, and we got them from  
Amazon.


http://www.amazon.com/Fat-Brain-Toys-FA042-1-Reptangles/dp/B00392NSQ4

Have fun!

  Phoebe

=
Phoebe A. Rice
Dept. of Biochemistry  Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es


Re: [ccp4bb] SeMET inconsistency

2011-10-22 Thread VAN RAAIJ , MARK JOHAN
Dear Kavya, 
I don't think it is likely you have five MSE and one MET. Rather, I would guess 
the side-chain has some disorder, i.e. one or more alternative conformations. 
If you don't see density for alternative conformations, the best way to model 
the disorder might be partial occupancy of the MSE that gives negative 
difference density peaks. 
Mark 

Quoting Kayashree M:

Dear users,

I had posted this question already but in a different context.

One of the Se-Met derivatised protein that we have solve is a
homodimer
(with 4 MET in the chains that crystallised) of which one chain has 3
MSE
residues, while the other chain has only 2 MSE.

Are there any such instances in PDB, where two homodimer (or any mer)
wherein each has different percentage of MSE?
Because when we change the only MET to MSE a negative density would
arise. The tools to analyse anomalous peaks is not giving peaks for
the
MSE residues as the data was collected at 1.541Ang wavelength.

Thank you
Kavya

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Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] Complex seeding

2011-09-22 Thread VAN RAAIJ , MARK JOHAN
agree, any crystallisation idea is worth pursuing, given you have or can make 
enough sample to try it with.
having said that, wouldn't you tend to select for the same crystals as the 
seed, i.e. crystals of the component on its own?
have you tried limited proteolysis of your sample, incl. a bit of protease in 
the drop - or can you think of ways to stabilise the complex?
Mark

Quoting Ed Pozharski:

 On Wed, 2011-09-21 at 18:04 +0100, Peter Hsu wrote:
 Or is this just a crazy/bad idea?

 If there is one thing that I learned about crystallization, is that very
 few ideas are so crazy that they are bad (i.e. not worth trying).  Well,
 if dried seaweed and ground horse hair are good for seeding, I don't see
 how actual protein crystal seeds can be dismissed.



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

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] Complex seeding

2011-09-21 Thread VAN RAAIJ , MARK JOHAN

agree, any crystallisation idea is worth pursuing, given you have or can make 
enough sample to try it with. 
having said that, wouldn't you tend to select for the same crystals as the 
seed, i.e. crystals of the component on its own? 
have you tried limited proteolysis of your sample, incl. a bit of protease in 
the drop - or can you think of ways to stabilise the complex?Mark 

Quoting Ed Pozharski:

 On Wed, 2011-09-21 at 18:04 +0100, Peter Hsu wrote:
 Or is this just a crazy/bad idea?

 If there is one thing that I learned about crystallization, is that very
 few ideas are so crazy that they are bad (i.e. not worth trying).  Well,
 if dried seaweed and ground horse hair are good for seeding, I don't see
 how actual protein crystal seeds can be dismissed.



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


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] Data from old tapes

2011-07-19 Thread VAN RAAIJ , MARK JOHAN
did you try looking if there is a company offering data recovery services from 
these kind of tapes? 
if there is, there may not be a need to buy a tape drive yourself.Mark 

Quoting Min, Xiaoshan:

 Dear CCP4 community,

 We have a few datasets that reside in tapes (Sony QG-112M 8 mm tape 
 and Maxell DDS-2 4 mm tape).  I have been searching the internet for 
 tape drives ( and cable) but haven't found anything.   Does anyone 
 know where we can purchase compatible tape drives for these lovely 
 tapes? Or if you have a spare working set sitting in your graphic 
 room and would like to sell them, that will be wonderful.   Thanks.


 Xiaoshan Min. Ph.D.
 Molecular Structure
 Amgen San Francisco
 1120 Veterans Blvd.
 South San Francisco, CA 94080



Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] Off topic question. NACCESS

2011-06-19 Thread VAN RAAIJ , MARK JOHAN
Dear Armando, 
don't know about NACCESS, but I guess it is superseded by AREAIMOL in CCP4 
(also in CCP4i); it outputs the accessible volume per atom in the pdb file and 
per residue and per chain and some other statistics in the log-file. 
Mark 

Quoting Armando Albert:

 Does anyone has got some information about how to get a mac version 
 (intel), of the old unix program naccess?. It was meant  to calculate 
 the solvent accessibility per residue from a pdb file.
 Armando

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] how to quantitate protein which dont have ne aromatic residue

2011-04-09 Thread VAN RAAIJ , MARK JOHAN
you can do amino acid analysis on your pure protein, using a commercial or 
academic service - I hope these are still around. You should only need to do 
this once, then relate the result to your A220, BCA and Bradford assays. 
Mark 

Quoting Arpit Mishra:

 hello everybody

 i am working on the protien which dont have any aromatic residue  i do fplc
 other purification using 220 absorption, but i want to quantitate protein
 precisely i have tried using BCA nd bradford but both methods quantification
 is not matching,,so any one is having sum idea how to quantitate it
 precisely

 thanks in advance for your valuable suggestion..


 Arpit Mishra


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] OT: PCR instrument

2011-04-03 Thread VAN RAAIJ , MARK JOHAN

if the PCR machine is just to be used for standard sub-cloning (amplifying 
fragments from other plasmids, cloned cDNA etc.), I would go for the cheapest 
one I could find. I guess there are few crystallography projects were the first 
PCR step turned out to be the most difficult. 
For more sophisticated applications there are probably forums where more 
knowledgeable people reside (on PCR that is...) 
Mark 

Quoting Bernhard Rupp (Hofkristallrat a.D.):

 Dear All,

 I was polled for a  recommendation for a  good PCR instrument,
 but I am not much of a molecular biology person - if someone could
 please help and kindly send some recommendations to

 Eric W. Reinheimer ewreinhei...@csupomona.edu

 Best regards, BR
 -
 Bernhard Rupp
 001 (925) 209-7429
 +43 (676) 571-0536
 b...@ruppweb.org
 hofkristall...@gmail.com
 http://www.ruppweb.org/ 
 -
 No animals were hurt or killed during the
 production of this email.
 -


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] what to do with disordered side chains

2011-03-30 Thread VAN RAAIJ , MARK JOHAN
yet, apart from (and additionally to) modelling two conformations of the 
side-chain, the B-factor is the only tool we have (now). 

Quoting Pavel Afonine:

 Hi  Quyen,


 (...) And if B-factor is an estimate of thermo-motion (or static disorder),
 then would it not be reasonable to accept that building the side-chain and
 let B-factor sky rocket might reflect reality more so than not building it?


 NO.  Your B-factors are valid within a harmonic (small) approximation of
 atomic vibrations. Larger scale motions you are talking about go beyond the
 harmonic approximation, and using the B-factor to model them is abusing the
 corresponding mathematical model.
 http://www.phenix-online.org/newsletter/CCN_2010_07.pdf

 Pavel.


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] off-topic: 2 peaks on Cation

2011-02-18 Thread VAN RAAIJ , MARK JOHAN

I observed 3-5 peaks for a baculovirus expressed protein once, and could only 
get good crystals if the peaks were crystallised separately, see: 
Virology 262, 333-343 (1999) 

Virology 262, 333–343 (1999)  
Mark 

Quoting Ulli Hain:

 Thanks for the suggestions/ideas. The protein is recombinantly 
 expressed in E.coli. It does in fact show a metal dependency. We mass 
 spec'd the peaks  once looking for phosphorylation, which was not 
 detected, but we only got about 60-70% sequence coverage so it was 
 not very helpful.

 Quoting Nadir T. Mrabet nadir.mra...@medecine.uhp-nancy.fr:

 Given no info on the protein, it can be anything.
 Is it recombinant? Which host? etc.

 Oxydation (cys, met) is also a possibility
 By the way, deamination concerns asn and gln, not lys.

 Best,

 Nadir

 Pr. Nadir T. Mrabet
 Structural  Molecular Biochemistry
 Nutrigenex - INSERM U-954
 Nancy University, School of Medicine
 9, Avenue de la Foret de Haye, BP 184
 54505 Vandoeuvre-les-Nancy Cedex
 France
 Phone: +33 (0)3.83.68.32.73
 Fax:   +33 (0)3.83.68.32.79
 E-mail: Nadir.Mrabetat  medecine.uhp-nancy.fr



 On 18/02/2011 19:45, Soisson, Stephen M wrote:
 Possibly deamidation of the protein, in particluar one or more
 lysines.  What does the Mass spec look like?
 Cheers,
 Steve

 
 *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On
 Behalf Of *Ulli Hain
 *Sent:* Friday, February 18, 2011 12:14 PM
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* [ccp4bb] off-topic: 2 peaks on Cation

 Hi, I was wondering if anyone had possible explanations for a
 recombinantly expressed soluble protein that runs as 2 equal,
 slightly overlapping peaks on a cation exhanger but as one peak on a
 size exclusion column and same electrophoretic mobility on SDS-PAGE.
 -Ulli


 Adelaide Ulricke Hain
 PhD Candidate
 Johns Hopkins Bloomberg School of Public Health
 Department of Biochemistry and Molecular Biology
 615 North Wolfe Street
 Baltimore, MD  21205
 Notice:  This e-mail message, together with any attachments, contains
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Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] Problems with auto-indexing

2010-11-29 Thread VAN RAAIJ , MARK JOHAN
Dear Chen, 

It looks like you have a unit cell with two relatively short axes and one long 
one - and some disorder. I have experienced a few examples of this with virus 
fibre proteins (adenovirus fibre and T4 short tail fibre). For the short tail 
fibre we also obtained images in which some lines of spots showed nice 
separation but others less so. 
You should try and mount the crystals with the long axis roughly parallel to 
the rotation axis to avoid overlaps. If you screen several (or many) crystals, 
you may find one with less disorder. In any case, collect complete datasets of 
the best ones and try to solve the structure, you may get lucky like we did. 

Greetings, 

Mark 

Quoting chen c:

 I attached two diffraction images of my crystal, of which one seems normal
 as protein crystal usually do, while the other one looks very strange ,with
 very continuous lines on the image.

 In fact, of the 180 crystal images diffracted by my crystal, there is a
 tendency between those two.

 I had thought that my crystal is a combination of many two-dimensional
 crystals, between wich there are translational or rotational translocations,
 namely resulting in a lack of translational symmetry in the third axes. As a
 result of this, when I tried to index them using HKL2000, one of the cell
 parameter is merely several angstroms.

 However, of the several data sets from different crystals, one data set is
 sucessfully indexed by the assistant professor of my laboratory and
 currently submitted to the operation of Molucular Replacement.

 This confused me a lot. Is what I thought wrong? Or is the very crystal that
 was indexed a special one?

 Thanks all

 chen


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es 

Re: [ccp4bb] Editorial policies (was Citations in supplementary material)

2010-11-19 Thread VAN RAAIJ , MARK JOHAN

Regarding editorial decisions, I actually welcome editors making more rejection 
decisions, i.e. reading the paper before sending it to referees, so I waste 
less time, waiting as author, or as referee reading and commenting on papers 
for which it would have been clear beforehand that they are not suitable for 
the journal. I realise this would put more burden on the editors, but then they 
could enlist more editor (I have never been asked to be editor for any journal 
yet (hint)...). 
Mark 

Quoting Anastassis Perrakis:

 Dear John,

 I did not have the IUCr journals specifically in mind while making  
 these remarks.
 Quite the contrary, I think due to you and other colleagues and  
 friends, they are
 run competently and to the benefit of the community and of science at  large.

 If I may though offer an opinion about the peer review system in IUCr 
  journals,
 I personally find the concept that the authors know the identity of  
 the managing
 editor, wrong. I am sure that in the majority of cases its not a  problem,
 but often a managing editor can hesitate to communicate a negative  
 referee report
 to e.g. an old colleague or good friend, whose manuscript she/he is  
 handling,
 even when one of the referees is negative.

 I much prefer the system of e.g. Proteins (where I act as a managing  
 editor),
 where authors never learn the identity of the managing editor far 
 more  comfortable
 (there is a few people that I would rather prefer if they don't know  
 for sure that I rejected their paper),
 and the current system of PNAS were you learn the identity of the
 editor only if your paper is accepted and after is published, far  
 superior (you make friends but not enemies ...)

 I would not mind to had seen IUCr journals adopting a similar system, 
  I think it would improve even further
 their good reputation.

 A.


 On Nov 19, 2010, at 12:32, John R Helliwell wrote:

 I don't wish to vear away from Victor's thrust with starting this
 thread and I would happily sign the petition you suggest.

 But I feel I should respond to the assertions about 'problems of peer
 review' at least with respect to Journals of my experience.
 Some 'Editor handling of submissions' statistics should help quantify
 such matters. These are a matter of public record re my IUCr Journals
 submission handling statistics ie therefore not confidential and which
 basically are:-
 approx 1000 article submissions;
 my rejection rate 20%;
 appeals against my rejections 0.5%;
 As Editor in Chief of Acta Cryst between 1996 to 2005 I received three
 appeals (out of approx tens of thousands of submissions through all
 Coeditors); I rejected these three. [My judgements were confidential
 re the details.]

 I can add that for the 2000 referees' reports or so for my article
 handling of submissions, that colleagues have kindly supplied to my
 Editor requests, problems involve:-
 about 1% where the report is 'publish as is' AND without any
 commendation given; these are in effect not terribly useful reports to
 me as an Editor. Another problem, which is growing, is the number of
 declines to my invites to referee (around 10%). Even worse are the no
 replies at all from invited referees as time is lost to the authors
 who rightly expect as prompt as possible handling.

 Re your points I offer replies as follows:-
 Let me outline what I think are problems of peer review:

 1. 'review by last author name'. Very often the last author is well
 known, or a friend, and the reviewers' critical judgement takes a
 temporary leave of abesnse.
 JRH reply:- Such reports would be easy to spot and are not a problem
 in my experience and so resort to double blind review is not necessary
 in my experience.

 2. 'preferred reviewers'. a double edged sword .. think about it.
 JRH reply; these are not so commonly offered suggestions by authors in
 fact and where they are one can follow or decide against (see point
 1).


 3. too much power of decision on editors (professional or academic)
 being able to reject papers without peer-review in many journals.
 JRH reply;This approach, 'insufficent general interest' is for the
 magazines we know and yet still love.

 4. Bad refereeing - sometimes I wonder if people read the paper.
 JRH reply;Such reports are very few and obvious. The other categories
 above are more common (ie 'publish as is' category).

 5. Lack of referee expertise: you get papers these days with: a
 structure, some biochemistry, some SAXS, some biophysics, and a cell
 based assay. Two or three people being
 able to pick up all the mistakes is very unlikely.
 JRH reply; Papers can be challenging re content and your example here
 is a good one. Other chalenging cases are where they include a lot of
 maths. That said peer review does its best but can occasionally fail;
 this level of failure can be measured by the number of criticism
 articles or formal retractions. These are also very few, but it is
 true, not zero.

 Yours sincerely,
 

Re: [ccp4bb] relationship between B factors and Koff

2010-11-19 Thread VAN RAAIJ , MARK JOHAN

Hi Sebastiano, 
I don't see how the k-off would influence this, given the timescale of growing 
crystals. 
An explanation in terms of high Kd and relative lack of crystal contacts for 
the component with higher temperature factors would sound more convincing to 
me. 
Mark 

Quoting Vellieux Frederic:

 I can direct you to PDB entry 1EWY, where the average isotropic 
 temperature factor for the major component of the complex is ca. 47 
 A**2 and that for the smaller component is ca. 69 A**2. Similar 
 values than the ones you are reporting. I am assuming some sort of 
 disorder, or if you prefer, wobbling of the smaller component at 
 the lever of the binding site.

 Fred.

 Sebastiano Pasqualato wrote:
 Hi all,
 I have a crystallographical/biochemical problem, and maybe some of 
 you guys can help me out.

 We have recently crystallized a protein:protein complex, whose Kd 
 has been measured being ca. 10 uM (both by fluorescence polarization 
 and surface plasmon resonance).
 Despite the 'decent' affinity, we couldn't purify an homogeneous 
 complex in size exclusion chromatography, even mixing the protein at 
 concentrations up to 80-100 uM each.
 We explained this behavior by assuming that extremely high Kon/Koff 
 values combine to give this 10 uM affinity, and the high Koff value 
 would account for the dissociation going on during size exclusion 
 chromatography. We have partial evidence for this from the SPR 
 curves, although we haven't actually measured the Kon/Koff values.

 We eventually managed to solve the crystal structure of the complex 
 by mixing the two proteins (we had to add an excess of one of them 
 to get good diffraction data).
 Once solved the structure (which makes perfect biological sense and 
 has been validated), we get mean B factors for one of the component 
 (the larger) much lower than those of the other component (the 
 smaller one, which we had in excess). We're talking about 48 Å^2 vs. 
 75 Å^2.

 I was wondering if anybody has had some similar cases, or has any 
 hint on the possible relationship it might (or might not) exist 
 between high a Koff value and high B factors (a relationship we are 
 tempted to draw).

 Thanks in advance,
 best regards,
 ciao
 s





Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es

Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

2010-10-27 Thread VAN RAAIJ , MARK JOHAN
perhaps we should campaign for it to be obligatory to provide the pdb and 
structure factor file to the journal, and thus referees, upon submission? Then 
he can look for himself to see that building and refinement have been performed 
satisfactorily. 
Mark

 Surely the best model is the one that the referees for your paper 
 are happy with?

 I have found referees to impose seemingly random and arbitrary 
 standards that sometime require a lot of effort to comply with but 
 result in little to no impact on the biology being described. Mind 
 you discussions on this email list can be a useful resource for 
 telling referee's why you don't think you should comply with their 
 rule of thumb.

 Simon



 On 27 Oct 2010, at 20:11, Bernhard Rupp (Hofkristallrat a.D.) wrote:

 Dear Young and Impressionable readers:

 I second-guess here that Robbie's intent - after re-refining many many PDB
 structures, seeing dreadful things, and becoming a hardened cynic - is to
 provoke more discussion in order to put in perspective - if not debunk-
 almost all of these rules.

 So it may be better to pretend you have never heard of these rules. Your
 crystallographic life might be a happier and less biased one.

 If you follow this simple procedure (not a rule)

 The model that fits the primary evidence (minimally biased electron density)
 best and is at the same time physically meaningful, is the best model, i.
 e., all plausibly accountable electron density (and not more) is modeled.

 This process of course does require a little work (like looking through all
 of the model, not just the interesting parts, and thinking what makes sense)
 but may lead to additional and unexpected insights. And in almost all cases,
 you will get a model with plausible statistics, without any reliance on
 rules.

 For some decisions regarding global parameterizations you have to apply more
 sophisticated test such as Ethan pointed out (HR tests) or Ian uses
 (LL-tests). And once you know how to do that, you do not need any rules of
 thumb anyhow.

 So I opt for a formal burial of these rules of thumb and a toast to evidence
 and plausibility.

 And, as Gerard B said in other words so nicely:

 Si tacuisses, philosophus mansisses.

 BR

 -Original Message-
 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Robbie
 Joosten
 Sent: Tuesday, October 26, 2010 10:29 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree)

 Dear Anthony,

 That is an excellent question! I believe there are quite a lot of 'rules of
 thumb' going around. Some of them seem to lead to very dogmatic thinking and
 have caused (refereeing) trouble for good structures and lack of trouble for
 bad structures. A lot of them were discussed at the CCP4BB so it may be nice
 to try to list them all.


 Rule 1: If Rwork  20%, you are done.
 Rule 2: If R-free - Rwork  5%, your structure is wrong.
 Rule 3: At resolution X, the bond length rmsd should be  than Y (What is
 the rmsd thing people keep talking about?) Rule 4: If your resolution is
 lower than X, you should not use_anisotropic_Bs/riding_hydrogens
 Rule 5: You should not build waters/alternates at resolutions lower than X
 Rule 6: You should do the final refinement with ALL reflections Rule 7: No
 one cares about getting the carbohydrates right


 Obviously, this list is not complete. I may also have overstated some of the
 rules to get the discussion going. Any addidtions are welcome.

 Cheers,
 Robbie Joosten
 Netherlands Cancer Institute

 Apologies if I have missed a recent relevant thread, but are lists of
 rules of thumb for model building and refinement?





 Anthony



 Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076


   =


Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es