Re: [ccp4bb] occupancy vs. Bfactors

[Jrh]

Ian, yes absolutely but your very description of where the unit cells are not 
identical is NOT the situation where we see fractional occupancy moieties. In 
such cases a large fraction of the unit cells ARE ordered. QED. John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 20 Nov 2012, at 17:33, Ian Tickle  wrote:

> John
> 
> Having begun my crystallographic life with small molecules (organic 
> semiconductors) and subsequently moved to PX, and having worked on SOD 
> crystals I stand in both camps (i.e. both meanings: site-occupancy disorder 
> and superoxide dismutase!).  It seems to me that static disorder is the 
> appropriate description of any situation where the time-averaged unit cells 
> are not all identical and the variations are more or less random throughout 
> the lattice.  This would then apply both to SOD and the more common (at least 
> in MX) positional disorder.
> 
> But I'm puzzled where you say "where there is disorder surely such a chemical 
> moiety would be invisible".  Surely if there is static disorder such that a 
> fraction x of the sites are randomly occupied, with the remaining fraction 
> 1-x vacant the moeity in question will be perfectly visible, just with 
> reduced occupancy x.  In fact I had an example of this: a 9-methyl anthracene 
> molecule sitting on an inversion centre with the Me group randomly occupied 
> with half occupancy.  The disordered Me was certainly visible in the map, 
> just with reduced density compared with the other C atoms.
> 
> -- Ian
> 
> 
> On 20 November 2012 17:58, Jrh  wrote:
> Nomenclature hazard warning:-
> 
> Ian, Thankyou for drawing attention to the nomenclature school:-
> Partial occupancy disorder
> Which I prefer to refer to as 
> Partial occupancy order.
> 
> Outside our MX field static disorder refers to what we call split occupancy 
> order. I like the latter and dislike the former. Ie where there is disorder 
> surely such a chemical moiety would be invisible,  let alone allowing us to 
> be able to determine its occupancy from Bragg intensities. 
> 
> I once tried to propose an amendment to the IUCr Nomenclature Committee to 
> replace static disorder terminology with split occupancy order terminology. 
> The forces to which you refer were too strong. Static disorder remains the 
> term in approved use.
> 
> 
> Prof John R Helliwell DSc 
>  
>  
> 
> On 20 Nov 2012, at 15:49, Ian Tickle  wrote:
> 
>> PS: Partial occupancy is not the same as disorder. You can have well-ordered 
>> different occupancies that manifest themselves then in superstructure 
>> patterns. Common in small molecule/materials.
>> 
>> 
>> Hello Bernhard
>> 
>> Agree with everything you said up till this point, but I think the owners of 
>> the "site occupancy disorder" websites below would disagree that partial 
>> occupancy is not the same as disorder!
>> 
>> http://www.ucl.ac.uk/~uccargr/sod.htm
>> 
>> http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/Html/thCastepDisorder.htm
>> 
>> There are also many research papers on partial occupancy disorder of 
>> superlattice materials in the solid state, eg:
>> 
>> http://www.researchgate.net/publication/226559734_Order-disorder_behavior_in_KNbO3_and_KNbO3KTaO3_solid_solutions_and_superlattices_by_molecular-dynamics_simulation
>> 
>> Cheers
>> 
>> -- Ian
>>  
>> 
>> 
> 

Re: [ccp4bb] occupancy vs. Bfactors

[James Holton]

Something you want to be very careful with here that appears to have not 
been mentioned yet is "phase bias".


If you have built in a wrong side chain or other entity that is not 
actually there, but still force it to have occupancy=1 and reasonable B 
factors (B factor restraints might do that) and then you refine the rest 
of the molecule to convergence, build in lots of waters, etc. it is 
quite astonishing how much "memory" the resulting phases can have for 
the incorrectly-placed atoms.  If you simply remove the wrong side chain 
atoms and then re-calculate the map with no refinement, then it is not 
unexpected that you will see "green" difference density for it.  This 
may persist even after a few cycles of refinement.


Best thing to do after removing a "questioned" feature is to jiggle the 
rest of the molecule a bit, remove all the waters, and then re-refine to 
convergence.  If the difference feature survives such a treatment, then 
it is probably for real.  This used to be called a "simulated annealing 
omit map".  Something that seems to have been lost in a few modern packages.


And yes, "phase bias" can work the other way as well.  If you really do 
have a low-occupancy feature, then not modeling it and re-refining 
everything else will result in "negative" phase bias: squashing your 
weak feature into oblivion.  Exactly what occupancy is required to be 
resistant to a "simulated annealing omit" procedure?  That's a good 
question.  However, I am reasonably confident that this "critical 
occupancy" is less than 1.0  And probably greater than zero as well.


-James Holton
MAD Scientist


On 11/20/2012 10:36 AM, GRANT MILLS wrote:

Hello all,

I'm currently working on a structure which if I stub a certain side 
chain phenix/coot shows me a large green blob which looks strikingly 
similar to the side chain, when I put it in and run another refinement 
the blob turns red.


Basically I was just playing around and I changed the occupancy of the 
side chain and now there are no complaints. But I was thinking, should 
I haven changed the Bfactors instead? Should I have left well enough 
alone? If I lower the occupancy manually and do not include alternate 
confirmations have I introduced modelling bias?


Could someone recommend some good articles I could read on exactly how 
to correctly fix this problem.


Thanks,
GM

Re: [ccp4bb] occupancy vs. Bfactors

[Pavel Afonine]

Dear Bernhard, dear John,

On 11/20/12 6:10 AM, Bernhard Rupp wrote:

As already mentioned by jrh, I again want to impress that B-factor and
occupancy are in principle two entirely different parameters.



They may appear as achieving the same thing upon refinement at the
resolution we deal with in most macromolecular structures.



The fact is that reduced occupancy just **scales down** the entire
scattering function at a given B, while an increased B-factor **changes the
shape** of the scattering curve, i.e. makes it narrower in reciprocal space
and thus in direct space gives a broader electron density. Reduced
occupancy just reduces electron density levels. Those are physically
distinctly different although not easily separable effects. I have an
applet that can be used to see the point



http://www.ruppweb.org/cgi-bin/webscat.exe?E1=O&B=50.0&Occupation_factor=0.5&B1=Submit


On 11/20/12 12:05 AM, Jrh wrote:

Dear Pavel,
Also worth mentioning the obvious that the mathematical functional form of
an occupancy and a B factor in its -ve exponential is very different BUT at
lower resolutions they behave similarly. Thus higher resolution refinement
allows an 'easier' determination of each parameter.


I surely agree about occupancy and B-factor having distinct and different
mathematical meaning and effects. It's obvious from the structure factor
formula being proportional to q*exp(-B*s**2). No plots needed to see it!
-;)

Unless we are going into subatomic resolution world with their deformation
density maps (most kinds of which are in fact model calculated maps!), at
typical macro-molecular resolutions we don't deal with electron density
distribution, but its Fourier image. Needless to say that such image may be
as far away from the true electron density as your set of Fobs is far away
from being fully complete. Whether the differences between "scaling" and
"changing the shape" are visible, significant or
reliably distinguishable in this context isn't very obvious to me.

As John pointed out, at lower resolution the effect of q or B is similar,
while it is less true as resolution becomes higher. Perhaps the line where
a) effects of q and B become (in)distinguishable and b) one should be used
instead of the other, is subtle.
I guess the original poster found the answer empirically by trying to do
both, and judging the trial success by flatness of residual map it
produced, which is probably the most robust way to figure this out (as long
as what you try makes sense).

   PS: Partial occupancy is not the same as disorder. You can have
well-ordered different occupancies that manifest themselves then in
superstructure

patterns. Common in small molecule/materials.


Put nomenclature rigor aside (bad idea?), my (rather simplistic!)
understanding is that both are disorder but of different kind and nature,
thus two different and simple parameters to model it, q and B. While
occupancy is to reflect the fraction of unit cells having that atom there,
the B-factor describes small (within harmonic approximation) vibration of
it. Larger-scale vibrations are accounted for by more complex models, such
as anharmonic approximations: Gram-Charier expansion or "bananas and pears"
of Reilly et al (Acta Cryst. A67, 346-356) (was a nice talk about it at
ECM27!).

All the best,
Pavel

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[Bosch, Juergen]

It probably had a functional Firewall under Linux that's why it survived :-)

Jürgen

P.S. note to myself, don't ever give George my laptop, as it might be 
mistreated - just for test purposes :-)

On Nov 20, 2012, at 12:57 PM, George M. Sheldrick wrote:

It is dual bootable Linux/Windows
George

On 11/20/2012 05:56 PM, William Scott wrote:
Presumably then it was running Linux?

On Nov 20, 2012, at 7:39 AM, "George M. Sheldrick" 
mailto:gshe...@shelx.uni-ac.gwdg.de>> wrote:

I have never understood why Macs are so popular, although in this part
of the world they are appreciably more expensive. My vintage 2005 Dell
laptop does not have the sex appeal of a MacBook, but it has survived a
fire (not its fault) as well as being under water (to put out the fire)
and then bounced down a stone staircase (my wife fortunately caught it
on the way down). Despite all my efforts to destroy it, it never needed
servicing or replacement parts and still works perfectly!

George
(PS I should add that I have no connection with or shares in Dell)


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

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

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[George M. Sheldrick]

It is dual bootable Linux/Windows
George

On 11/20/2012 05:56 PM, William Scott wrote:
> Presumably then it was running Linux?
> 
> On Nov 20, 2012, at 7:39 AM, "George M. Sheldrick" 
>  wrote:
> 
>> I have never understood why Macs are so popular, although in this part
>> of the world they are appreciably more expensive. My vintage 2005 Dell
>> laptop does not have the sex appeal of a MacBook, but it has survived a
>> fire (not its fault) as well as being under water (to put out the fire)
>> and then bounced down a stone staircase (my wife fortunately caught it
>> on the way down). Despite all my efforts to destroy it, it never needed
>> servicing or replacement parts and still works perfectly!
>>
>> George
>> (PS I should add that I have no connection with or shares in Dell)
>>

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

Re: [ccp4bb] Collecting native data at an absorption edge

[Pete Meyer]

native datasets?  And would a native dataset for refinement be 
compromised by friedel pair differences collected at an edge?


If you've got anomalous data available, you may get better results by 
using your friedel pair differences in refinement - especially if your 
diffraction stays in the ~ 4 Angstrom range.


This was originally implemented in refmac5D, and has been in the main 
refmac releases for a while (not sure about cns or phenix.refine - last 
I checked they didn't have a friedle pair refinement target).



Pete

Re: [ccp4bb] Collecting native data at an absorption edge

[Bosch, Juergen]

You'll see the zinc also at the Semet peak edge already check out Ethan's edge 
plot web server. If you used his-tag purification methods it would be wiser to 
collect passed the edge of either Ni or Co so you can distinguish them from Zn 
sites.

Jürgen 

..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://lupo.jhsph.edu

On Nov 20, 2012, at 9:26, "Alan Cheung"  wrote:

> Dear all - we have a synchrotron trip coming up and have crystals that 
> are likely to contain intrinsically bound zinc atoms.  The crystals 
> diffract to 4A-ish so far.  We're hoping to collect both native datasets 
> at higher dose, and phasing datasets at lower dose (on separate 
> crystals).  Can we do the lot at the zinc edge wavelength, or should we 
> be worried about radiation damage, and move away from the edge for the 
> native datasets?  And would a native dataset for refinement be 
> compromised by friedel pair differences collected at an edge?
> 
> Alan
> 
> 
> 
> 
> -- 
> Alan Cheung
> Gene Center
> Ludwig-Maximilians-University
> Feodor-Lynen-Str. 25
> 81377 Munich
> Germany
> Phone:  +49-89-2180-76845
> Fax:  +49-89-2180-76999
> E-mail: che...@lmb.uni-muenchen.de

Re: [ccp4bb] occupancy vs. Bfactors

[Ian Tickle]

John

Having begun my crystallographic life with small molecules (organic
semiconductors) and subsequently moved to PX, and having worked on SOD
crystals I stand in both camps (i.e. both meanings: site-occupancy disorder
and superoxide dismutase!).  It seems to me that static disorder is the
appropriate description of any situation where the time-averaged unit cells
are not all identical and the variations are more or less random throughout
the lattice.  This would then apply both to SOD and the more common (at
least in MX) positional disorder.

But I'm puzzled where you say "where there is disorder surely such a
chemical moiety would be invisible".  Surely if there is static disorder
such that a fraction x of the sites are randomly occupied, with the
remaining fraction 1-x vacant the moeity in question will be perfectly
visible, just with reduced occupancy x.  In fact I had an example of this:
a 9-methyl anthracene molecule sitting on an inversion centre with the Me
group randomly occupied with half occupancy.  The disordered Me was
certainly visible in the map, just with reduced density compared with the
other C atoms.

-- Ian


On 20 November 2012 17:58, Jrh  wrote:

> Nomenclature hazard warning:-
>
> Ian, Thankyou for drawing attention to the nomenclature school:-
> Partial occupancy disorder
> Which I prefer to refer to as
> Partial occupancy order.
>
> Outside our MX field static disorder refers to what we call split
> occupancy order. I like the latter and dislike the former. Ie where there
> is disorder surely such a chemical moiety would be invisible,  let alone
> allowing us to be able to determine its occupancy from Bragg intensities.
>
> I once tried to propose an amendment to the IUCr Nomenclature Committee to
> replace static disorder terminology with split occupancy order terminology.
> The forces to which you refer were too strong. Static disorder remains the
> term in approved use.
>
>
> Prof John R Helliwell DSc
>
>
>
> On 20 Nov 2012, at 15:49, Ian Tickle  wrote:
>
> PS: Partial occupancy is not the same as disorder. You can have
>> well-ordered different occupancies that manifest themselves then in
>> superstructure patterns. Common in small molecule/materials.
>>
>
> Hello Bernhard
>
> Agree with everything you said up till this point, but I think the owners
> of the "site occupancy disorder" websites below would disagree that partial
> occupancy is not the same as disorder!
>
> http://www.ucl.ac.uk/~uccargr/sod.htm
>
>
> http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/Html/thCastepDisorder.htm
>
> There are also many research papers on partial occupancy disorder of
> superlattice materials in the solid state, eg:
>
>
> http://www.researchgate.net/publication/226559734_Order-disorder_behavior_in_KNbO3_and_KNbO3KTaO3_solid_solutions_and_superlattices_by_molecular-dynamics_simulation
>
> Cheers
>
> -- Ian
>
>>
>>
>
>

[ccp4bb] Collecting native data at an absorption edge

[Alan Cheung]

Dear all - we have a synchrotron trip coming up and have crystals that 
are likely to contain intrinsically bound zinc atoms.  The crystals 
diffract to 4A-ish so far.  We're hoping to collect both native datasets 
at higher dose, and phasing datasets at lower dose (on separate 
crystals).  Can we do the lot at the zinc edge wavelength, or should we 
be worried about radiation damage, and move away from the edge for the 
native datasets?  And would a native dataset for refinement be 
compromised by friedel pair differences collected at an edge?


Alan




--
Alan Cheung
Gene Center
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:  +49-89-2180-76999
E-mail: che...@lmb.uni-muenchen.de

Re: [ccp4bb] occupancy vs. Bfactors

[Jrh]

Nomenclature hazard warning:-

Ian, Thankyou for drawing attention to the nomenclature school:-
Partial occupancy disorder
Which I prefer to refer to as 
Partial occupancy order.

Outside our MX field static disorder refers to what we call split occupancy 
order. I like the latter and dislike the former. Ie where there is disorder 
surely such a chemical moiety would be invisible,  let alone allowing us to be 
able to determine its occupancy from Bragg intensities. 

I once tried to propose an amendment to the IUCr Nomenclature Committee to 
replace static disorder terminology with split occupancy order terminology. The 
forces to which you refer were too strong. Static disorder remains the term in 
approved use.

Prof John R Helliwell DSc 
 
 

On 20 Nov 2012, at 15:49, Ian Tickle  wrote:

> PS: Partial occupancy is not the same as disorder. You can have well-ordered 
> different occupancies that manifest themselves then in superstructure 
> patterns. Common in small molecule/materials.
> 
> 
> Hello Bernhard
> 
> Agree with everything you said up till this point, but I think the owners of 
> the "site occupancy disorder" websites below would disagree that partial 
> occupancy is not the same as disorder!
> 
> http://www.ucl.ac.uk/~uccargr/sod.htm
> 
> http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/Html/thCastepDisorder.htm
> 
> There are also many research papers on partial occupancy disorder of 
> superlattice materials in the solid state, eg:
> 
> http://www.researchgate.net/publication/226559734_Order-disorder_behavior_in_KNbO3_and_KNbO3KTaO3_solid_solutions_and_superlattices_by_molecular-dynamics_simulation
> 
> Cheers
> 
> -- Ian
>  
> 
> 

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[William Scott]

Presumably then it was running Linux?

On Nov 20, 2012, at 7:39 AM, "George M. Sheldrick" 
 wrote:

> I have never understood why Macs are so popular, although in this part
> of the world they are appreciably more expensive. My vintage 2005 Dell
> laptop does not have the sex appeal of a MacBook, but it has survived a
> fire (not its fault) as well as being under water (to put out the fire)
> and then bounced down a stone staircase (my wife fortunately caught it
> on the way down). Despite all my efforts to destroy it, it never needed
> servicing or replacement parts and still works perfectly!
> 
> George
> (PS I should add that I have no connection with or shares in Dell)
> 
> On 11/20/2012 10:25 AM, Charles Ballard wrote:
>> To add to the general list (and future class action).  I have just had the 
>> battery expansion on one  for the second time.  Added to the number of them 
>> I have bricked by letting the charge run down to low by unplugging them.  
>> Interestingly apple agreed to replace the bricked batteries free of charge, 
>> for their US customers.  But, us foreigners had to pay for the pleasure...
>> 
>> Charles
>> 
>> On 18 Nov 2012, at 17:30, Bosch, Juergen wrote:
>> 
>>> Bill I think that's crap.
>>> I had issues on a 2005 MacBook Pro with inflating battery and it was 
>>> replaced (after about 6 months). There were troubles with those batteries 
>>> and impurities but mine still had apple care at that time and the batteries 
>>> were exchangeable. 
>>> I have not heard of the build in batteries to have problems but yours sure 
>>> did. Send Tim Cook an email with the picture. This should not have happened 
>>> and also keeping the power cord on leading to this problem should not have 
>>> happened. For what did they introduce the trickling charging ? If you can't 
>>> leave the coord plugged in how many nice wooden US households gave caught 
>>> fire due to Apple products ?
>>> 
>>> Jürgen 
>>> ..
>>> Jürgen Bosch
>>> Johns Hopkins Bloomberg School of Public Health
>>> Department of Biochemistry & Molecular Biology
>>> Johns Hopkins Malaria Research Institute
>>> 615 North Wolfe Street, W8708
>>> Baltimore, MD 21205
>>> Phone: +1-410-614-4742
>>> Lab:  +1-410-614-4894
>>> Fax:  +1-410-955-3655
>>> http://lupo.jhsph.edu
>>> 
>>> On Nov 17, 2012, at 16:28, "William G. Scott"  wrote:
>>> 
 Hi folks:
 
 I'm trying to get a sense for how frequently this sort of thing occurs:
 
 
 
 That was a macbook air that served me well for four years, but then 
 self-destructed. (I took it to the Apple store.  They generously offered 
 to repair it for $800 or to sell me a new one, and suggested this was 
 normal if you leave the power cord attached after the battery charges, 
 even while giving a lecture or seminar.)  It strikes me as a bit dangerous.
 
 --Bill Scott
 
 
 
 
 
 William G. Scott
 Professor
 Department of Chemistry and Biochemistry
 and The Center for the Molecular Biology of RNA
 228 Sinsheimer Laboratories
 University of California at Santa Cruz
 Santa Cruz, California 95064
 USA
 
 
 
>> 
> 
> -- 
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-22582

Re: [ccp4bb] dihedral backbone generator

[Ed Pozharski]

On Mon, 2012-11-12 at 13:47 -0500, Ed Pozharski wrote:
> Does anyone know of a tool that would generate a protein molecule
> backbone from a set of phi/psi angles?
> 

For the record.

Thanks to all who responded.  Here is what I found out:

1. MOLEMAN works best. The most cumbersome part is to transfer phi/psi
from one structure to another.  If anyone is ever interested, I have a
bash script that does it in automated manner, all you need to do is to
provide the list of residues to be corrected.

2. Other options include TINKER and fortran code by Edward Berry.  I
couldn't use the second one because it does not do omegas and I have
some cis-prolines in the model.  TINKER is an awesome MD package from
what I can tell.  I abandoned it for moleman after concluding that it
takes integers values, but I didn't investigate if that is actually true
and if it is really a big problem (see below).

3.  On the scientific side, it appears that updating phi/psi angles is
not enough.  Basically, even if I transfer all the angles from one model
to another, models match well only in the N-terminal domain.  The
C-terminal domain which in this case undergoes about 45 degrees
closure-type rotation is very much messed up.  Perhaps the conclusion is
that changes other than phi/psi contribute significantly.  Which is, on
the second thought, not that surprising.

Cheers,

Ed.  

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

Re: [ccp4bb] occupancy vs. Bfactors

[Ian Tickle]

>
> PS: Partial occupancy is not the same as disorder. You can have
> well-ordered different occupancies that manifest themselves then in
> superstructure patterns. Common in small molecule/materials.
>

Hello Bernhard

Agree with everything you said up till this point, but I think the owners
of the "site occupancy disorder" websites below would disagree that partial
occupancy is not the same as disorder!

http://www.ucl.ac.uk/~uccargr/sod.htm

http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/Html/thCastepDisorder.htm

There are also many research papers on partial occupancy disorder of
superlattice materials in the solid state, eg:

http://www.researchgate.net/publication/226559734_Order-disorder_behavior_in_KNbO3_and_KNbO3KTaO3_solid_solutions_and_superlattices_by_molecular-dynamics_simulation

Cheers

-- Ian

>
>

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[George M. Sheldrick]

I have never understood why Macs are so popular, although in this part
of the world they are appreciably more expensive. My vintage 2005 Dell
laptop does not have the sex appeal of a MacBook, but it has survived a
fire (not its fault) as well as being under water (to put out the fire)
and then bounced down a stone staircase (my wife fortunately caught it
on the way down). Despite all my efforts to destroy it, it never needed
servicing or replacement parts and still works perfectly!

George
(PS I should add that I have no connection with or shares in Dell)

On 11/20/2012 10:25 AM, Charles Ballard wrote:
> To add to the general list (and future class action).  I have just had the 
> battery expansion on one  for the second time.  Added to the number of them I 
> have bricked by letting the charge run down to low by unplugging them.  
> Interestingly apple agreed to replace the bricked batteries free of charge, 
> for their US customers.  But, us foreigners had to pay for the pleasure...
> 
> Charles
> 
> On 18 Nov 2012, at 17:30, Bosch, Juergen wrote:
> 
>> Bill I think that's crap.
>> I had issues on a 2005 MacBook Pro with inflating battery and it was 
>> replaced (after about 6 months). There were troubles with those batteries 
>> and impurities but mine still had apple care at that time and the batteries 
>> were exchangeable. 
>> I have not heard of the build in batteries to have problems but yours sure 
>> did. Send Tim Cook an email with the picture. This should not have happened 
>> and also keeping the power cord on leading to this problem should not have 
>> happened. For what did they introduce the trickling charging ? If you can't 
>> leave the coord plugged in how many nice wooden US households gave caught 
>> fire due to Apple products ?
>>
>> Jürgen 
>> ..
>> Jürgen Bosch
>> Johns Hopkins Bloomberg School of Public Health
>> Department of Biochemistry & Molecular Biology
>> Johns Hopkins Malaria Research Institute
>> 615 North Wolfe Street, W8708
>> Baltimore, MD 21205
>> Phone: +1-410-614-4742
>> Lab:  +1-410-614-4894
>> Fax:  +1-410-955-3655
>> http://lupo.jhsph.edu
>>
>> On Nov 17, 2012, at 16:28, "William G. Scott"  wrote:
>>
>>> Hi folks:
>>>
>>> I'm trying to get a sense for how frequently this sort of thing occurs:
>>>
>>> 
>>>
>>> That was a macbook air that served me well for four years, but then 
>>> self-destructed. (I took it to the Apple store.  They generously offered to 
>>> repair it for $800 or to sell me a new one, and suggested this was normal 
>>> if you leave the power cord attached after the battery charges, even while 
>>> giving a lecture or seminar.)  It strikes me as a bit dangerous.
>>>
>>> --Bill Scott
>>>
>>>
>>>
>>>
>>>
>>> William G. Scott
>>> Professor
>>> Department of Chemistry and Biochemistry
>>> and The Center for the Molecular Biology of RNA
>>> 228 Sinsheimer Laboratories
>>> University of California at Santa Cruz
>>> Santa Cruz, California 95064
>>> USA
>>>
>>>
>>>
> 

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

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[Peter Artymiuk]

Just to indicate, amidst all these tales of disaster, that not everyone has bad 
experiences with Apple laptops. 

I bought my first generation MacBook Air in February 2008, one week after they 
were first announced. I have been using it pretty much  permananently since 
then. I have not had any catastrophic battery issues, although a charge is now 
only good for about 3 hours continuous use. Still, mustn't be complacent, so I 
won't leave it to recharge on the sofa overnight from now on...

However, a few months ago one of the hinges on the screen broke so I took it 
along to the local Apple Store and they replaced it with a new screen free of 
charge even though the machine was more than 4 years old. (By the way, I am not 
a regular customer of theirs and don't know anyone there personally.) In a way 
I was a little disappointed because I wanted an excuse to buy one of the newer 
MBAs with more than the 2 Gbyte memory and 80 Gbyte disk that my early model 
has (you can now get them with 8 Gbyte and a 256 Gbyte SSD)...

best wishes
Pete

Prof Peter Artymiuk
Krebs Institute
Department of Molecular Biology & Biotechnology
University of Sheffield
Sheffield
S10 2TN
ENGLAND





On 20 Nov 2012, at 09:25, Charles Ballard wrote:

> To add to the general list (and future class action).  I have just had the 
> battery expansion on one  for the second time.  Added to the number of them I 
> have bricked by letting the charge run down to low by unplugging them.  
> Interestingly apple agreed to replace the bricked batteries free of charge, 
> for their US customers.  But, us foreigners had to pay for the pleasure...
> 
> Charles
> 
> On 18 Nov 2012, at 17:30, Bosch, Juergen wrote:
> 
>> Bill I think that's crap.
>> I had issues on a 2005 MacBook Pro with inflating battery and it was 
>> replaced (after about 6 months). There were troubles with those batteries 
>> and impurities but mine still had apple care at that time and the batteries 
>> were exchangeable. 
>> I have not heard of the build in batteries to have problems but yours sure 
>> did. Send Tim Cook an email with the picture. This should not have happened 
>> and also keeping the power cord on leading to this problem should not have 
>> happened. For what did they introduce the trickling charging ? If you can't 
>> leave the coord plugged in how many nice wooden US households gave caught 
>> fire due to Apple products ?
>> 
>> Jürgen 
>> ..
>> Jürgen Bosch
>> Johns Hopkins Bloomberg School of Public Health
>> Department of Biochemistry & Molecular Biology
>> Johns Hopkins Malaria Research Institute
>> 615 North Wolfe Street, W8708
>> Baltimore, MD 21205
>> Phone: +1-410-614-4742
>> Lab:  +1-410-614-4894
>> Fax:  +1-410-955-3655
>> http://lupo.jhsph.edu
>> 
>> On Nov 17, 2012, at 16:28, "William G. Scott"  wrote:
>> 
>>> Hi folks:
>>> 
>>> I'm trying to get a sense for how frequently this sort of thing occurs:
>>> 
>>> 
>>> 
>>> That was a macbook air that served me well for four years, but then 
>>> self-destructed. (I took it to the Apple store.  They generously offered to 
>>> repair it for $800 or to sell me a new one, and suggested this was normal 
>>> if you leave the power cord attached after the battery charges, even while 
>>> giving a lecture or seminar.)  It strikes me as a bit dangerous.
>>> 
>>> --Bill Scott
>>> 
>>> 
>>> 
>>> 
>>> 
>>> William G. Scott
>>> Professor
>>> Department of Chemistry and Biochemistry
>>> and The Center for the Molecular Biology of RNA
>>> 228 Sinsheimer Laboratories
>>> University of California at Santa Cruz
>>> Santa Cruz, California 95064
>>> USA
>>> 
>>> 
>>> 
> 
> --
> Scanned by iCritical.

[ccp4bb] areaimol bugs

[Ben Eisenbraun]

Hi CCP4bb,

I updated our CCP4 6.3.0 for x86_64 linux to the September 21 CCP4 update
when it came out. The release notes said it had a patched areaimol in it,
and it did update the binary, but we are still seeing segfaults and NaN
values, etc.

The all-in-one update also contains an areaimol binary, and both that one
and the one I have installed after the update have md5 sum:

08798443e2154e90703378f0b6702aba 
/programs/x86_64-linux/ccp4/6.3.0/ccp4-6.3.0/bin/areaimol 

But on the CCP4 problems page, there is a totally different binary linked:

ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/updates/Linux-x86_64/areaimol

And it has md5 sum:

0e438e2710e6dd8df902073e50318313

All of these binaries report themselves as:

### CCP4 6.3: AREAIMOL version 6.3 : 17/08/12##

I'll have my user test the binary on the problems page, but I figured this
confusion should get sorted out upstream regardless of whether that is the
correct solution.

So which binary should we be using?

Thanks.

-ben

--
| Ben Eisenbraun
| SBGrid Consortium  | http://sbgrid.org   |
| Harvard Medical School | http://hms.harvard.edu  |

Re: [ccp4bb] occupancy vs. Bfactors

[Bernhard Rupp]

As already mentioned by jrh, I again want to impress that B-factor and
occupancy are in principle two entirely different parameters.

 

They may appear as achieving the same thing upon refinement at the
resolution we deal with in most macromolecular structures.

 

The fact is that reduced occupancy just *scales down* the entire scattering
function at a given B, while an increased B-factor *changes the shape* of
the scattering curve, i.e. makes it narrower in reciprocal space and thus in
direct space gives a broader electron density. Reduced occupancy just
reduces electron density levels. Those are physically distinctly different
although not easily separable effects. I have an applet that can be used to
see the point

 

http://www.ruppweb.org/cgi-bin/webscat.exe?E1=O
 &B=50.0&Occupation_factor=0.5&B1=Submit

 

(disregard the core dump in the cgi)

 

and a figure from the book also shows this:

 

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallograph
y_Fig_9-06.htm

 

Note that by reducing occupancy I can achieve a *similar* overall effect
than by increasing B, but not the *same* electron density distribution!

If the data are good enough (and reasonably high resolution), a refinement
program can refine both parameters simultaneously, although with a high
covariance.

 

In summary, similar appearance is not caused by the same effect.

 

Best, BR

 

PS: Partial occupancy is not the same as disorder. You can have well-ordered
different occupancies that manifest themselves then in superstructure

patterns. Common in small molecule/materials.

 

PPS: Neither n or B have anything to do with reflection spot width, btw!

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Monday, November 19, 2012 3:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] occupancy vs. Bfactors

 

Hi Grant,

 

sounds like you did the right thing (as far as I can guess given the amount
of information you provided).

 

In a nutshell, both, B-factors and occupancies, model disorder. The
difference is that occupancies model larger scale disorder (such as distinct
conformations) than B-factors (smearing due to temperature vibrations, etc).

 

Perhaps in you case the side chain has several conformations among which you
can see only one, and therefore it's valid to model it with occupancy less
than 1 (I presume you refined one occupancy per all atoms in that side
chain).

 

Pavel

On Mon, Nov 19, 2012 at 3:36 PM, GRANT MILLS
 wrote:

Hello all,

I'm currently working on a structure which if I stub a certain side chain
phenix/coot shows me a large green blob which looks strikingly similar to
the side chain, when I put it in and run another refinement the blob turns
red.

Basically I was just playing around and I changed the occupancy of the side
chain and now there are no complaints. But I was thinking, should I haven
changed the Bfactors instead? Should I have left well enough alone? If I
lower the occupancy manually and do not include alternate confirmations have
I introduced modelling bias?

Could someone recommend some good articles I could read on exactly how to
correctly fix this problem.

Thanks,
GM 

 

Re: [ccp4bb] CONECT Records

[Jenny Harmer]

Didn't have the latest version of Coot but can now make the LINKs. 

Many thanks for your help.

Re: [ccp4bb] how many cycles to settle B-factor?

[Robbie Joosten]

Hi Jim,

The speed at which the B-factor converges depends on many factors. The B-factor 
restraint weight that Herman and I mentioned (the one you should optimise 
before changing occupancies!) is an important factor. Also the position of your 
atomic coordinates WRT where they should end up is important. In Refmac, there 
is a big difference between isotropic and anisotropic B-factors (the latter 
converge much slower). So all in all it is very difficult to predict when the 
B-factor converges. The good news however is that more cycles of refinement 
should not hurt your model (if they do, your refinement settings are 
non-optimal). So grab a cup of coffee and run enough cycles. In Refmac 30 
cycles is enough for most isotropic B-factors, but in some cases I use many 
more.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Jim Brannigan
> Sent: Tuesday, November 20, 2012 10:49
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] how many cycles to settle B-factor?
> 
> As an adjunct to B-factor vs occupancy thread, i might expect the b-factor to
> halve if the occupancy is set to 0.5 (but I'm only a molecular 
> biologist), if so
> how many cycles of refmac would it take for the value to settle? My limited
> experience is that it dosn't exactly halve but i do tend to use fewer cycles 
> at
> later stages of refinement?
> 
> thanks
> 
> Jim Brannigan

[ccp4bb] how many cycles to settle B-factor?

[Jim Brannigan]

As an adjunct to B-factor vs occupancy thread, i might expect the b-factor to 
halve if the occupancy is set to 0.5 (but I'm only a molecular biologist), 
if so how many
cycles of refmac would it take for the value to settle? My limited experience 
is that it dosn't exactly halve but i do tend to use fewer cycles at later 
stages of refinement?

thanks

Jim Brannigan

Re: [ccp4bb] ctruncate/scapepacktomtz : terminate called after throwing an instance of clipper::Message_fatal

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Hari,

this is hard to tell without debugging, but I have two guesses:
1) did you untick 'use anomalous data' but the script only partially
picked this up? In that case, the 'colano'-columns would not be present
2) some column name is too long given your suffix "B8-C7-A_P21" -
although this should not be too long, mtz column labels can be up to
30 characters long - but maybe give it a try without it or with
shorter suffix.

Regards,
Tim

On 11/20/2012 12:02 AM, hari jayaram wrote:
> Hi All, I am running the latest ccp4 ( auto-updated using the new
> autoupdate tool built into ccp4i)
> 
> I was running what should be a routine scalepack to mtz conversion
> and I got an error which I have never seen before with ctruncate.
> 
> 
> When I run the same job with old truncate it succeeds.
> 
> 
> Any ideas what may be causing this. I hope I snipped the correct
> part of the error message.
> 
> 
> Thanks Hari
> 
> 
> 
> ***
>
> 
* Information from CCP4Interface script
> ***
>
> 
The program run with command:
> /home/hari/ccp4-6.3-download/ccp4-6.3.0/bin/ctruncate -hklin 
> "/tmp/hari/B8-C7-A_P21_4_1_mtz.tmp" -hklout 
> "/tmp/hari/B8-C7-A_P21_4_3_mtz.tmp" -colin
> "/*/*/\[IMEAN,SIGIMEAN\]" -colano
> "/*/*/\[I(+),SIGI(+),I(-),SIGI(-)\]" -colout B8-C7-A_P21 -nres 150 
> has failed with error message CCP4MTZfile - internal error 
> terminate called after throwing an instance of
> 'clipper::Message_fatal' 
> ***
>
> 
> 
> #CCP4I TERMINATION STATUS 0 "CCP4MTZfile - internal error terminate
> called after throwing an instance of 'clipper::Message_fatal'" 
> #CCP4I TERMINATION TIME 19 Nov 2012  16:50:26 #CCP4I MESSAGE Task
> failed
> 

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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQq036UxlJ7aRr7hoRAq2dAKChGzAnUXloxQIr56rv9XAECmCp0ACfUOAR
W6I0zJJWMustOTLvyVBoir8=
=Hgbi
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[ccp4bb] CCP4 Study Weekend, early bird deadline

[Charles Ballard]

Dear All,

A quick reminder to you all about this coming January's CCP4 Study Weekend 
entitled "Molecular Replacements" (January 3rd-5th 2010). As the title 
suggests, the meeting will be all about the latest developments in molecular 
replacement with many leading crystallographers and software developers giving 
presentations on the subject. The deadline for the first round of registrations 
will be the 23rd of November after which the registration price will increase 
from £210 to £260. So please get your registration in before then. 

After a few years in Warwick, the meeting will be returning to the East 
Midlands Conference Centre at Nottingham University in the UK. For more details 
and to register please see the Study Weekend website at:

http://www.cse.scitech.ac.uk/events/CCP4_2013/

We hope to see you there.

Best wishes

Charles

Organisers: Helen Walden, Pietro Roversi, along with Airlie McCoy
-- 
Scanned by iCritical.

Re: [ccp4bb] OT: Has anyone experienced problems with Apple laptop battery expansion?

[Charles Ballard]

To add to the general list (and future class action).  I have just had the 
battery expansion on one  for the second time.  Added to the number of them I 
have bricked by letting the charge run down to low by unplugging them.  
Interestingly apple agreed to replace the bricked batteries free of charge, for 
their US customers.  But, us foreigners had to pay for the pleasure...

Charles

On 18 Nov 2012, at 17:30, Bosch, Juergen wrote:

> Bill I think that's crap.
> I had issues on a 2005 MacBook Pro with inflating battery and it was replaced 
> (after about 6 months). There were troubles with those batteries and 
> impurities but mine still had apple care at that time and the batteries were 
> exchangeable. 
> I have not heard of the build in batteries to have problems but yours sure 
> did. Send Tim Cook an email with the picture. This should not have happened 
> and also keeping the power cord on leading to this problem should not have 
> happened. For what did they introduce the trickling charging ? If you can't 
> leave the coord plugged in how many nice wooden US households gave caught 
> fire due to Apple products ?
> 
> Jürgen 
> ..
> Jürgen Bosch
> Johns Hopkins Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Phone: +1-410-614-4742
> Lab:  +1-410-614-4894
> Fax:  +1-410-955-3655
> http://lupo.jhsph.edu
> 
> On Nov 17, 2012, at 16:28, "William G. Scott"  wrote:
> 
>> Hi folks:
>> 
>> I'm trying to get a sense for how frequently this sort of thing occurs:
>> 
>> 
>> 
>> That was a macbook air that served me well for four years, but then 
>> self-destructed. (I took it to the Apple store.  They generously offered to 
>> repair it for $800 or to sell me a new one, and suggested this was normal if 
>> you leave the power cord attached after the battery charges, even while 
>> giving a lecture or seminar.)  It strikes me as a bit dangerous.
>> 
>> --Bill Scott
>> 
>> 
>> 
>> 
>> 
>> William G. Scott
>> Professor
>> Department of Chemistry and Biochemistry
>> and The Center for the Molecular Biology of RNA
>> 228 Sinsheimer Laboratories
>> University of California at Santa Cruz
>> Santa Cruz, California 95064
>> USA
>> 
>> 
>> 

--
Scanned by iCritical.

[ccp4bb] Invitation to the "Mini-Symposium in Honor of the Retirement of Prof. Jorge Navaza"

[Diego Marcelo Guerin Aguilar]

Dear CCP4 colleagues & AMoRe's funs.
We are organizing a mini-symposium (two days long) in honor of the
retirement of Jorge Navaza. If you are interested on attending this
meeting, please go to the link indicated below and input the dates of your 
preference.
Please, feel free to distribute this invitation to other colleagues.
Thanks very much for join us.
Diego

PS: By now, we don't know where this meeting will take place. The three
candidate cities are Sitges (near Barcelona), Madrid, and Bilbao, but for sure 
will be in Spain.

http://doodle.com/ughnhb6pik7yssqz

--
***
Dr Diego M.A. Guerin
Unidad de Biofisica (CSIC-UPV/EHU) - Fundacion Biofisica Bizkaia
Barrio Sarriena S/N, 48940, Leioa, Vizcaya, Spain
E-mail: diego.gue...@ehu.es
http://www.ehu.es/biofisica http://sici.umh.es http://www.redtrv.org
Tel: +34 94 601 3345 Fax: +34 94 601 3360
ADVERTENCE: The email and any files attached with this email are
confidential. Any unauthorised dissemination or any use or disclosure
of any information contained in them, is strictly prohibited and
may be illegal. Please let me know if you received this message
in error, and delete it from your computer. Thank you.
***

Re: [ccp4bb] occupancy vs. Bfactors

[Herman . Schreuder]

What of course also could have happened, is that the Bfactor restraints
are too tight, forcing, too low Bfactors for the flexible side chain.
Especially after rotatable bonds, Bfactors can increase much more
sharply than many of the older parameter files would allow. In this
case, reducing these restraints would solve the problem.
Herman




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of herman.schreu...@sanofi.com
Sent: Tuesday, November 20, 2012 9:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] occupancy vs. Bfactors


Hi Robby and Grant,
Here I must second Pavel. As Grant just discovered, modern
refinement programs have improved so much, that they will no longer
allow to fudge a low occupancy (sharper but less density) with a high
Bfactor (broader and more density), especially at higher resolutions. In
this case, I would scroll down the contour level and look for
alternative conformations. Even if you don't find any, the most correct
approach in my view would still be to lower the occupancy, although I am
personnally too lazy to do this.
 
My two cents,
Herman
 




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
On Behalf Of Robbie Joosten
Sent: Tuesday, November 20, 2012 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] occupancy vs. Bfactors


Hi Grant,

This is part of the recurring side chain discussion.
There is no consensus in the community about what the optimal approach
is.
In your current approach you are adding a model
parameter (occupancy) to improve the fit with the experimental data
(remove negative difference density). You should ask yourself whether
you really need to add that parameter. Are you not overfitting? Is there
any clear evidence that the atoms are not always there?
The alternative model you propose (full occupancy, high
B) has fewer parameters and explains more of the strucure (you account
for all atoms the protein has, prior knowledge). This model probably
also better reflects the uncertainty of the coordinates of the side
chains involved. If your B-factor restraints are not too tight, the
difference densitty should also disappear (equal explanation of the
experimental data). To me that would be a better model.

HTH,
Robbie




Date: Mon, 19 Nov 2012 23:36:56 +
From: gdmi...@students.latrobe.edu.au
Subject: [ccp4bb] occupancy vs. Bfactors
To: CCP4BB@JISCMAIL.AC.UK


Hello all,

I'm currently working on a structure which if I stub a
certain side chain phenix/coot shows me a large green blob which looks
strikingly similar to the side chain, when I put it in and run another
refinement the blob turns red.

Basically I was just playing around and I changed the
occupancy of the side chain and now there are no complaints. But I was
thinking, should I haven changed the Bfactors instead? Should I have
left well enough alone? If I lower the occupancy manually and do not
include alternate confirmations have I introduced modelling bias?

Could someone recommend some good articles I could read
on exactly how to correctly fix this problem.

Thanks,
GM 

Re: [ccp4bb] occupancy vs. Bfactors

[Herman . Schreuder]

Hi Robby and Grant,
Here I must second Pavel. As Grant just discovered, modern refinement
programs have improved so much, that they will no longer allow to fudge
a low occupancy (sharper but less density) with a high Bfactor (broader
and more density), especially at higher resolutions. In this case, I
would scroll down the contour level and look for alternative
conformations. Even if you don't find any, the most correct approach in
my view would still be to lower the occupancy, although I am personnally
too lazy to do this.
 
My two cents,
Herman
 




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Robbie Joosten
Sent: Tuesday, November 20, 2012 6:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] occupancy vs. Bfactors


Hi Grant,

This is part of the recurring side chain discussion. There is no
consensus in the community about what the optimal approach is.
In your current approach you are adding a model parameter
(occupancy) to improve the fit with the experimental data (remove
negative difference density). You should ask yourself whether you really
need to add that parameter. Are you not overfitting? Is there any clear
evidence that the atoms are not always there?
The alternative model you propose (full occupancy, high B) has
fewer parameters and explains more of the strucure (you account for all
atoms the protein has, prior knowledge). This model probably also better
reflects the uncertainty of the coordinates of the side chains involved.
If your B-factor restraints are not too tight, the difference densitty
should also disappear (equal explanation of the experimental data). To
me that would be a better model.

HTH,
Robbie




Date: Mon, 19 Nov 2012 23:36:56 +
From: gdmi...@students.latrobe.edu.au
Subject: [ccp4bb] occupancy vs. Bfactors
To: CCP4BB@JISCMAIL.AC.UK


Hello all,

I'm currently working on a structure which if I stub a certain
side chain phenix/coot shows me a large green blob which looks
strikingly similar to the side chain, when I put it in and run another
refinement the blob turns red.

Basically I was just playing around and I changed the occupancy
of the side chain and now there are no complaints. But I was thinking,
should I haven changed the Bfactors instead? Should I have left well
enough alone? If I lower the occupancy manually and do not include
alternate confirmations have I introduced modelling bias?

Could someone recommend some good articles I could read on
exactly how to correctly fix this problem.

Thanks,
GM 

Re: [ccp4bb] occupancy vs. Bfactors

[Jrh]

Dear Pavel,
Also worth mentioning the obvious that the mathematical functional form of an 
occupancy and a B factor in its -ve exponential is very different BUT at lower 
resolutions they behave similarly. Thus higher resolution refinement allows an 
'easier' determination of each parameter. 
Greetings,
John

Prof John R Helliwell DSc 
 
 

On 19 Nov 2012, at 23:54, Pavel Afonine  wrote:

> Hi Grant,
> 
> sounds like you did the right thing (as far as I can guess given the amount 
> of information you provided).
> 
> In a nutshell, both, B-factors and occupancies, model disorder. The 
> difference is that occupancies model larger scale disorder (such as distinct 
> conformations) than B-factors (smearing due to temperature vibrations, etc).
> 
> Perhaps in you case the side chain has several conformations among which you 
> can see only one, and therefore it's valid to model it with occupancy less 
> than 1 (I presume you refined one occupancy per all atoms in that side chain).
> 
> Pavel
> 
> On Mon, Nov 19, 2012 at 3:36 PM, GRANT MILLS 
>  wrote:
> Hello all,
> 
> I'm currently working on a structure which if I stub a certain side chain 
> phenix/coot shows me a large green blob which looks strikingly similar to the 
> side chain, when I put it in and run another refinement the blob turns red.
> 
> Basically I was just playing around and I changed the occupancy of the side 
> chain and now there are no complaints. But I was thinking, should I haven 
> changed the Bfactors instead? Should I have left well enough alone? If I 
> lower the occupancy manually and do not include alternate confirmations have 
> I introduced modelling bias?
> 
> Could someone recommend some good articles I could read on exactly how to 
> correctly fix this problem.
> 
> Thanks,
> GM 
>