Re: [ccp4bb] Ramachandran outliers

[Phoebe A. Rice]

In this sort of case, I find that often the Rama-bad residues appear unfixable 
because small distortions in many bond lengths and angles have made the side 
chain appear correctly fit even though the rotamer choice was wrong.

My recipe for fixing that:

  *   Mutate the offending residue to glycine or alanine in coot
  *   Optimize the bond lengths & angles of the backbone
 *   If that doesn’t move the residue into an allowed region, manually fix 
it and re-optimize the bond lengths & angles
  *   Then put the side chain back on and choose the rotamer that best fits the 
density.  You’ll probably fit it to be different than the original one.

My colleagues wrote a rebuild + refine server based on automating, more 
rigorously, that sort of logic:
https://godzilla.uchicago.edu/pages/projects.html
In my own experience at least, you should use the results from their server as 
a buffet of (often quite useful) suggestions for how to rebuild your refmac- or 
phenix- refined model.

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/



From: CCP4 bulletin board  on behalf of Tereza Skalova 

Reply-To: Tereza Skalova 
Date: Friday, March 8, 2019 at 3:08 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] Ramachandran outliers

Dear all,

I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based on PDB 
structures (identical molecules with high resolution) and I use NCS, medium 
between AB (protein 1) and loose between CDE (protein 2). I use overall 
B-factor and 8 TLS groups.
Is it possible to optimize Ramachandran plot directly in Refmac?

Thank you

Tereza Skalova







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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Change dimer assembly in ASU

[Herman . Schreuder]

Dear Ezequiel,

Be careful, it also happens that the asymmetric contains two half-dimers, with 
the other half of the dimers being generated by crystallographic operators.

In this case it is not possible to rearrange the monomers such that the 
asymmetric unit contains one biological dimer and for refinement, one has to 
stick to the arrangement obtained by molecular replacement. However, for 
analysis and the making of pictures, it is perfectly valid to generate the two 
biological dimers using the appropriate crystallographic symmetry operators. 
WITHIN the dimers generated that way, the monomers will be identical, however, 
BETWEEN the two dimers, there might be (small) differences, which may or may 
not be biologically relevant.

Good luck!
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Eleanor 
Dodson
Gesendet: Dienstag, 5. März 2019 13:04
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Change dimer assembly in ASU

I tend to use PISA for suggesting biologically relevant complexes.  And you can 
modify the MR solution to replace a molecule with  any symmetry generated copy 
of it..

But check Phaser has put your molecule reasonably close to the origin.



On Mon, 4 Mar 2019 at 19:52, Randy Read 
mailto:rj...@cam.ac.uk>> wrote:
Dear Ezequiel,

There is nothing special about which particular symmetry copies a molecular 
replacement program chooses, so there is no good reason to stick to those 
symmetry copies.  On the other hand, there are very good reasons to present a 
molecule that is as close as possible to what is biologically relevant, so you 
should definitely change the choices of symmetry copies to make a proper 
heterodimer in your PDB entry.  The easiest way I know to do that is with the 
option in coot: Extensions->Modelling->Symm Shift Reference Chain Here (after 
centering on an atom in a symmetry copy that you want to make the master copy).

Best wishes,

Randy Read

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

> On 4 Mar 2019, at 17:27, Eze Chivi 
> mailto:ezech...@outlook.com.ar>> wrote:
>
> Dear CCP4bb community:
> My crystal is a heterodimeric complex. I solved the structure using MR with a 
> related structure (containig the dimer), using a highly automated pipeline. 
> However, the MR solution is not the dimer of biological relevance. The 
> experimentally validated dimer is formed between a protomer in the ASU and 
> one from the adjacent symmetry-related pair of molecules. Is it correct to 
> use a modelling program to assemble the "biologically correct" dimer and then 
> proceed to refinement? Or... is it need to keep the MR solution and inform in 
> the PDB header how the relevant dimer is formed? Many Thanks
>
> Ezequiel
>
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>



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Re: [ccp4bb] Ramachandran outliers

[Tristan Croll]

Dear Tereza,

First, a shameless plug for ISOLDE (https://isolde.cimr.cam.ac.uk). It’s built 
specifically for working with models around your resolution.

Other than that, I’d suggest having a close look at the corresponding sites in 
your high-resolution reference models as a sanity check. Remember: just because 
a model is built into high-resolution data doesn’t mean it’s completely correct 
- mistakes happen at all resolutions. Conversely, some outliers are real - if 
it’s an outlier in the reference model *and* well-supported by the 
high-resolution density, you can tick it off your list of things to worry about.

Best regards,

Tristan
 

> On 8 Mar 2019, at 09:08, Tereza Skalova  wrote:
> 
> Dear all,
> 
> I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
> Do you have any idea how to reduce the number?
> I refine in Refmac, using h-bond based Prosmart restraints based on PDB 
> structures (identical molecules with high resolution) and I use NCS, medium 
> between AB (protein 1) and loose between CDE (protein 2). I use overall 
> B-factor and 8 TLS groups.
> Is it possible to optimize Ramachandran plot directly in Refmac?
> 
> Thank you
> 
> Tereza Skalova
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Ramachandran outliers

[Nicolas FOOS]

Dear Tereza,

In certain cases it could be better to do a step back to be able to 
rebuild properly.


Did you look carefully in the real-space the agreement between your 
model and the visible density.


If you "over"refined your model in reciprocal space only you can loose 
some information.


I comment you last comments :

1) Density too weak. Was it like that from the beginning, what happen if 
you remove the "invisible" parts, is any differences green or red 
density visible in the vicinity? Is that a flexible loop ?


The "systematic" coincidence between weak density and ramachandran 
outlier is suspicious.


2) Manual NCS definition could help in a first approach but once your 
model is complet enough it could be good to relax this constrain, 
because you are actually fitting the model with what you think it should 
be and what it actually is. In my opinion it's interesting to at least 
try to use automatic which maybe will keep as NCS only the parts which 
are really NCS. Sometimes very similar conformation of domain or 
sub-units are close to be an NCS but not anymore NCS because already too 
different (I am not sure to be clear ;-) ).


4) pdb redo even if really powerful and efficient can't be magic, if 
your model suffer from mistake such as really bad rotamer or 
ramachandran outlier, it  could be impossible to revert that. Only a 
manual intervention could fix it.


If the ramachandran outlier are in a weak density area, I would probably 
try to fix that localy based on geometrical constraint (included 
ramachandran) and then redo a round of refinement in reciprocal space to 
see what happen. Sometimes the distortion is that important that you 
need to re-build more than the residues directly involved especially at 
relatively "low" resolution.


Hope this help.

Nicolas

Nicolas Foos
PhD
Structural Biology Group
European Synchrotron Radiation Facility (E.S.R.F)
71, avenue des Martyrs
CS 40220
38043 GRENOBLE Cedex 9
+33 (0)6 76 88 14 87
+33 (0)4 76 88 45 19

On 08/03/2019 10:36, Tereza Skalova wrote:

Thank you for your comments.

1) manual correction in Coot does not work - the density is too weak
2) manual NCS is substantially better than automatic local NCS in this 
case

3) CPP4i2 might be good idea
4) PDB REDO is great, however no more help in this case
5) Prosmart - I use "prosmart -id -p1 target.pdb -p2 external.pdb" , I 
will study other possibilities


Tereza



pá 8. 3. 2019 v 10:25 odesílatel Robert Nicholls 
mailto:nicho...@mrc-lmb.cam.ac.uk>> napsal:


Dear Tereza,

It is highly recommended that you do not attempt to directly
optimise the Ramachandran plot during refinement. Doing so would
not guarantee you a better model, and would mean that you could no
longer use the Ramachandran plot for validation purposes.

I suggest that you inspect each of the residues corresponding to
the outliers, and assess the conformation, geometry and density
fit of that residue and residues in the surrounding region. There
are various tools in Coot to help you with this. It should be
clear which regions are in need of attention (outliers that should
be fixed) and which "outliers" should be considered acceptable.
Indeed, ensuring that there are no Ramachandran outliers is not an
objective/requirement for a good model.


I refine in Refmac, using h-bond based Prosmart restraints based
on PDB structures (identical molecules with high resolution)


Prosmart h-bond based restraints, and Prosmart restraints based on
PDB structures are two different things. Are you using Prosmart
h-bond restraints, or Prosmart restraints to a high-resolution
homologous model? If you're using restraints to a high-resolution
homologue, are you generating restraints for all of your chains,
or just some of them? If you're just generating restraints for
some of them, then you should ensure that the others are
appropriately restrained also.


I use NCS, medium between AB (protein 1) and loose between CDE
(protein 2).


From your mention of "medium" and "loose" NCS restraints, I'm
guessing you're using CCP4i. Why not try using CCP4i2? This is the
currently recommended and supported interface for CCP4 software.
Don't use manual NCS restraints (medium, loose, etc.). Try using
automatically generated local NCS restraints - we find they work
better.

How are your R/Rfree behaving in refinement? If you're using
Prosmart restraints to homologous models then do you need/benefit
from the use of NCS restraints too, or are they working against
each other?

Best regards,
Rob




On 8 Mar 2019, at 09:08, Tereza Skalova mailto:t.skalova.c...@gmail.com>> wrote:

Dear all,

I have structure at 3.3A resolution and I have ca. 35
Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based
on PDB 

Re: [ccp4bb] Discrepancy between (initially indistinguishable) space groups in mtz and pdb

[CCP4BB]

Hi

Just to make sure about this - you do NOT need to reprocess the data (i.e. You 
don't need to repeat the indexing) you only need to change the space group in 
the way that Eleanor has indicated. 

Harry
--
Dr Harry Powell

> On 7 Mar 2019, at 21:36, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Yes - I think you do need to assign the space group in the mtz file to be the 
> same as that in the coordinate file header. I believe that REFMAC will stop 
> with an error message if there is inconsistency between the two sets of 
> header information.
> 
> It is easy to change the spacegroup.
> In GUI2 there is a task to do this, but this is equivalent to typing on the 
> command line
> mtzutils hklin1 I23.mtz hklout  I213.mtz
> SYMM I213
> end
> 
> all that does is rewrite the header of the mtz file with the correct symmetry 
> operators.
> 
> eleanor
> 
> 
> 
>> On Thu, 7 Mar 2019 at 21:26, Eze Chivi  wrote:
>> Dear CCP4bb community:
>> 
>> My data set was indexed assuming the space group "I 2 3" (SG number 197), 
>> however it is indistinguishable from "I 21 3" (SG number 199). Refinement 
>> was carried out initially by a colleague in Phenix picking the SG "I 21 3" 
>> from the two listed SG (this is the correct one judging from refinement 
>> results). Now, I'm conducting some "polishing" tasks and comparing results 
>> from Phenix and Refmac. However, 1) I cant't see the option in Refmac to 
>> choose the "alternative" SG, and 2) Is it need to repeat the indexing in the 
>> final SG? Does it create some conflict with the refinement task conducted so 
>> far (i.e. different data flagged for Rfree)?
>> Thank you in advance
>> 
>> SG in mtz: I 2 3
>> SG in pdb: I 21 3 (this is the correct SG)
>> 
>> Ezequiel
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
> 
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Re: [ccp4bb] Ramachandran outliers

[Tereza Skalova]

Thank you for your comments.

1) manual correction in Coot does not work - the density is too weak
2) manual NCS is substantially better than automatic local NCS in this case
3) CPP4i2 might be good idea
4) PDB REDO is great, however no more help in this case
5) Prosmart - I use "prosmart -id -p1 target.pdb -p2 external.pdb" , I will
study other possibilities

Tereza



pá 8. 3. 2019 v 10:25 odesílatel Robert Nicholls 
napsal:

> Dear Tereza,
>
> It is highly recommended that you do not attempt to directly optimise the
> Ramachandran plot during refinement. Doing so would not guarantee you a
> better model, and would mean that you could no longer use the Ramachandran
> plot for validation purposes.
>
> I suggest that you inspect each of the residues corresponding to the
> outliers, and assess the conformation, geometry and density fit of that
> residue and residues in the surrounding region. There are various tools in
> Coot to help you with this. It should be clear which regions are in need of
> attention (outliers that should be fixed) and which "outliers" should be
> considered acceptable. Indeed, ensuring that there are no Ramachandran
> outliers is not an objective/requirement for a good model.
>
> I refine in Refmac, using h-bond based Prosmart restraints based on PDB
> structures (identical molecules with high resolution)
>
>
> Prosmart h-bond based restraints, and Prosmart restraints based on PDB
> structures are two different things. Are you using Prosmart h-bond
> restraints, or Prosmart restraints to a high-resolution homologous model?
> If you're using restraints to a high-resolution homologue, are you
> generating restraints for all of your chains, or just some of them? If
> you're just generating restraints for some of them, then you should ensure
> that the others are appropriately restrained also.
>
> I use NCS, medium between AB (protein 1) and loose between CDE (protein 2).
>
>
> From your mention of "medium" and "loose" NCS restraints, I'm guessing
> you're using CCP4i. Why not try using CCP4i2? This is the currently
> recommended and supported interface for CCP4 software. Don't use manual NCS
> restraints (medium, loose, etc.). Try using automatically generated local
> NCS restraints - we find they work better.
>
> How are your R/Rfree behaving in refinement? If you're using Prosmart
> restraints to homologous models then do you need/benefit from the use of
> NCS restraints too, or are they working against each other?
>
> Best regards,
> Rob
>
>
>
> On 8 Mar 2019, at 09:08, Tereza Skalova  wrote:
>
> Dear all,
>
> I have structure at 3.3A resolution and I have ca. 35 Ramachandran
> outliers.
> Do you have any idea how to reduce the number?
> I refine in Refmac, using h-bond based Prosmart restraints based on PDB
> structures (identical molecules with high resolution) and I use NCS, medium
> between AB (protein 1) and loose between CDE (protein 2). I use overall
> B-factor and 8 TLS groups.
> Is it possible to optimize Ramachandran plot directly in Refmac?
>
> Thank you
>
> Tereza Skalova
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>



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Re: [ccp4bb] Ramachandran outliers

[Robert Nicholls]

Dear Tereza,

It is highly recommended that you do not attempt to directly optimise the 
Ramachandran plot during refinement. Doing so would not guarantee you a better 
model, and would mean that you could no longer use the Ramachandran plot for 
validation purposes.

I suggest that you inspect each of the residues corresponding to the outliers, 
and assess the conformation, geometry and density fit of that residue and 
residues in the surrounding region. There are various tools in Coot to help you 
with this. It should be clear which regions are in need of attention (outliers 
that should be fixed) and which "outliers" should be considered acceptable. 
Indeed, ensuring that there are no Ramachandran outliers is not an 
objective/requirement for a good model.

> I refine in Refmac, using h-bond based Prosmart restraints based on PDB 
> structures (identical molecules with high resolution)

Prosmart h-bond based restraints, and Prosmart restraints based on PDB 
structures are two different things. Are you using Prosmart h-bond restraints, 
or Prosmart restraints to a high-resolution homologous model? If you're using 
restraints to a high-resolution homologue, are you generating restraints for 
all of your chains, or just some of them? If you're just generating restraints 
for some of them, then you should ensure that the others are appropriately 
restrained also.

> I use NCS, medium between AB (protein 1) and loose between CDE (protein 2).


From your mention of "medium" and "loose" NCS restraints, I'm guessing you're 
using CCP4i. Why not try using CCP4i2? This is the currently recommended and 
supported interface for CCP4 software. Don't use manual NCS restraints (medium, 
loose, etc.). Try using automatically generated local NCS restraints - we find 
they work better.

How are your R/Rfree behaving in refinement? If you're using Prosmart 
restraints to homologous models then do you need/benefit from the use of NCS 
restraints too, or are they working against each other?

Best regards,
Rob



> On 8 Mar 2019, at 09:08, Tereza Skalova  wrote:
> 
> Dear all,
> 
> I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
> Do you have any idea how to reduce the number?
> I refine in Refmac, using h-bond based Prosmart restraints based on PDB 
> structures (identical molecules with high resolution) and I use NCS, medium 
> between AB (protein 1) and loose between CDE (protein 2). I use overall 
> B-factor and 8 TLS groups.
> Is it possible to optimize Ramachandran plot directly in Refmac?
> 
> Thank you
> 
> Tereza Skalova
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Ramachandran outliers

[Robbie Joosten]

Hi Tereza,

Rather than opting for a technological fix in a reciprocal space refinement 
program you should look at all the outliers in Coot and see if they are 
fixable. If they are severe outliers, you need to rebuild by peptide flipping 
and possibly by more invasive actions. If you have small outliers (just outside 
the distribution), see if this general fit is okay. If so, just tighten the 
overall restraints a bit and refine some more. If not, rebuild.

Generally in Refmac you should use local NCS restraints rather that chain-level 
restraints like you use now. This can be part of the problem.

If you insists on solving the problem by automation you can try PDB-REDO which 
will do peptide flipping for you and will try to optimize settings for Refmac. 
That may solve some of your outliers, but you really need to look at them in 
Coot as well.

Cheers,
Robbie

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tereza 
Skalova
Sent: Friday, March 08, 2019 10:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Ramachandran outliers

Dear all,

I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based on PDB 
structures (identical molecules with high resolution) and I use NCS, medium 
between AB (protein 1) and loose between CDE (protein 2). I use overall 
B-factor and 8 TLS groups.
Is it possible to optimize Ramachandran plot directly in Refmac?

Thank you

Tereza Skalova







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[ccp4bb] Ramachandran outliers

[Tereza Skalova]

Dear all,

I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based on PDB
structures (identical molecules with high resolution) and I use NCS, medium
between AB (protein 1) and loose between CDE (protein 2). I use overall
B-factor and 8 TLS groups.
Is it possible to optimize Ramachandran plot directly in Refmac?

Thank you

Tereza Skalova



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Re: [ccp4bb] change in unit cell volume

[Elspeth Garman]

Dear Murpholino
Unfortunately no rule of thumb has been established, although I have only seen 
contraction once and have seen expansion for very many proteins.
Seems to depend critically on the particular crystal (and probably its density 
of stacking imperfections/dislocations) and even crystals of the same protein 
from the same growth drop do not behave in the same way, as shown in 2 
systematic studies of this phenomenon:
Ravelli et al., JSR (2002) 9
Murray and Garman, JSR (2002) 9, 347-354.
Best wishes
Elspeth


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward 
Snell
Sent: 07 March 2019 20:56
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] change in unit cell volume

Hi Murpholino,

I’ve looked at this with respect to metals in the protein and found that it was 
very informative to compare fractional coordinates which compensate for the 
volume expansion. When that is done, some apparent motions may be simply due to 
unit cell expansion (waters, metals, ligands etc.), while others can be very 
specific and produce structural non-isomorphism.

I suspect the chemical damage has much more of an impact. Owen, Rudino-Pinera 
and Garman (PNAS, 2006) recommend an absolute maximum dose of 30 MGy. I’ve not 
compared cell expansion as a function of dose for a large sample of proteins 
but in a recent study (conveniently just heading for publication) I have seen a 
linear ~0.3% expansion per MGy which gives ~1% at 30 MGy. I don’t know if it’s 
the same for other proteins but I seem to remember a study or two on this and 
fully expect the authors to give me grief for forgetting them at the moment!

Unit cell decreases could possibly be an impact of specific damage to 
crystallization contacts, off center crystals (if it’s within a data set), 
detector shifts or energy changes (both unlikely). I’ve not heard of a unit 
cell decrease being driven by damage but that’s not to say that it doesn’t 
happen.

Best,

Eddie

PS. Shameless plug –- http://getacrystal.com

Edward Snell Ph.D.

Biological Small Angle Scattering Theory and Practice, Eaton E. Lattman, Thomas 
D. Grant, and Edward H. Snell.
Available through all good bookshops, or direct from Oxford University Press

Director of the NSF BioXFEL Science and Technology Center
President and CEO Hauptman-Woodward Medical Research Institute
BioInnovations Chaired Professorship, University at Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone:   (716) 898 8631 Fax: (716) 898 8660
Skype:eddie.snell Email: 
esn...@hwi.buffalo.edu
Webpage: https://hwi.buffalo.edu/scientist-directory/snell/

[cid:image002.png@01D4D58B.E18F91C0]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Murpholino Peligro
Sent: Thursday, March 7, 2019 3:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] change in unit cell volume

Let's say I have a protein crystal from which I collected 30 datasets. If I 
plot the unit cell volume per dataset the volume rises.
My question is: Is there a rule of thumb of some sort* to consider the 
initial/final datasets isomorphous still?

* Something like if the unit cell volume changes more than 1% then the crystal 
is not isomorphous.

My second question is: Meents already said that the unit cell volume expansion 
is a consequence of hydrogen gas building up inside the crystal. But...what if 
the unit cell volume decreases? Is there an explanation for that?


Thank you very much.



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