Re: [ccp4bb] 3D

[Shaun Lott]

I'm still using passive, interleaved 3D, Zalman-style... Hopefully coot etc 
will retain support for that...!



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Re: [ccp4bb] 3D

[Paul Emsley]

On 11/03/19 15:55, Pedro Matias wrote:
>
> Reading the news piece, I would hardly consider the present-day VR
> headsets to be "affordable" - except perhaps for the PSVR. With the
> added downside that they are single-user.
>
> When can we expect a CootVR release ?
>
>

VR is not really a substitute for stereo I feel (or vice versa).

CootVR is available from github: it's in "beta" at the moment

https://github.com/hamishtodd1/CVR

The author of CootVR is Hamish Todd. There is a release planned for May
(2019).

Regards,

Paul



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[ccp4bb] 77th Annual Pittsburgh Diffraction Conference: First Announcement

[Leighton Coates]

Dear Colleagues

You are invited to the 77th Annual Pittsburgh Diffraction Conference
which will be hosted onsite at Oak Ridge National Laboratory in Oak
Ridge, Tennessee, USA

Start Date: 24th Oct 2019
End Date:  26th Oct 2019

URL: https://conference.sns.gov/event/78/

The conference will take place over three days and feature sessions
focused on all areas of diffraction, from powders to protein crystals.
Topics will include emerging technologies/techniques, Total
scattering, Magnetic scattering, small molecules and Integrative
Structural Biology. The Chung Soo Yoo Award, established by the
Pittsburgh Diffraction Society to honor Dr. Yoo’s memory, and a $400
cash prize will be given to the graduate student having the best
poster presentation at the conference. Registration for the conference
is only $100 and abstract submission for talks and posters is now
open.

Best Wishes

Leighton Coates

Contact:  Leighton Coates
Email: coat...@ornl.gov
URL:   https://conference.sns.gov/event/78/



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[ccp4bb] Wednesday 3.30pm (UTC) - Webinar: PDBe-KB Aggregated views

[David Armstrong]

On behalf of PDBe, I invite you to attend a webinar on the new PDBe 
Knowledge Base (PDBe-KB) resource. This webinar will introduce you to 
the new PDBe-KB Aggregated views: brand new pages presenting PDB data in 
a different context.


For more information and to register for the webinar, please visit the 
following link:


bit.ly/PDBe-KB-webinar

Kind Regards,

David Armstrong

--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544



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[ccp4bb] R Associate II or Associate Scientist I - Protein Engineering

[Oganesyan, Vaheh]

Posting on behalf of colleague (please, do not reply to me):

·
o
§
US - Gaithersburg - MD
· Apply
· Apply with 
LinkedIn
· MedImmune is the worldwide biologics research and development arm of 
AstraZeneca. Here, you’ll have the opportunity to make a difference in people’s 
lives every day. As one of the world’s premier biotechnology companies, our 
mission is centered on delivering life-changing products that advance world 
health, and help fight and cure disease.
We’re constantly pushing the boundaries of science to deliver life-changing 
medicines to patients, with a passion for discovery and a pipeline to show for 
it. We’re pioneering innovative research and exploring novel pathways across 
key therapeutic areas including oncology, respiratory, inflammation and 
autoimmunity, cardiovascular and metabolic disease, and infection and vaccines. 
And we’re industry-leading in immunology, protein engineering and translational 
science. We offer a unique and strong collaborative network as part of the 
AstraZeneca family, as together we explore synergies between small and large 
molecules.

MedImmune has a dynamic environment that fosters collaboration and innovation. 
We attract top minds, and we nurture and build top talent.
Main Duties and Responsibilities
Major responsibilities include planning and executing experiments related to 
developing protein engineering platforms for therapeutic antibody generation 
and optimization. She/he will work with scientists to create research plans, 
execute experiments, analyze and interpret data and present results to the 
group and the department. She/he is expected to have a strong work ethic, 
excellent organizational skills and keep good records. Strong team-based 
communication and presentation skills will be required.
Essential Requirements
· The ideal candidate should have strong hands-on experience in 
Molecular Biology or Biochemistry, particularly PCR and molecular cloning 
techniques.
· Protein expression, purification and characterization experience is 
also required.
· Experience in cell culture, FACS and antibody engineering 
(phage/yeast display-based selections) is not required but is also highly 
desirable.
Education and Experience
· Research Associate II - Bachelor’s Degree in Molecular Biology or 
other related fields with two to five years of relevant experience in industry 
(preferred) or academia, or Master’s Degree with zero to two years of relevant 
experience in industry (preferred) or academia
· Associate Scientist I – Bachelor’s Degree in Molecular Biology or 
other related fields with five to eight years of relevant experience in 
industry (preferred) or academia, or Master’s Degree with two to five years of 
relevant experience in industry (preferred) or academia
Knowledge
· Hands-on experience with advanced PCR and molecular cloning 
techniques, particularly where troubleshooting was required to drive a project 
forward
· Familiarity with cell culture, recombinant protein production and 
purification. Biochemical characterization such as affinity determination and 
immunoassays (ELISA).
· Experience with antibody engineering and FACS is highly desirable.
· The ability to learn and embrace new technologies quickly, work 
independently and communicate well with the team.




Regards,

Vaheh Oganesyan, PhD
www.medimmune.com




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



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[ccp4bb] Demonstrations of the Fourier series with epicycles

[Bryan Lepore]

Greetings - I just learned about a nifty representation of the Fourier
series using epicycles, perhaps the CCP4 readers would be interested in -
there's an animated gif here :

https://twitter.com/johncarlosbaez/status/1094671748501405696?lang=en

This longer video shows more detail of this approach, where a refinement
process is used to draw a fairly complex two-dimensional picture:

What is a Fourier series? (Explained by drawing circles) - Smarter Every
Day 205
https://youtu.be/ds0cmAV-Yek

finally, the video above originated from this blog :
Turkish language : http://bilimneguzellan.net/fuyye-serisi/
part 2 : http://bilimneguzellan.net/en/follow-up-to-fourier-series-2/

Enjoy,

-Bryan W. Lepore



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Re: [ccp4bb] problem with the symmetry water molecule

[Eleanor Dodson]

You need to set the occupancy to 0.5 though..
Eleanor

On Mon, 11 Mar 2019 at 16:17, Phil Jeffrey  wrote:

> Hello Firdous
>
> You are seeing two because you are displaying crystallographic symmetry
> and you are seeing its symmetry mate.  Coot only places one (check the
> PDB file) but displays the second generated by symmetry.  It pays to
> place that water molecule as precisely as possible on the symmetry axis
> so that refinement programs will treat this as a special position water
> and eliminate the extra one - i.e. make it as close as possible to its
> symmetry mate.
>
> Phil Jeffrey
> Princeton
>
> On 3/11/19 12:09 PM, Firdous Tarique wrote:
> > Hello everyone
> >
> > I am having a difficult time fitting a water molecule which is right at
> > the centre of symmetry. Every time I am trying to fit one water molecule
> > it fits two because of the symmetry atom is at the same place. What is
> > the best way to solve this problem? I am talking about the water
> > molecule where two molecules are paced at one place (4th position in the
> > semicircle having both pink and purple).
> >
> > Thanks
> >
> > Firdous
> > Screen Shot 2019-03-11 at 12.00.21 PM.png
>
> 
>
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>



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Re: [ccp4bb] problem with the symmetry water molecule

[Mark J van Raaij]

and set the occupancy of that water molecule to 0.50

> On 11 Mar 2019, at 17:17, Phil Jeffrey  wrote:
> 
> Hello Firdous
> 
> You are seeing two because you are displaying crystallographic symmetry and 
> you are seeing its symmetry mate.  Coot only places one (check the PDB file) 
> but displays the second generated by symmetry.  It pays to place that water 
> molecule as precisely as possible on the symmetry axis so that refinement 
> programs will treat this as a special position water and eliminate the extra 
> one - i.e. make it as close as possible to its symmetry mate.
> 
> Phil Jeffrey
> Princeton
> 
> On 3/11/19 12:09 PM, Firdous Tarique wrote:
>> Hello everyone
>> I am having a difficult time fitting a water molecule which is right at the 
>> centre of symmetry. Every time I am trying to fit one water molecule it fits 
>> two because of the symmetry atom is at the same place. What is the best way 
>> to solve this problem? I am talking about the water molecule where two 
>> molecules are paced at one place (4th position in the semicircle having both 
>> pink and purple).
>> Thanks
>> Firdous
>> Screen Shot 2019-03-11 at 12.00.21 PM.png
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] problem with the symmetry water molecule

[Phil Jeffrey]

Hello Firdous

You are seeing two because you are displaying crystallographic symmetry 
and you are seeing its symmetry mate.  Coot only places one (check the 
PDB file) but displays the second generated by symmetry.  It pays to 
place that water molecule as precisely as possible on the symmetry axis 
so that refinement programs will treat this as a special position water 
and eliminate the extra one - i.e. make it as close as possible to its 
symmetry mate.


Phil Jeffrey
Princeton

On 3/11/19 12:09 PM, Firdous Tarique wrote:

Hello everyone

I am having a difficult time fitting a water molecule which is right at 
the centre of symmetry. Every time I am trying to fit one water molecule 
it fits two because of the symmetry atom is at the same place. What is 
the best way to solve this problem? I am talking about the water 
molecule where two molecules are paced at one place (4th position in the 
semicircle having both pink and purple).


Thanks

Firdous
Screen Shot 2019-03-11 at 12.00.21 PM.png




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[ccp4bb] Refmac5 refinement question

[Raymond Brown]

Hi folks,

What are acceptable values for RMS Bond length, RMS Bond angle and RMS Chiral 
volume?

The tutorial suggests RMS Bond length of 0.0200?

I would like to hear your suggestions and/or rationale.

Many thanks

Ray Brown



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Re: [ccp4bb] 3D

[Pedro Matias]

Reading the news piece, I would hardly consider the present-day VR
headsets to be "affordable" - except perhaps for the PSVR. With the
added downside that they are single-user.

When can we expect a CootVR release ?

Às 15:45 de 11/03/2019, Joern Krausze escreveu:
>
> The legacy drivers will not be affected, will they?
>
> On 3/11/19 4:22 PM, David Schuller wrote:
>>
>> https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/
>>
>>
>>   NVIDIA will stop supporting 3D glasses in April
>>
>>
>> -- 
>> ===
>> All Things Serve the Beam
>> ===
>>David J. Schuller
>>modern man in a post-modern world
>>MacCHESS, Cornell University
>>schul...@cornell.edu
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
> -- 
> *
> Address:
>
> Joern Krausze
> Department of Plant Biology
> Braunschweig University of Technology
> Spielmannstr. 7
> 38106 Braunschweig
> Germany
>
> Email:  j.krau...@tu-braunschweig.de
> Phone:  +49 (0)531 3915858 
> * 
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
-- 

Industry and Medicine Applied Crystallography
Macromolecular Crystallography Unit
___
Phones : (351-21) 446-9100 Ext. 1669
 (351-21) 446-9669 (direct)
 Fax   : (351-21) 441-1277 or 443-3644

email : mat...@itqb.unl.pt

http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography
http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit

Mailing address :
Instituto de Tecnologia Quimica e Biologica António Xavier
Universidade Nova de Lisboa
Av. da República
2780-157 Oeiras
PORTUGAL

ITQB NOVA, a great choice for your PhD
https://youtu.be/de6j-aaTWNQ

Master Programme in Biochemistry for Health
https://youtu.be/UKstDCFjYI8




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Re: [ccp4bb] 3D

[Joern Krausze]

The legacy drivers will not be affected, will they?

On 3/11/19 4:22 PM, David Schuller wrote:


https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/


  NVIDIA will stop supporting 3D glasses in April


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



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--
*
Address:

Joern Krausze
Department of Plant Biology
Braunschweig University of Technology
Spielmannstr. 7
38106 Braunschweig
Germany

Email:  j.krau...@tu-braunschweig.de
Phone:  +49 (0)531 3915858
*




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Re: [ccp4bb] 3D

[Francis Reyes]

I’m crossing my fingers, or should I say my eyes, that they don’t!

> On Mar 11, 2019, at 9:22 AM, David Schiller  wrote:
> 
> https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/
> 
> NVIDIA will stop supporting 3D glasses in April
> 
> 
> 
> -- 
> ===
> All Things Serve the Beam
> ===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu
> 
> To unsubscribe from the CCP4BB list, click the following link:
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[ccp4bb] 3D

[David Schuller]

https://www.engadget.com/2019/03/11/nvidia-ends-3d-vision-support/


 NVIDIA will stop supporting 3D glasses in April


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




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[ccp4bb] Correct link: 3 year PhD fellowship in the Group of Structural Biology and Drug Development (Luecke group) at the Centre for Molecular Medicine Norway (NCMM), University of Oslo (UiO).

[Luecke, Hartmut]

A 3 year PhD fellowship is available in the Group of Structural Biology and 
Drug Development (Luecke 
group) at the Centre 
for Molecular Medicine Norway (NCMM), University of Oslo (UiO).

The Group for Structural Biology and Drug Development investigates medically 
relevant proteins and protein complexes using biophysical, biochemical and 
structural approaches.  The projects aim at understanding structure-function 
relationships with an emphasis on drug discovery.  We employ a variety of 
biochemical and biophysical techniques (x-ray crystallography, single particle 
cryo electron microscopy, DSF, ITC, SPR, HDX-MS, SAXS, molecular dynamics 
simulations etc.).  Externally funded projects include inhibitor discovery 
targeting the Helicobacter pylori pH acclimation system (a pH-gated urea 
channel and a cytoplasmic urease), and discovery of compounds that reactivate 
p53 cancer mutants in vitro and in vivo.  Additional projects are available.

The PhD student will also benefit from career development programs offered both 
at UiO, the Norwegian BioCat initiative  as well as 
the Nordic EMBL network of the Centre for Molecular Medicine, Norway.
Online application required, deadline 31 Mar 2019:

https://www.jobbnorge.no/en/available-jobs/job/165866/phd-research-fellowship-in-structural-biology-and-drug-development


--
Prof. Hartmut Luecke
Structural Biology and Drug Discovery Group
Norwegian Centre for Molecular Medicine (NCMM), Nordic EMBL Partnership
and Institute of Clinical Medicine, University of Oslo
Dept. of Medical Biochemistry, Oslo University Hospital
Oslo, Norway




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transmission cannot be guaranteed to be secure or error-free as information 
could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or 
contain viruses. The sender therefore does not accept liability for any errors 
or omissions in the contents of this message, which arise as a result of e-mail 
transmission.



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[ccp4bb] 3 year PhD fellowship in the Group of Structural Biology and Drug Development (Luecke group) at the Centre for Molecular Medicine Norway (NCMM), University of Oslo (UiO).

[Luecke, Hartmut]

A 3 year PhD fellowship is available in the Group of Structural Biology and 
Drug Development (Luecke 
group) at the Centre 
for Molecular Medicine Norway (NCMM), University of Oslo (UiO).

The Group for Structural Biology and Drug Development investigates medically 
relevant proteins and protein complexes using biophysical, biochemical and 
structural approaches.  The projects aim at understanding structure-function 
relationships with an emphasis on drug discovery.  We employ a variety of 
biochemical and biophysical techniques (x-ray crystallography, single particle 
cryo electron microscopy, DSF, ITC, SPR, HDX-MS, SAXS, molecular dynamics 
simulations etc.).  Externally funded projects include inhibitor discovery 
targeting the Helicobacter pylori pH acclimation system (a pH-gated urea 
channel and a cytoplasmic urease), and discovery of compounds that reactivate 
p53 cancer mutants in vitro and in vivo.  Additional projects are available.

The PhD student will also benefit from career development programs offered both 
at UiO, the Norwegian BioCat initiative  as well as 
the Nordic EMBL network of the Centre for Molecular Medicine, Norway.
Online application required, deadline 31 Mar 2019:

https://www.jobbnorge.no/en/available-jobs/job/164159/two-2-postdoctoral-fellowships-in-structural-biology-and-drug-development

--
Prof. Hartmut Luecke
Structural Biology and Drug Discovery Group
Norwegian Centre for Molecular Medicine (NCMM), Nordic EMBL Partnership
and Institute of Clinical Medicine, University of Oslo
Dept. of Medical Biochemistry, Oslo University Hospital
Oslo, Norway




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distribute, or copy this e-mail. Please notify the UC Irvine Health – 
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888-456-7006 immediately if you have received this e-mail in error. E-mail 
transmission cannot be guaranteed to be secure or error-free as information 
could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or 
contain viruses. The sender therefore does not accept liability for any errors 
or omissions in the contents of this message, which arise as a result of e-mail 
transmission.



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[ccp4bb] Postdoctoral position in structural biology at SGC-UNICAMP, Brazil

[Rafael COUNAGO]

We are looking to recruit a highly motivated and ambitious individual to
take a leading role in developing new inhibitors for putative drug targets
in Neglected and Emerging Infectious Diseases.

The Structural Genomics Consortium at UNICAMP (SGC-UNICAMP, Brazil)
combines protein structure, biochemistry and medicinal chemistry to develop
small molecule inhibitors that can be used to validate potential drug
targets.

The successful candidate should have a strong background and interest in
biochemistry and structural biology. We are looking for a creative and
ambitious person with good communication skills and keen to work on
challenging projects.

For further details and to apply for this position, please follow the link
below:
https://www.nature.com/naturecareers/job?id=679937

Our lab is situated in Campinas, São Paulo Brazil and is one of the
laboratories of the Structural Genomics Consortium (https://www.thesgc.org/
).

Rafael M. Couñago
SGC - CQMED - Unicamp (www.thesgc.org)
Av. Dr. André Tosello, 550
Cidade Universitária
CEP 13083-886
Campinas, SP, Brazil



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Re: [ccp4bb] change in unit cell volume

[Clemens Vonrhein]

On Thu, Mar 07, 2019 at 02:32:53PM -0600, Murpholino Peligro wrote:
> 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.

You also have to be sure that

 (1) there is no significant energy drift during those experiments
 (which if not modelled could be compensated by a change in
 refined cell dimensions)

 (2) each dataset has been collected identically (over the same part
 of the crystal) and contains enough observations to give a stable
 refinement of your cell parameters

I would also check the values of crystal-detector distance as a
function of dose - since these should stay stable and not drift as
well. Sometimes instrumentation changes/drifts can be compensated by a
change in refined cell dimensions while the physical cell within the
crystal actually stays static.

Assuming you have high quality data for each of those datasets, a good
test is to refine your model to convergence against each of those and
see if the final (standard) bonds are systematically shorter or longer
than the expected values (e.g. Engh for protein). WhatCheck does
a check for that and correlates it with a nice suggestion about wrong
cell parameters ... which can highlight e.g. errors in energy or
wavelength values as written by beamlines into image headers ;-)

Cheers

Clemens



> 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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-- 

*--
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
* Global Phasing Ltd., Sheraton House, Castle Park 
* Cambridge CB3 0AX, UK   www.globalphasing.com
*--



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