Re: [ccp4bb] change in unit cell volume

[Rosenbaum, Gerold]

Hi Murpholino and Eddie,

I looked up what we found in our study of the decay of thaumatin crystals at 3 
energies (Acta Cryst. (2015). D71, 772-778).
Figure 2 shows the unit cell parameter a vs. dose for 5 crystals (all from the 
same batch). One crystal shows a fairly linear expansion of +0.06% per MGy up 
to 16 MGy. Two other crystals show about the same initial expansion of 
0.06%/MGy up to 8 and 10 MGy which then decreases with one of the two shown no 
expansion from 13 to 16 MGy. Crystal 4 starts with about 0.04%/MGy up to 2 MGy 
and shows no expansion from 6 to 16 MGy. Crystal 5 starts expanding at 
0.03%/MGy up to 4 MGy, no expansion between 6 and 8 MGy, and contracting 
between 8 and 15 MGy at a final rate of -0.05%/MGy between 12 and 15 MGy.

Fig. 2 shows data measured at 6.33 keV. Similar disparity was observed for the 
5 crystals each measured at 12.66 keV and at 19 keV. We were not the first 
observing contraction instead of expansion.

We did not address the question of isomorphism. For our study, the change of 
unit-cell parameters was only of concern to make sure we used only those 
reflections that were fully recorded from zero to the maximum dose.

I agree with Eddie that the chemical changes due to radiation damage contribute 
much more to non-isomorphism than the small changes in unit-call parameters.

By the way, we found that, on average, at a dose of about 11 MGy the average 
diffraction intensities had decayed to 70% of the initial value at 12.66 keV 
and 19 keV and at about 7.5 MGy at 6.33 keV. Much lower than 30 MGy as reported 
by Owen et al. Others have also reported dose limits similar to ours.

Gerd

On 07.03.2019 14:56, Edward Snell wrote:
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:part3.F0916F99.BC7F8DEA@anl.gov]
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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Re: [ccp4bb] Discrepancy between (initially indistinguishable) space groups in mtz and pdb

[Eleanor Dodson]

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

[Eze Chivi]

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



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Re: [ccp4bb] change in unit cell volume

[Edward Snell]

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:image001.png@01D4D4FE.49ECE2B0]
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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[ccp4bb] change in unit cell volume

[Murpholino Peligro]

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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Re: [ccp4bb] Cryo-EM Full Professor position at Strasbourg University

[Bruno KLAHOLZ]

Dear all,

kind reminder for those interested to apply for the cryo-EM full professor 
position in Strasbourg, the deadline for the registration via the Galaxie Web 
site is approaching (March 26th 2019).
Please note that there is either
a) a qualification step to have done already, or b) no need for that if you 
have an equivalent position elsewhere (e.g. associate professor or full 
professor in any other University in France or abroad).

If you are interested or have questions about the position please write to the 
contact persons indicated below.

Best regards,

Bruno Klaholz





From: Bruno KLAHOLZ
Sent: Monday, October 01, 2018 8:45 PM
To: 3...@ncmir.ucsd.edu; CCP4BB@JISCMAIL.AC.UK; 'cc...@jiscmail.ac.uk' 

Subject: RE: Cryo-EM Full Professor position at Strasbourg University


Dear all,

kind reminder for those interested to apply for the cryo-EM full professor 
position in Strasbourg, the deadline for the pre-registration to the 
qualification step is approaching (14.10.2018).
If you are interested or have questions about the procedure please write to the 
contact persons indicated below.

Best regards,

Bruno Klaholz





INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

CALL FOR APPLICATIONS
FOR A PROFESSOR AND GROUP LEADER POSITION
IN MOLECULAR AND CELLULAR CRYO ELECTRON MICROSCOPY


A full professor position is open at the Strasbourg University to establish a 
research team in molecular or cellular cryo electron microscopy. Candidates 
should have excellent international visibility in the field of molecular 
(single particles) or cellular (tomography, FIB / SEM imaging) electron 
microscopy. Their scientific profile may include the development of image 
processing methods (3-D reconstruction and refinement, 3-D classification of 
structures, subtomogram averaging, 3-D image segmentation), multi-scale 
analysis (correlative microscopy, integration of complementary methods, 
integration of multi-scale data) or sample preparation (controlled and 
time-resolved vitrification, cryo-sectioning, cryo-lamellas for cell 
tomography).

With a strong background in biophysics and structural biology, the candidate 
will consolidate and extend the teaching program in life sciences centered on 
multiscale imaging of biological macromolecules at the master level and in the 
newly funded graduate school for integrative molecular and cellular biology at 
Strasbourg University 
http://www.igbmc.fr/formation/imcbio and 
the associated Research Institutes. The applicant is also expected to have a 
leading role in cryo-EM trainings program developed at the national (FRISBI 
http://frisbi.eu) and ReNaFoBiS https://www.renafobis.fr and 
international level (Instruct-ERIC https://www.structuralbiology.eu).

The research team will be hosted at the Centre for Integrative Biology (CBI) 
http://www.igbmc.fr/grandesstructures/cbi at the Institute of Genetics and 
Molecular and Cellular Biology (IGBMC http://www-igbmc.fr) and the Department 
of Integrated Structural Biology (ISB 
http://www-igbmc.u-strasbg.fr/research/department/3)
 in Illkirch, France. IGBMC is one of the leading biomedical research centres 
in Europe and brings together more than 700 researchers, PhD students and 
scientific staff grouped into 50 research teams and over a dozen core 
facilities. IGBMC is dedicated to fundamental and applied research in life 
sciences, in the fields of gene expression regulation, epigenetics, 
developmental biology and human genetics. Researchers have access to a wide 
range of methods including structural and functional analysis of biomolecules, 
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The research teams in the ISB Department address fundamental biological 
questions mainly in the field of gene expression regulation at the 
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the translational level (RNA stability, protein synthesis, ribosome structure). 
The recruited candidate is expected to develop an ambitious, innovative and 
collaborative research program creating a strong synergy with other IGBMC teams.

The professorship is expected to start in September 2019. An attractive 
start-up package will be provided and the selected candidate will have access 
to the cutting-edge facilities at the CBI that hosts the French and European 
Infrastructures for Integrated Structural Biology FRISBI and Instruct-ERIC: 
http://frisbi.eu and https://www.structuralbiology.eu.

Your application:

If you hold an equivalent position (e.g. associate professor or full professor) 
or have gone through the qualification procedure described below you can now 
apply through the following website:
https://galaxie.enseignementsup-recherche.gouv.fr/antares/can/index.jsp
Deadline is 26.3.2019.

Re: [ccp4bb] Visualisation software supporting ChromaDepth

[Thomas Holder]

Hi Jan,

Chromadepth is actually in Open-Source PyMOL since version 2.2. I see the 
ChangeLog only mentions "Graphics refactoring, ported from Incentive PyMOL". 
I'll fix the related documentation.

Cheers,
  Thomas

> On Mar 7, 2019, at 12:38 PM, Jan Gebauer  wrote:
> 
> Dear all,
> 
> I know it's not quite the topic of this list, but hopefully related enough.
> 
> I am looking for a free software,able to render PDB structures in ChromaDepth 
> colours (Meaning from blue to red based on the distance from the viewer - 
> https://en.wikipedia.org/wiki/ChromaDepth). I'd like to print some structure 
> for an "open-day" of our faculty.
> 
> I found that the incentive version of PyMol supports it, but this is a little 
> bit to expensive.
> 
> Is there any free software out there? Or potentially a plugin? If not is 
> there a function to determine distances of atoms from the viewer in Chimera 
> -- I could write my own python script then...
> 
> Thanks for all help,
> 
> Jan Gebauer
> --
> Dr. Jan Gebauer
> Structural Biologist
> px.uni-koeln.de / c2f.uni-koeln.de / pipc.uni-koeln.de
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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[ccp4bb]

[Robert Nicholls]

Or you can use ViewHKL if you want a graphical interface.

Rob


> On 7 Mar 2019, at 12:58, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> mtzdump hklin my.mtz
> 
> That reads the header and the first 10 lines
> 
> or if you want all as ASCII
> mtzdump hklin my.mtz > mine.hkl
> nref 1
> end
> 
> and that will list the first 1 reflections to an ascii file..
> 
> 
> On Thu, 7 Mar 2019 at 12:52, Sanaz Asadollahpour 
>  > wrote:
> Dears,
> with which program in CCP4 I can read MTZ file?
> 
> regards,
> S.A.
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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[ccp4bb]

[Eleanor Dodson]

mtzdump hklin my.mtz

That reads the header and the first 10 lines

or if you want all as ASCII
mtzdump hklin my.mtz > mine.hkl
nref 1
end

and that will list the first 1 reflections to an ascii file..


On Thu, 7 Mar 2019 at 12:52, Sanaz Asadollahpour <
sanaz.asadollahp...@ocbc.uni-freiburg.de> wrote:

> Dears,
> with which program in CCP4 I can read MTZ file?
>
> regards,
> S.A.
>
> 
>
> 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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[ccp4bb]

[Robbie Joosten]

Hi Sanaz,

That is not a very well-defined question. To just get some info on an mtz file 
you can use mtzdmp from the command line (mtzdmp foo.mtz). 

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Sanaz Asadollahpour
> Sent: Thursday, March 07, 2019 13:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb]
> 
> Dears,
> with which program in CCP4 I can read MTZ file?
> 
> regards,
> S.A.
> 
> ##
> ##
> 
> 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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[ccp4bb]

[Almudena Ponce Salvatierra]

Just run mtzdump or do it here http://services.mbi.ucla.edu/SAVES/MTZ/

Best,

Almu


El jue., 7 mar. 2019 a las 13:52, Sanaz Asadollahpour (<
sanaz.asadollahp...@ocbc.uni-freiburg.de>) escribió:

> Dears,
> with which program in CCP4 I can read MTZ file?
>
> regards,
> S.A.
>
> 
>
> 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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[ccp4bb]

[Sanaz Asadollahpour]

Dears,
with which program in CCP4 I can read MTZ file?

regards,
S.A.



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[ccp4bb] Visualisation software supporting ChromaDepth

[Jan Gebauer]

Dear all,

I know it's not quite the topic of this list, but hopefully related enough.

I am looking for a free software,able to render PDB structures in 
ChromaDepth colours (Meaning from blue to red based on the distance from 
the viewer - https://en.wikipedia.org/wiki/ChromaDepth). I'd like to 
print some structure for an "open-day" of our faculty.


I found that the incentive version of PyMol supports it, but this is a 
little bit to expensive.


Is there any free software out there? Or potentially a plugin? If not is 
there a function to determine distances of atoms from the viewer in 
Chimera -- I could write my own python script then...


Thanks for all help,

Jan Gebauer
--
Dr. Jan Gebauer
Structural Biologist
px.uni-koeln.de / c2f.uni-koeln.de / pipc.uni-koeln.de



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Re: [ccp4bb] Racemic crystallography and structure solving problem

[CCP4BB]

Sorry, I meant to write "note that not all achiral space groups are 
centrosymmetric", since most are. However, even as written it's true, but less 
obvious...

Harry
--
Dr Harry Powell

> On 7 Mar 2019, at 10:23, CCP4BB  wrote:
> 
> Hi all
> 
> A genuine question; I'm wondering how well Phaser (or other MR programs) 
> deals with achiral space groups and the presence of both hands of a molecule 
> (just because you can have both hands of a chiral molecule related 
> crystallographically in a crystal, you don't need a centrosymmetric space 
> group - note that not all achiral space groups are not centrosymmetric...).
> 
> Harry
> --
> Dr Harry Powell
> 
>> On 7 Mar 2019, at 10:11, Prasun Kumar  wrote:
>> 
>> Hi Tim: 
>> 
>> Thanx for your response and sorry for late acknowledgment . 
>> You are right, the peptide is forming an oligomer. I have used Xia2 and 
>> pipeline 3dii with small_molecule=true option as suggested earlier by 
>> Pierre. Now the space group is P-1.
>> I will check for SHELXT. 
>> So far the molecular replacement is a problem for me. However, I am on it. 
>> 
>> Regards
>> Prasun
>> From: Tim Gruene 
>> Sent: 05 March 2019 10:02:53
>> To: Prasun Kumar
>> Cc: CCP4BB@jiscmail.ac.uk
>> Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem
>>  
>> Dear Prasun,
>> 
>> in case you get atomic resolution (better than about 1.2A), you should be 
>> able 
>> to solve the structure with direct methods, e.g. SHELXT.  You may want to 
>> check the processing if the cell is really this big. Unless you have several 
>> copies in the asymmetric unit, one might expect a smaller cell for only 30 
>> residues. You can also try alternative programs, like XDS - start with 
>> XDSGUI 
>> in case you are not familiar with XDS from the command line.
>> 
>> Best,
>> Tim
>> 
>> 
>> On Monday, March 4, 2019 4:33:20 PM CET Prasun Kumar wrote:
>> > Hi All:
>> > 
>> > I have performed racemic crystallography and got crystals that diffracted.
>> > The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK)
>> > gives the space group as P1 and cell dimension
>> > 42.78 52.16   54.49   114.11  92.16   92.31.
>> > 
>> > Challanges start from here:
>> > 
>> > 1) How much I should be assured of the space group as I expect my peptides
>> > to get crystallized in the same group, but by default we get the same space
>> > group. 2) Is there any seperate method for processing the raw images in my
>> > case.
>> > 
>> > I used the merged .mtz file for phasing. However, I always get the warning
>> > that eLLG score is low and it is difficult to fit a single copy of the
>> > ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also
>> > more than 95%.
>> > 
>> > My peptides, 30 residues long, form an oligomer. However, I do not have
>> > reliable model of oligomers to start with. I have taken a single helix of
>> > length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines
>> > will be really helpful.
>> > 
>> > I am happy to provide any other relevant information, if one wants.
>> > 
>> > Thanx in advance
>> > Prasun
>> > 
>> > 
>> > 
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>> -- 
>> --
>> Tim Gruene
>> GPG Key ID = A46BEE1A
>> 
>> 
>> 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] Racemic crystallography and structure solving problem

[CCP4BB]

Hi all

A genuine question; I'm wondering how well Phaser (or other MR programs) deals 
with achiral space groups and the presence of both hands of a molecule (just 
because you can have both hands of a chiral molecule related 
crystallographically in a crystal, you don't need a centrosymmetric space group 
- note that not all achiral space groups are not centrosymmetric...).

Harry
--
Dr Harry Powell

> On 7 Mar 2019, at 10:11, Prasun Kumar  wrote:
> 
> Hi Tim: 
> 
> Thanx for your response and sorry for late acknowledgment . 
> You are right, the peptide is forming an oligomer. I have used Xia2 and 
> pipeline 3dii with small_molecule=true option as suggested earlier by Pierre. 
> Now the space group is P-1.
> I will check for SHELXT. 
> So far the molecular replacement is a problem for me. However, I am on it. 
> 
> Regards
> Prasun
> From: Tim Gruene 
> Sent: 05 March 2019 10:02:53
> To: Prasun Kumar
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem
>  
> Dear Prasun,
> 
> in case you get atomic resolution (better than about 1.2A), you should be 
> able 
> to solve the structure with direct methods, e.g. SHELXT.  You may want to 
> check the processing if the cell is really this big. Unless you have several 
> copies in the asymmetric unit, one might expect a smaller cell for only 30 
> residues. You can also try alternative programs, like XDS - start with XDSGUI 
> in case you are not familiar with XDS from the command line.
> 
> Best,
> Tim
> 
> 
> On Monday, March 4, 2019 4:33:20 PM CET Prasun Kumar wrote:
> > Hi All:
> > 
> > I have performed racemic crystallography and got crystals that diffracted.
> > The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK)
> > gives the space group as P1 and cell dimension
> > 42.78 52.16   54.49   114.11  92.16   92.31.
> > 
> > Challanges start from here:
> > 
> > 1) How much I should be assured of the space group as I expect my peptides
> > to get crystallized in the same group, but by default we get the same space
> > group. 2) Is there any seperate method for processing the raw images in my
> > case.
> > 
> > I used the merged .mtz file for phasing. However, I always get the warning
> > that eLLG score is low and it is difficult to fit a single copy of the
> > ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also
> > more than 95%.
> > 
> > My peptides, 30 residues long, form an oligomer. However, I do not have
> > reliable model of oligomers to start with. I have taken a single helix of
> > length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines
> > will be really helpful.
> > 
> > I am happy to provide any other relevant information, if one wants.
> > 
> > Thanx in advance
> > Prasun
> > 
> > 
> > 
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> -- 
> --
> Tim Gruene
> GPG Key ID = A46BEE1A
> 
> 
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Re: [ccp4bb] Racemic crystallography and structure solving problem

[Prasun Kumar]

Hi Tim:


Thanx for your response and sorry for late acknowledgment .

You are right, the peptide is forming an oligomer. I have used Xia2 and 
pipeline 3dii with small_molecule=true option as suggested earlier by Pierre. 
Now the space group is P-1.

I will check for SHELXT.

So far the molecular replacement is a problem for me. However, I am on it.


Regards

Prasun


From: Tim Gruene 
Sent: 05 March 2019 10:02:53
To: Prasun Kumar
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem

Dear Prasun,

in case you get atomic resolution (better than about 1.2A), you should be able
to solve the structure with direct methods, e.g. SHELXT.  You may want to
check the processing if the cell is really this big. Unless you have several
copies in the asymmetric unit, one might expect a smaller cell for only 30
residues. You can also try alternative programs, like XDS - start with XDSGUI
in case you are not familiar with XDS from the command line.

Best,
Tim


On Monday, March 4, 2019 4:33:20 PM CET Prasun Kumar wrote:
> Hi All:
>
> I have performed racemic crystallography and got crystals that diffracted.
> The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK)
> gives the space group as P1 and cell dimension
> 42.78 52.16   54.49   114.11  92.16   92.31.
>
> Challanges start from here:
>
> 1) How much I should be assured of the space group as I expect my peptides
> to get crystallized in the same group, but by default we get the same space
> group. 2) Is there any seperate method for processing the raw images in my
> case.
>
> I used the merged .mtz file for phasing. However, I always get the warning
> that eLLG score is low and it is difficult to fit a single copy of the
> ensemble. CC1/2 and I/SigI are in acceptable range. Completeness is also
> more than 95%.
>
> My peptides, 30 residues long, form an oligomer. However, I do not have
> reliable model of oligomers to start with. I have taken a single helix of
> length 24, 12 and 6 residues to phase, but no luck so far. Any guidelines
> will be really helpful.
>
> I am happy to provide any other relevant information, if one wants.
>
> Thanx in advance
> Prasun
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

--
--
Tim Gruene
GPG Key ID = A46BEE1A




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