Re: [ccp4bb] Completeness question

[Robbie Joosten]

Hi Clemens,

Thanks for pointing out the table in the PDBpeep log file. It has the data I 
need and since the issue only applies to deposited PDB entries it does the 
trick quite nicely.

Cheers,
Robbie

> -Original Message-
> From: Clemens Vonrhein 
> Sent: Wednesday, June 3, 2020 14:18
> To: Robbie Joosten 
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Completeness question
> 
> Dear Robbie,
> 
> On Sat, May 30, 2020 at 08:36:06AM +, Robbie Joosten wrote:
> > I've been looking at some recent PDB entries that have much lower
> > spherical) completeness than reported in the coordinate file. One
> > reason for this is that the data were anisotropicly truncated, another
> > reason is some mess-up with the deposition of the reflection data.
> > There is a lot of discussion about the former practice and I don't
> > want to go in to that, but the second one is obviously an error. Now
> > how do I distinguish these cases?
> >
> > Sometimes, you can look at the reported number of reflections and
> > compare that to the deposited reflection file and you will find that
> > something has clearly gone wrong. However, the reported number of
> > reflections is not entirely reliable because of other issues so I'd
> > rather not use it. If you use PDBpeep (e.g. for 6rjy) you can see
> > something is wrong, but that is completely visual. Is there a tool in
> > CCP4 that reports both spherical and ellipsoidal completeness (on
> > merged reflection data)? That would make it easy to distinguish such
> > cases.
> 
> One needs a description of the anisotropy in a form that allows for a simple
> computation ("Is a reflection above a significance limit or
> not?") to relate this to the completeness of reflections above such a
> significance level. That model could e.g. be the ellipsoid fitted to the
> significance (local ) cutoff surface as done by STARANISO [1]. You can
> see that information e.g. at the PDBpeep server [2]:
> 
>   http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6rjy
> 
> as
> 
>   Diffraction limits & principal axes of ellipsoid fitted to diffraction 
> cut-off
> surface:
> 
>   1.747 1.   0.   0.   a*
>   1.777 0.   1.   0.   b*
>   1.465 0.   0.   1.   c*
> 
> Of course, if this information is already present in deposited PDB entries of
> interest, no additional computation is required. We are currently working
> with our colleagues from the PDBx/mmCIF working group on definitions and
> items that would extend the current PDBx/mmCIF dictionary so that the
> above information could be deposited to and retrieved from the PDB
> database.
> 
> In any case, this information is then used for computation of the spherical
> and ellipsoidal completness e.g. within STARANISO - see link to the
> "complete log file" at the bottom of the page:
> http://staraniso.globalphasing.org/PDB/6rjy.log. It contains a table
> ("Statistics for isotropic, anisotropic & ellipsoidal diffraction
> cut-offs") where Cmeas_sph and Cmeas_ell should give the above
> information (showing clearly that for 6rjy something else went wrong during
> deposition).
> 
> If there is unmerged data deposited, one could give that ellipsoid description
> e.g. to MRFANA [3] via
> 
>   mrfana -ell 1.747 1.0 0.0 0.0 1.777 0.0 1.0 0.0 1.465 0.0 0.0 1.0
> unmerged.mtz
> 
> to get the same information (but maybe use different binning, limit
> resolution ranges etc).
> 
> Cheers
> 
> Clemens, Claus, Ian & Gerard
> 
> [1] http://staraniso.globalphasing.org/
> [2] http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi
> [3] https://github.com/githubgphl/MRFANA, a result of the Data Quality
> Metrics Workshop organised by Global Phasing at the ESRF in April
> 2019



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Re: [ccp4bb] Question about small molecule crystallography

[Navdeep Sidhu]

Dear Jiyuan,

There was a similar question on the bulletin board some 6 years ago; my
response then (links below) complements some of the other great
suggestions already made in answer to your question:

,
and
.

I believe some 90% of small molecule structures are solved using the
SHELX suite of programs by Prof. Sheldrick, so that should be a great
start. The programs are very easy to use, with great defaults. (There
used to be a joke that to solve this or that problem, all you had to do
is start one of his programs and press enter 5 times.)

As before, I'd highly recommend you read Mueller et al.'s excellent book
with detailed tutorials. It provides the data and walks you through
detailed examples in solving and refining small molecule structures:

Peter Müller, Regine Herbst-Irmer, Anthony Spek, Thomas Schneider and
Michael Sawaya. IUCr/Oxford, 2006
.

I'm sure you'll have much fun doing small molecules in addition to large
molecules. We all did.

All the best,
Navdeep


---
On 01.06.20 23:50, Jiyuan Ke wrote:
> Hi Everyone,
> 
> I want to crystallize a small organic molecule. I have very limited
> experience in small molecule crystallography. I found that the Crystal
> Screen HT from the Hampton research is good for both small molecule and
> macromolecule crystallization. Plan to set up a sitting drop screen just
> like setting up protein crystallization. I don’t know if this is the
> proper way to do it. Is the MRC sitting drop 2-well plate (HR3-083) used
> for protein crystallization good for small molecule crystallization? Are
> there any special plates used for small molecule crystallization? Is
> room temperature ok or not? 
> 
> For data collection, can I use the beamline for protein crystals to
> collect data on small molecule crystals? Larger oscillation angle,
> shorter exposure, reduced beam intensity? 
> 
> For structure determination, is SHELXL the preferred software for
> solving small molecule structures?
> 
> If anyone has experience in small molecule crystallography, please
> help.  Thanks!
> 
> Best Regards,
> 
> -- 
> 
> *Jiyuan Ke, Ph.D.*
> 
> *
> *
> 
> Research Investigator
> 
> H3 Biomedicine Inc.
> 
> 300 Technology Square, Floor 5
> 
> Cambridge, MA 02139
> 
> Phone: 617-252-3923
> 
> Email: jiyuan...@h3biomedicine.com 
> 
> Website: www.h3biomedicine.com 
> 
> 
>  
> 
>  
> 
> 
> [This e-mail message may contain privileged, confidential and/or
> proprietary information of H3 Biomedicine. If you believe that it has
> been sent to you in error, please contact the sender immediately and
> delete the message including any attachments, without copying, using, or
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> 
> 
> 
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> 



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Re: [ccp4bb] Completeness question

[Clemens Vonrhein]

Dear Robbie,

On Sat, May 30, 2020 at 08:36:06AM +, Robbie Joosten wrote:
> I've been looking at some recent PDB entries that have much lower
> spherical) completeness than reported in the coordinate file. One
> reason for this is that the data were anisotropicly truncated,
> another reason is some mess-up with the deposition of the reflection
> data. There is a lot of discussion about the former practice and I
> don't want to go in to that, but the second one is obviously an
> error. Now how do I distinguish these cases?
> 
> Sometimes, you can look at the reported number of reflections and
> compare that to the deposited reflection file and you will find that
> something has clearly gone wrong. However, the reported number of
> reflections is not entirely reliable because of other issues so I'd
> rather not use it. If you use PDBpeep (e.g. for 6rjy) you can see
> something is wrong, but that is completely visual. Is there a tool
> in CCP4 that reports both spherical and ellipsoidal completeness (on
> merged reflection data)? That would make it easy to distinguish such
> cases.

One needs a description of the anisotropy in a form that allows for a
simple computation ("Is a reflection above a significance limit or
not?") to relate this to the completeness of reflections above such a
significance level. That model could e.g. be the ellipsoid fitted to
the significance (local ) cutoff surface as done by STARANISO
[1]. You can see that information e.g. at the PDBpeep server [2]:

  http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi?ID=6rjy

as

  Diffraction limits & principal axes of ellipsoid fitted to diffraction 
cut-off surface:

  1.747 1.   0.   0.   a*
  1.777 0.   1.   0.   b*
  1.465 0.   0.   1.   c*

Of course, if this information is already present in deposited PDB
entries of interest, no additional computation is required. We are
currently working with our colleagues from the PDBx/mmCIF working
group on definitions and items that would extend the current
PDBx/mmCIF dictionary so that the above information could be deposited
to and retrieved from the PDB database.

In any case, this information is then used for computation of the
spherical and ellipsoidal completness e.g. within STARANISO - see link to
the "complete log file" at the bottom of the page:
http://staraniso.globalphasing.org/PDB/6rjy.log. It contains a table
("Statistics for isotropic, anisotropic & ellipsoidal diffraction
cut-offs") where Cmeas_sph and Cmeas_ell should give the above
information (showing clearly that for 6rjy something else went wrong
during deposition).

If there is unmerged data deposited, one could give that ellipsoid
description e.g. to MRFANA [3] via

  mrfana -ell 1.747 1.0 0.0 0.0 1.777 0.0 1.0 0.0 1.465 0.0 0.0 1.0 unmerged.mtz

to get the same information (but maybe use different binning, limit
resolution ranges etc).

Cheers

Clemens, Claus, Ian & Gerard

[1] http://staraniso.globalphasing.org/
[2] http://staraniso.globalphasing.org/cgi-bin/PDBpeep.cgi
[3] https://github.com/githubgphl/MRFANA, a result of the Data Quality
Metrics Workshop organised by Global Phasing at the ESRF in April
2019



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Re: [ccp4bb] Question about small molecule crystallography

[Bernhard Spingler]

Dear Jiyuan,
May I make some advertisement for our tutorial, we published some time ago? Our 
article "Some thoughts about the single crystal growth of small molecules" 
(https://pubs.rsc.org/en/content/articlelanding/2012/ce/c1ce05624g#!divAbstract)
 should exactly answer most of your questions. You will find descriptions about 
different crystallization techniques and which (organic) solvents you can use 
for a start.
If you have further questions, just send me an email.
Best regards
Bernhard


Prof. Dr. Bernhard Spingler
Department of Chemistry
University of Zurich, 34F42
Winterthurerstr. 190
CH 8057 Zurich
Switzerland
http://www.chem.uzh.ch/en/research/spingler.html
sping...@chem.uzh.ch



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