Re: [ccp4bb] AI papers in experimental macromolecular structure determination

[Shekhar Mande]

In particle picking, you may wish to include the following:

George, B., Assaiya, A., Roy, R.J. *et al.* CASSPER is a semantic
segmentation-based particle picking algorithm for single-particle
cryo-electron microscopy. *Commun Biol* 4, 200 (2021).
https://doi.org/10.1038/s42003-021-01721-1

On Tue, Aug 3, 2021 at 9:17 PM Guillaume Gaullier <
guillaume.gaull...@icm.uu.se> wrote:

> Hello,
>
> In the particle picking section, you may want to include these two:
>
> Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P,
> Sitsel O, Raisch T, Prumbaum D, et al (2019) SPHIRE-crYOLO is a fast and
> accurate fully automated particle picker for cryo-EM. Communications
> Biology 2: 218 https://doi.org/10.1038/s42003-019-0437-z
>
> Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ & Berger B (2019)
> Positive-unlabeled convolutional neural networks for particle picking in
> cryo-electron micrographs. Nat Methods: 1–8
> https://doi.org/10.1038/s41592-019-0575-8
>
> And this paper on micrograph denoising could go in the "micrograph
> preparation" section I suppose, or in its own section:
>
> Bepler T, Kelley K, Noble AJ & Berger B (2020) Topaz-Denoise: general deep
> denoising models for cryoEM and cryoET. Nature Communications 11: 5208
> https://doi.org/10.1038/s41467-020-18952-1
>
> I hope this is useful.
> Cheers,
>
> Guillaume
>
>
> On 3 Aug 2021, at 13:43, Thorn, Dr. Andrea 
> wrote:
>
> Dear colleagues,
> I have compiled a list of papers that cover the application of AI/machine
> learning methods in single-crystal structure determination (mostly
> macromolecular crystallography) and single-particle Cryo-EM. The draft list
> is attached below.
>
> If I missed any papers, please let me know. I will send the final list
> back here, for the benefit of all who are interested in the topic.
>
> Best wishes,
>
>
> Andrea.
>
>
> __
> General:
> - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. &
> Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716.
> - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143.
>
> Micrograph preparation:
> - (2020). Journal of Structural Biology. 210, 107498.
>
> Particle Picking:
> - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. & Sorzano,
> C. O. S. (2018). IUCrJ. 5, 854–865.
> - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC
> Bioinformatics. 20, 1–26.
> - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., Paul,
> G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12.
> - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58,
> 381–391.
> - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A. (2021).
> BMC Bioinformatics. 22, 1–28.
> - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & Zeng, J.
> (2016). Journal of Structural Biology. 195, 325–336.
> - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004).
> Journal of Structural Biology. 145, 157–167.
>
> Motion description in Cryo-EM:
> - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & Okuno, Y.
> (2021). Nat Mach Intell. 3, 153–160.
> - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat Methods.
> 18, 176–185.
>
> Local resolution:
> - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S.,
> Vargas, J. & Si, D. (2019). Molecules. 24, 1181.
> - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, C.
> O. S. (2019). IUCrJ. 6, 1054–1063.
> - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein
> Crystal Structures Using Machine Learning.
>
> Map post-processing:
> - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M.,
> Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296.
>
> Secondary structure assignment in map:
> - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat Methods.
> 16, 911–917.
> - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE
> International Conference on Bioinformatics and Biomedicine (BIBM), Vol. pp.
> 41–46.
> - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, 698–708.
> - He, J. & Huang, S.-Y. Brief Bioinform.
> - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers in
> Bioengineering and Biotechnology. 9,.
> - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A. (2020).
> Angewandte Chemie International Edition.
>
> Automatic structure building:
> - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82.
> - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T. &
> Cheng, J. (2020). Sci Rep. 10, 1–22.
> - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang, L. &
> Si, D. (2019).
> - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D. 75,
> 753–763.
>
> Crystallization:
> - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 1187–1195.
> - (2004). Methods. 34, 390–407.
> - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R.,
> Vanhoucke, V., Watkins, C. J., Williams, S.

Re: [ccp4bb] just out of totally idle curiosity ...

[Shekhar Mande]

All the refugees after Brexit, and the latest in the "most
powerful"country, can seek refuge in India. Since several millennia we have
offered- and continue to offer total detachment from anything and
everything happening around oneself, mental peace and ultimate pleasure in
the spirituality. I guess many of our friends do require a dose of
spirituality after today's development.

On 9 Nov 2016 11:08, "William G. Scott"  wrote:

> What’s the job situation in Europe looking like for refugee scientists
> these days?
>
>
>
> William G. Scott
> Director, Program in Biochemistry and Molecular Biology
> Professor, Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
>
> http://scottlab.ucsc.edu
>

Re: [ccp4bb] asymmetric homotrimer in the asu

[Shekhar Mande]

Several years ago, we had an interesting case, where the molecule - a
tetramer, did not possess the classical 222 or 4-fold symmetry.
Rather, two monomers were related by a 2-fold, and other two monomers were
related by yet another 2-fold.  Ofcourse, the confirmation that it was
indeed a tetramer was shown biochemically too!  Our paper describing the
"open" quaternary structure is:

Banerjee et al., Proc Natl Acad Sci USA (1994) v. 91, 227- 231.

Shekhar

On Fri, Dec 12, 2014 at 12:30 AM, Oganesyan, Vaheh  wrote:

>  This fact by itself is unusual to say the least (for me):
>
> “ we have *NO* rotational symmetry (2, 3, or 4-fold) whatsoever between
> interacting monomers in the ASU or relating those built up by the
> crystallographic symmetry”
>
> There might be several ways of choosing molecules to represent the
> asymmetric unit. Is it possible to find ones that are related? Say
> something like non-crystallographic translation (or pseudo translation) +
> non-crystallographic rotation.
>
>
>
> For long time I was thinking about such a possibility of having more than
> one molecule in au but no rotation or pst. May be I’ve missed but never
> found an evidence, nor can I explain why would that be impossible.
>
>
>
>
>
> *Vaheh Oganesyan*
>
> *www.medimmune.com *
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Hay
> Dvir
> *Sent:* Thursday, December 11, 2014 12:04 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] asymmetric homotrimer in the asu
>
>
>
> Dear Michael,
>
>
>
> Thank you very much for the useful comments.
>
>
>
> Indeed, we are of course looking at it biochemically, which isn't a clear
> cut so far..
>
> As you pointed out it could be a monomer in solution, but the interface
> between monomers within this asymmetric trimer seems too extensive
> (compared to those responsible for the lattice packing) not to suspect a
> trimer as a solution assembly. PISA suggested this asymmetric trimer as the
> most likely assembly but it falls into the grey region of their criteria
> (see attached pic.)
>
>
>
>
>
>
>
> Since it's rare, we are interested to know of other similar reports, if
> any, to learn how they were resolved/concluded. I believe the case you
> describe is not similar, as we have *NO* rotational symmetry (2, 3, or
> 4-fold) whatsoever between interacting monomers in the ASU or relating
> those built up by the crystallographic symmetry. Therefore I can't see how
> the space group information may help, but it is p212121 in case it helps
> boosting your morning coffee experience with symmetry pondering ... :).
>
>
>
> Cheers,
>
> Hay
>
>
>
>
>
>
>
> On Dec 11, 2014, at 3:47 PM, R. M. Garavito wrote:
>
>
>
>   Dear Hay,
>
>
>
> And your point is?  I am not trying to be snarky (although I am just
> starting my morning coffee), but to bring up the fact that CCP4BB readers
> need more info to comment on your case, like space group, local
> interactions, and how packed is "tightly packed."
>
>
>
> I have had two cases of "trimers," as my students initially called them,
> that were actually a dimer and a half.  The "half" dimer had its mate in
> another ASU.   Can it be a biological monomer that just happened to
> crystallize 3 monomers to an ASU?  Non-symmetric homo-oligomers are rare,
> but sadly cannot be absolutely confirmed by crystallography alone, but by
> good old biochemistry.  The PISA website (
> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html) can give you
> estimations of the strengths of the interfacial interactions, but they are
> mere estimates.  What does gel filtration say or cross linking? Does it fit
> with the biology/biochemistry expected of this protein?
>
>
>
> Anyway, have fun with your structure, but use a lot of skepticism in your
> interpretation.  That will help you convince the reviewers.
>
>
>
> Cheers,
>
>
>
> Michael
>
>
>
> **
>
> *R. Michael Garavito, Ph.D.*
>
> *Professor of Biochemistry & Molecular Biology*
>
> *603 Wilson Rd., Rm. 513   *
>
> *Michigan State University  *
>
> *East Lansing, MI 48824-1319*
>
> *Office:  (517) 355-9724 Lab:  (517) 353-9125*
>
> *FAX:  (517) 353-9334Email:  rmgarav...@gmail.com
> *
>
> **
>
>
>
>
>
>
>
> On Dec 11, 2014, at 7:27 AM, Hay Dvir  wrote:
>
>
>
>  Dear all,
>
>
>
>
>
> We have a structure of a rather tightly packed homotrimer protein in the
> ASU with no apparent crystallographic or non-crystallographic rotational
> symmetry between monomers.
>
> Attempting to establish the biological assembly, we are very interested to
> hear about additional similar cases you might know of.
>
>
>
> Thanks in advance,
>
> Hay
>
>
>
>
>
> ---
> Hay Dvir   Ph. D.
> Head   Technion Center for Structural Biology
> TechnionHaifa 323, Israel
> Tel:   +(972)-77

Re: [ccp4bb] Normal mode refinement

[Shekhar Mande]

 I agree with Ethan.

In philosophy, NMA is a useful analysis  to study low frequency collective
motions.  That is true by taking  a stand-alone structure and explore such
motions of biological interest.  Domain motions in the crystallographic
environment need not necessarily correspond to those of the isolated
molecule.  Also, please remember, many a times the most significant modes
(say mode 7 or mode 8) in NMA do not represent the motions of biological
interest.  One is usually recommended to analyze many significant modes to
extract the useful information, and in the extremes of argument, making at
times this as a subjective exercise.

In any case, I would strongly argue for TLSMD, as Ethan has pointed out, as
that represents modeling disorder in crystallographic environment. In one
of the examples where we were studying the relationship between NMA (for a
stand-alone molecule) and TLS, we could correlate the two for the 11th and
the 12th mode, suggesting clearly that 7th- 10th modes did not show a good
correlation.  By incorporating the 7-10th modes in crystallographic
refinement, we would have clearly not made the model better!

Shekhar

On Tue, Oct 21, 2014 at 6:22 AM, Ethan A Merritt 
wrote:

> On Monday, 20 October, 2014 18:10:03 Appu kumar wrote:
> > Dear CCP4 Users,
> > I seek your valuable advice and suggestion in carrying out the normal
> mode
> > structure refinement which manifest the dynamics of protein as linear
> > combination of harmonic modes, used to describe the motion of protein
> > structure in collective fashion. Studies suggest that it is highly useful
> > in refining the protein structure which harbors a considerable magnitude
> of
> > flexibility in atomic position owing to high thermal factors.
> > Therefor I want to know is there any software/script available to execute
> > the normal mode of refinement. Thanks a lot in advance for your
> imperative
> > suggestions
>
> The previously published examples of normal-mode refinement that I know
> about used private external programs to generate thermal ellipsoids for
> each
> atom, and then used those as fixed ADPs while refining coordinates in
> refmac or similar standard program.  Again speaking only of the examples
> I have looked at in detail, the result was "better" (had lower R factors)
> than a conventional isotropic refinement but was not nearly as good as a
> multi-group TLS refinement of the same structure (TLSMD + refmac).
>
> On the other hand, there is a quite different way normal modes can be used
> in refinement.   As I understand it (perhaps Garib will add addtional
> details)
> the "jellybody" refinement mode of recent refmac versions can be viewed
> as restraining the model shifts to be consistent with the principle normal
> mode.
> In this way the normal mode contributes to the path of the refinement,
> but is not explicitly part of the final model.
>
> So it may be that using TLSMD + refmac jellybody TLS refinement
> would get you the best of both approaches, though I have not gone back
> to look again at the published example structures since the advent of
> jellybody refinement.  But note that jellybody is primarily useful when
> you already have a high-qualityl, good geometry, starting model.
>
> Ethan
>
> --
> Ethan A Merritt
> Biomolecular Structure Center,  K-428 Health Sciences Bldg
> MS 357742,   University of Washington, Seattle 98195-7742
>



-- 
Shekhar C. Mande (शेखर चिं मांडे)
Director, National Centre for Cell Science
Ganeshkhind, Pune 411 007
Email: shek...@nccs.res.in, direc...@nccs.res.in
Phone: +91-20-25708121
Fax:+91-20-25692259

[ccp4bb] Beamline Scientist opening

[Shekhar Mande]

I am posting this job opening for a beamline Scientist position on behalf
of Prof. D D Sarma.  Interested candidates may write to him directly.  The
advertisement reads as below:

*Beam-line Scientist and Engineer Positions*

*at Elettra, Italian Synchrotron source, Trieste, ITALY*



Two beam-lines dedicated to high pressure x-ray diffraction and
Macromolecular Crystallographic studies are being commissioned at the
Elettra synchrotron source in Trieste, Italy, as a part of an Indo-Italian
collaboration funded by the Department of Science and Technology on the
Indian side.

These beam-lines presently have three openings at the level of beam-line
scientists and engineers and we seek applications from suitable Indian
candidates for these positions.

The applicants should have backgrounds in x-ray diffraction and structural
studies. Expertise in macromolecular crystallography and/or high pressure
crystallographic studies including a working knowledge of diamond anvil
cells is desirable.  Prior experience in instrumentation and data analysis
will be considered as an advantage. Familiarity with computer programming
and interest and knowledge in instrumentation and software packages like
such as MATLAB, LABVIEW, EPICS etc. would be added assets.

Selected candidates will be expected to assist in the commissioning of the
beam-lines, installation of end-stations, carry out test experiments and
later provide support to users at the beam lines.  The compensation package
is highly attractive for suitable candidates with the possibility of yearly
visit to India, higher than the average salary structure as well as the
possibility of having synchrotron beamtime to run one's own research
program.

Candidates below the age of 35 years would be preferred. For the post of
beam-line scientist, the candidate should have a doctoral degree in
physics, chemistry, earth sciences, any branches of life sciences or any
other relevant or related field. For the post of beam-line engineer, the
candidate with either BTech/ MSc physics or MSc Chemistry may apply.  Both
the posts would prefer a work experience at synchrotron beam-lines and/or
high-pressure laboratories and an outstanding R & D record.

Interested candidates should apply within three weeks of the publication of
this advertisement, sending a detailed CV, along with a list of
publications, and the names and addresses of three references to the
following address:

Prof. D. D. Sarma; Solid State and Structural Chemistry Unit, Indian
Institute of Science, Bangalore 560012. Email: sa...@sscu.iisc.ernet.in &
sarma...@gmail.com






Shekhar

-- 
Shekhar C. Mande (शेखर चिं मांडे)
Director, National Centre for Cell Science
Ganeshkhind, Pune 411 007
Email: shek...@nccs.res.in, direc...@nccs.res.in
Phone: +91-20-25708121
Fax:+91-20-25692259

Re: [ccp4bb] popular piece on X-ray crystallography

[Shekhar Mande]

Following up on the original post, I was recently asked to give a popular
account of 100 years of X-ray diffraction in about 6 minutes :)  This was
broadcast on All India Radio from New Delhi on the 12th April across India,
but the conservative estimates suggest that no more than 5 persons heard it
live.  I have a mp3 of the same (~6 MB).  I will post it on my Facebook
today.  It will also be available on the Facebook of our Centre- National
Centre for Cell Science, Pune, hopefully posted on Monday or Tuesday.

Shekhar


On Sat, Apr 20, 2013 at 9:37 AM, James Holton  wrote:

>
> It was the observation that atoms have "size".
>
> Rutherford's alpha-particle experiment had shown that the nucleus was
> incredibly small, very much smaller than the distances between atoms,
> bringing about the "solar system" idea, which right away came into question
> because such atoms would produce synchrotron radiation and the electrons
> would rapidly decay from their orbits.  So, every nanosecond that the
> universe has not tuned itself into powdered neutronium is evidence against
> electrons in "orbit".  I think it was Laue who then proposed that the
> electrons must be bound very close to the nucleus (somehow).  Making the
> atoms very sharp points, and separated from each other by vast distances
> (relative to their size).  However, if the electrons really were confined
> to very sharp points, then the x-ray diffracted intensities from things
> like perfect rock salt crystals would not fall off with increasing
> sin(theta)/lambda.  They would be relatively constant (much like the
> scattering profile of Rutherford's experiment).  This was explained away as
> thermal vibrations "blurring" the atomic positions, making them look like
> they have "size", and causing the spots to fade with increasing resolution.
>
> What Debye showed was that the temperature-dependence of this falloff was
> insufficient to give the atoms zero size, even when extrapolated to
> absolute zero (yes, they had liquid air in 1914), and this residual "size"
> was still comparable to bond lengths.  That meant the electrons really were
> distributed in a "cloud" very far from the nucleus, and apparently not
> falling in.  The only explanation is that the electron must be
> de-localised.  And that is a quantum effect.
>
> I always thought that the paper Debye (1914) Ann. Phys. 348, 49-92 is
> perhaps one of the most remarkable in all of science.  It is the original
> reference for the B factor, the Lorentz factor, and also the paper that
> ended determinism.
>
> At least, that is how I understand it.  I had to return my English
> translation of the Debye paper to the library.  I'll order my own copy.
>
> -James Holton
> MAD Scientist
>
>
>
> On Fri, Apr 19, 2013 at 2:38 PM,  wrote:
>
>> James
>>
>> In 1915, I thought Debye and Scherrer were testing for interference
>> between the electrons in different orbits within atoms. This was in order
>> to test the Bohr model. They got rings but they were powder diffraction
>> rings. The method never did identify planetary type orbitals. However Debye
>> eventually adjusted his aims and the method did become useful despite "the
>> requirement for objects to force themselves into ordered arrays"
>>
>> Was there some other key observation Debye made in 1915 which you refer
>> to?
>>
>> Colin
>>
>>
>>
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> James Holton
>> Sent: 19 April 2013 18:27
>> To: ccp4bb
>> Subject: Re: [ccp4bb] popular piece on X-ray crystallography
>>
>> Because there is never more than one photon "in flight" at any given
>> time.  Even at 1 photon/s, we still eventually get spots.
>>
>> Atoms also don't emit synchrotron radiation, despite there being charged
>> particles accelerating around their little "orbits" in there.
>>
>> But yes, in 1913, people were still hoping there was another explanation
>> for these two observations, other than that pesky quantum theory.  It was
>> in 1915 that Debye made the key observation that collapsed determinism as
>> we knew it.  I don't think he was very happy about that.
>> Neither was Einstein.
>>
>> -James Holton
>> MAD Scientist
>>
>> On 4/19/2013 9:43 AM, Tim Gruene wrote:
>> > -BEGIN PGP SIGNED MESSAGE-
>> > Hash: SHA1
>> >
>> > Hello Bernhard,
>> >
>> > could you explain this? A photon is the exchange particle of the
>> > electromagnetic force, i.e. as soon as you have more than two charged
>> > particles interacting there is more than one photon - why is it
>> > incorrect to use the term "multi-photon process" in the context of
>> > X-ray diffraction?
>> >
>> > Cheers,
>> > Tim
>> >
>> > On 04/19/2013 06:19 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
>> >> However, a reviewer could reject the method on theoretical grounds
>> >> - the explanation of X-ray diffraction as a multi-photon process is
>> >> not correct
>> >>
>> >> BR
>> >>
>> >> -Original Message- From: CCP4 

Re: [ccp4bb] Who invented PDB format?

[Shekhar Mande]

As a person who wears two hats- "we- the crystallographers" and "they- the
bioinformaticians" it is interesting to see that the world can be divided
by one of the most trivial issues- coordinate formats!  Enjoying the debate
:)

Shekhar


On Sun, Jan 6, 2013 at 8:02 PM, Boaz Shaanan wrote:

>  Dear George,
>
> "Those folks" (bioinformaticiens ?) are not interested in inter-molecular
> contacts, as far as I'm aware so they can't bothered less by the orthogonal
> coordinates used in pdb files.
>
>  Cheers,
>
>  Boaz
>
> *Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: bshaa...@bgu.ac.il
> Phone: 972-8-647-2220  Skype: boaz.shaanan
> Fax:   972-8-647-2992 or 972-8-646-1710*
> **
> **
> *
>
> *
>   --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of George
> T. DeTitta [deti...@hwi.buffalo.edu]
> *Sent:* Sunday, January 06, 2013 3:48 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Who invented PDB format?
>
>  While it is certainly a simple coding job to convert back and forth
> between orthogonal and fractional coordinates there is perhaps something
> lost in the former and that is the notion of a molecule embedded in a
> crystal structure. Generally speaking, it's the latter that we determine.
> George may well be right that orthogonalization made it easier for those
> non-crystallographers who use structures but I wonder if those folk are
> aware of all the information about intermolecular contacts that you lose by
> looking at the molecular structure only. Sure, you can recover that
> information from orthogonalized coordinates (please consult a
> crystallographer if you are in need of guidance) but will you?
> Sent via BlackBerry by AT&T
> --
> *From: *George Sheldrick 
> *Sender: *CCP4 bulletin board 
> *Date: *Sun, 6 Jan 2013 09:57:28 +0100
> *To: *
> *ReplyTo: *George Sheldrick 
> *Subject: *Re: [ccp4bb] Who invented PDB format?
>
>  Chemical crystallographers have always used fractional coordinates, it
> makes it so
> much easier to handle symmetry, special positions etc. But if the PDB
> hadn't
> used orthogonal coordinates, bioinformatics might never have taken off.
>
> George
>
> On 01/06/2013 09:34 AM, Eleanor Dodson wrote:
>
> Some of us resisted using an orthogonal format for coordinates, arguing
> that the output from a crystal structure should refer to crystal axes.
> And since symmetry was a crystal property it was important that we could
> "see" it easily.  The PDB format won out,  but I still use *coordconv* a
> lot
> to turn back the orthogonalised PDB style to fractional coordinates - to
> see if this heavy atom solution is the same as that one, given an origin
> shift, etc etc.
> Eleanor
>
>  On 4 Jan 2013, at 20:44, Soisson, Stephen M wrote:
>
>
> --
> 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
>
>
>


-- 
Shekhar C. Mande (शेखर चिं मांडे)
Director, National Centre for Cell Science
Ganeshkhind, Pune 411 007
Email: shek...@nccs.res.in, direc...@nccs.res.in
Phone: +91-20-25708120
Fax:+91-20-25692259

Re: [ccp4bb] Water

[Shekhar Mande]

Welljust to add, it has been our contention that many of the metal ions
have been modelled as waters in several structures- due perhaps to the lack
of sufficiently high resolution data.  We published some of the potential
metal binding sites in many structures a few years ago:

Proteins. 2008 Mar;70(4):1206-18.

Shekhar

On Thu, Mar 8, 2012 at 9:42 AM, Parthasarathy Sampathkumar <
spart...@gmail.com> wrote:

> Dear Uma,
>
> The water pictured in W12-1.jpg: could this be a potential metal ion? If
> you flip the side chain on Asn at 3.08Angstrom, then this has 3 or 4
> coordination with oxygen atoms. So, provided your crystallization condition
> or buffer contains metal ion(s), you could attempt to see if it fits better
> with a refinement cycle.
>
> May be a similar situation with the water described in W11-1.jpg as well?
> Difficult to say from these figures.
>
> COOT within the "validate" wizard has an option to search for
> "hihgly-coordinated waters" like the one you have pictured.
>
> Hope this helps,
> Partha
>
> On Wed, Mar 7, 2012 at 4:21 PM, Uma Ratu  wrote:
>
>> Dear Roger:
>>
>> Thank you very much for your comments. I use them as guideline and remove
>> many 'false waters".
>>
>> Still, I am not clear of some of these 'waters' are real or not. I have
>> the pic attached.
>>
>> In Pic-W11-1, the 'water' is connected to the adjust residues with 4
>> contacts, which are 'N' or 'O' atoms. I would consider this 'water' is
>> false. My question is: if these 4 contacts include "C" from residues, will
>> it be a polar contact or not?
>>
>> In Pic-W12-1, the 'water' is connected to the adjust residues with 3
>> contacts. The 4th is to another 'water'.
>> Will this 'water' is true or not? Similar case is seen in Pic-W190-1
>>
>> In Pic-W109-1, some 'waters' are connected to adjust residues, some not.
>> Are these 'water' true or not?
>>
>> Further more,
>> > and the b-factors are not way out of line,
>>
>> I am not clear on how to define "out of line".
>> How to find b-factor of individual residue in Coot? I search the web, but
>> find no answer.
>>
>> Thank you for advice
>>
>> Uma
>>
>> On Wed, Mar 7, 2012 at 11:44 AM, Roger Rowlett wrote:
>>
>>> Uma,
>>>
>>> Remember that your structure, ultimately, is a model. A model is your
>>> best judgment of the true representation of the protein structure in your
>>> crystal. Your model should make chemical sense. Coot is pretty good at
>>> placing waters, but it cannot substitute entirely for the experimentalist.
>>> Coot will miss some waters, and mis-assign others into weak, unmodeled or
>>> alternate side- or main-chain density, or into density that might be
>>> attributable to cations and anions or other crystallization materials. Your
>>> waters should be subjected to inspection and verification. It is really
>>> helpful to turn on environment distances in Coot when you do this. Even in
>>> a large protein model, it is possible to inspect all waters for
>>> reasonableness pretty quickly. If you have no significant positive or
>>> negative difference density, and the b-factors are not way out of line, and
>>> hydrogen bonding partners are reasonable, then modeling a water is probably
>>> a good call.
>>>
>>> Waters should have hydrogen bonding partners with side chains or
>>> main-chain polar atoms, within reasonable distances, or be withing hydrogen
>>> bonding distance of other waters that are (chains of waters). If a "water"
>>> has strong electron density and more than 4 polar contacts, you might
>>> consider anion or cation occupancy. Most anions and cations will have
>>> higher electron density, and appropriately different types of polar
>>> contacts. (e.g. you might find sulfates near a cluster of basic residues).
>>> Low occupancy anions can often look a lot like water. PEGs can create ugly
>>> "snakes" of variable density that may be challenging to model. Modeling
>>> non-protein structural bits is endlessly entertaining for the protein
>>> crystallographer. ;)
>>>
>>> Cheers,
>>>
>>> ___
>>> Roger S. Rowlett
>>> Gordon & Dorothy Kline Professor
>>> Department of Chemistry
>>> Colgate University
>>> 13 Oak Drive
>>> Hamilton, NY 13346
>>>
>>> tel: (315)-228-7245
>>> ofc: (315)-228-7395
>>> fax: (315)-228-7935
>>> email: rrowl...@colgate.edu
>>>
>>>
>>> On 3/7/2012 11:20 AM, Uma Ratu wrote:
>>>
>>> Dear All:
>>>
>>> I try to add water to my model.
>>>
>>> Here is how I did:
>>> Coot: Find Wates
>>>  Map: FWT PHWT;  1.8 rmsd; Distances to protein atoms:
>>> 2.4 min/3.2 max
>>>
>>> Coot found 270 water molecules.
>>>
>>> I then examed these waters. Most of them had ball shape. Some had two or
>>> more balls together. Some had irregular shape (not glabol shape).
>>>
>>> I run Water Check. The program did not find any mis-matched water.
>>>
>>> Here is my question: how could I tell the waters are real? Or something
>>> else?
>>>
>>> Thank you for advice
>>>
>>> Ros
>>>
>>>
>>>
>>>
>>>
>>
>


-- 
Sh

Re: [ccp4bb] Strange density on Serine oxygen.

[Shekhar Mande]

Phosphoserine ?

शेखर चिं मांडे
हैदराबाद


On Wed, Nov 24, 2010 at 5:40 PM, Vinson LIANG
wrote:

> Dear all,
>
> I'm refining a structure and find some strange triangle density on the
> oxygen of Ser and Thr at the C terminus. One picture of the strange density
> is attached here. Could anyone please give me some suggestions on what this
> could be?
>
> The buffer used during purification is PBS, Tris and NaCl. And
> crystallization condition contains PEG3,350 and Mg(NO3)2.
>
> Thank you all in advance for any suggestion.
>
> Best,
>
> Vinson Liang
>
>
>
>
>



--

Re: [ccp4bb] Will 3mFo-2DFc maps have less model bias than 2mFo-DFc maps?

[Shekhar Mande]

One of the early references for mFo- nFc is:

Vijayan, *Acta Cryst.* (1980). A*36*, 295-298

You may also like to read the book on Fourier transforms in crystallography
by Ramachandran and Srinivasan.

Shekhar

On Fri, Jul 30, 2010 at 4:25 AM, Pavel Afonine  wrote:

>  Hi Ian,
>
> please correct me if I'm wrong in what I'm writing below...
>
> My reasoning for writing it like this
>
>
> 2Fo-Fc = Fo + (Fo-Fc)
>
> is:
>
> 1) the map (Fo, Pcalc) shows density for missing atoms at half size
> (approximately)
> 2) the map (Fo-Fc, Pcalc) shows density for missing atoms at half size
> (approximately)
> 3) then the map (2Fo-Fc, Pcalc) shows density for missing atoms at full
> size (approximately), and this is why this map is preferred over (Fo,
> Pcalc).
>
> And maximum-likelihood weighted map 2mFo-DFc is even better since in
> addition it is expected to be less model biased.
>
> This was my "rationale" to write 2Fo-Fc = Fo + (Fo-Fc) and not Fc +
> 2(Fo-Fc) .
>
> Pavel.
>
>
>
> On 7/29/10 2:38 PM, Ian Tickle wrote:
>
>> On Thu, Jul 29, 2010 at 8:25 PM, Pavel Afonine  wrote:
>>
>>> Speaking of 3fo2fc or 5fo3fc, ... etc maps (see classic works on this
>>> published 30+ years ago), I guess the main rationale for using them in
>>> those
>>> cases arises from the facts that
>>>
>>> 2Fo-Fc = Fo + (Fo-Fc),
>>> 3Fo-2Fc = Fo +2(Fo-Fc)
>>>
>>> To be precise, it is actually
>>>
>>> 2mFo-DFc for acentric reflections
>>> and mFo for centric reflections
>>>
>> I prefer to think of it rather as
>>
>> 2mFo - DFc = DFc + 2(mFo-DFc)   for acentrics and
>> mFo = DFc + (mFo-DFc)   for centrics.
>>
>> Then it also becomes clear that to be consistent the corresponding
>> difference map coefficients should be 2(mFo-DFc) for acentrics and
>> (mFo-DFc) for centrics.
>>
>> Cheers
>>
>> -- Ian
>>
>


-- 
Shekhar C. Mande
Centre for DNA Fingerprinting and Diagnostics
Bldg.7, Gruhakalpa
5-4-399/B, Nampally
Hyderabad- 51  INDIA
Phone: +91-40-24749401
Fax: +91-40-24749448

Re: [ccp4bb] non-symmetric tetramer ?

[Shekhar Mande]

Peanut lectin, when we solved the structure in the 90's, had a very unusual
non-symmetric tetramer.  Till we solved the structure, there were examples
only of symmetric tetramers 222 (say, ConA), or 4 (e.g. Neuraminadase) in
the literature.  Peanut lectin had two dimers, each with a two-fold
symmetry, but the two dimers were not related by mutually perpendicular
two-fold axes (PNAS, 1994, vol 91, 227- 231).

Shekhar

On Thu, Jul 29, 2010 at 1:05 PM, Vellieux Frederic  wrote:

> Non-symmetric tetramers: you can check out Tete-Favier et al (1993), Acta
> Cryst. D49, 246: the quaternary structure was assumed to have local 222
> symmetry. It turned out this was not exactly the case: the actual symmetry
> of the object (the molecule) was "pseudo" 2t2t2t. So in addition to 2-fold
> axes being common as an assembly mechanism (leading to the quite common 222
> symmetry) you can have deviations from this symmetry.
>
> Fred.
>
> Fred wrote:
>
>> Dear CCP4bb,
>> Could someone please, point me to some references about non-symmetric
>> tetramers? If I have a tetramer composed by 4 identical subunits, it'll
>> always have a P4 point group symmetry?
>> Thank in advance,
>> Tomb
>>
>>
>>


-- 
Shekhar C. Mande
Centre for DNA Fingerprinting and Diagnostics
Bldg.7, Gruhakalpa
5-4-399/B, Nampally
Hyderabad- 51  INDIA
Phone: +91-40-24749401
Fax: +91-40-24749448