Re: [ccp4bb] Mac M2 chip

[Joel Sussman]

Dear Shai
These are very widely used Python codes for crystallography that run slower on 
an M2 than an Intel Mac(!)
Apparently threre IS a solution, and this bulletin board is trying to ask 
someone to find the way to make it run faster than the Intel version.
You were right(!)
but there will be a fix
abah


> On 5 Jul 2023, at 18:21, Daniel Bonsor 
>  wrote:
> 
> Dear All,
> 
> Has anyone encountered problems with CCP4i/Phenix/XDS/etc on Macs with the M2 
> chip? I saw a post from 2020 on the M1 chip, but was curious about if there 
> are any issues between the M2 chip and our crystallographic software.
> 
> Thanks for any information.
> 
> Dan
> 
> 
> 
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Re: [ccp4bb] sequence search

[Joel Sussman]

Dear Eleanor
Suggest you look at OCA at: http://oca.weizmann.ac.il/oca-bin/ocamain
it has a simple to use but powerful sequence search
best regards
Joel


On 24 Jun 2022, at 17:36, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

The pdb seems to have gone so up market I can no longer see how to submit a 
simple sequence search or rum SSM

I get offered multiple options to use services I do not want to use!
But asking for
"sequence search" or Search sequences" gives lots and lots of non-intuitive 
choices!
Grrr
Eleanor

Any advice?



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Re: [ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Joel Sussman]

The PROSS (Protein Repair One-Stop Shop) at: 
https://pross.weizmann.ac.il/step/pross-terms
was used to both express and be able to crystallize human acetylcholinesterase 
in E. coli, which prior to using PROSS had been impossible.

See paper:

Goldenzweig, A., Goldsmith, M., Hill, S. E., Gertman, O., Laurino, P., Ashani, 
Y., Dym, O., Unger, T., Albeck, S.,
Prilusky, J., Lieberman, R. L., Aharoni, A., Silman, I., Sussman, J. L., 
Tawfik, D. S., & Fleishman, S. J. (2016).
Automated structure- and sequence-based design of proteins for high bacterial 
expression and stability.
Molecular Cell, 63(2), 337–346. https://doi.org/10.1016/j.molcel.2016.06.012

and Proteopedia's Interactive 3D Complement (I3DC) page:

https://proteopedia.org/w/Journal:Molecular_Cell:1

Best regards
Joel

-
Prof. Joel L. Sussman   
joel.suss...@weizmann.ac.il
Dept. of Chemical and Structural Biologytel: +972  (8) 934 6309  
www.weizmann.ac.il/~joel
Weizmann Institute of Science   fax: +972  (8) 934 6312  
proteopedia.org
Rehovot 76100 ISRAELmob: +972 (50) 510 9600
-


On 4 Apr 2022, at 22:06, Scott Classen 
mailto:sclas...@lbl.gov>> wrote:

Hello CCP4,

Has anyone successfully used the available ML/AI protein folding tools to guide 
crystallization construct design? Maybe you had a protein or domain that was 
resistant to crystallization efforts and the folding algorithms  predicted some 
loops or termini that were disordered? Then you trimmed or modified them in 
some way to aid in crystallization? Or if you haven’t done this yourself, are 
you aware of anyone who has?

Thanks,
Scott


~~
Scott Classen, Ph.D.
ALS-ENABLE
TomAlberTron Beamline 8.3.1
SIBYLS Beamline 12.3.1
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
mobile 510.206.4418
desk 510.495.2697
beamline 510.495.2134
~~




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Re: [ccp4bb] new page in Proteopedia on "SARS-CoV-2 spike protein mutations" by Eric Martz

[Joel Sussman]

This msg is sent on behalf of Prof. Eric Martz, University of Massachusetts, 
Amherst MA US

Coronavirus mutations reported within the past week by scientists in the UK 
have raised concern about an increased transmission rate of COVID-19. The 
report even temporarily closed the borders between the UK, France, and other EU 
countries, causing huge backups of trucking and supply concerns.

See the locations of the 4 most concerning mutations on a rotating 3D model of 
spike protein with interpretations of their likely consequences at this article 
posted December 22, 2020:

http://proteopedia.org/w/SARS-CoV-2_spike_protein_mutations

The article is written to be suitable for high-school students and higher. 
There are links to additional background material as well as references to 
reliable scientific publications and news sources.

The article offers a downloadable movie of the spike protein, slide 
presentation-ready, showing the conformational change when it is primed, with 
the locations of mutations indicated.

-Eric Martz

Professor Emeritus, Dept Microbiology (he/him/his)
University of Massachusetts, Amherst MA US
Martz.MolviZ.Org 
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Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Joel Sussman]

I'm curious how well AlphaFold would do on an Intrinsically Disordered Protein 
(IDP),
would it recognize that it is an "IDP" or predict that it has a structure (or 
structures)?
It would be interesting to test such a sequence and see what comes out.
Possibly AlphaFold might be the best IDP predictor too.

Joel


On 4 Dec 2020, at 6:29, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hello James, that's really strange - I've used refmac et al., to do poor man's 
energy minimizations of models and they've generally come out fine, unless the 
restraints, etc, are wildly off-target. I wasn't playing with X-ray weights 
though, since there never was a dataset, of course.

Cheers, Jon.C.

Sent from ProtonMail mobile



 Original Message 
On 4 Dec 2020, 01:34, James Holton < jmhol...@lbl.gov> 
wrote:

It is a major leap forward for structure prediction for sure.  A hearty 
congratulations to all those teams over all those years.

The part I don't understand is the accuracy.  If we understand what holds 
molecules together so well, then why is it that when I refine an X-ray 
structure and turn the X-ray weight term down to zero ... the molecule blows up 
in my face?

-James Holton
MAD Scientist


On 12/3/2020 3:17 AM, Isabel Garcia-Saez wrote:
Dear all,

Just commenting that after the stunning performance of AlphaFold that uses AI 
from Google maybe some of us we could dedicate ourselves to the noble art of 
gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or 
everything together (just in case I have already prepared my subscription to 
Netflix).

https://www.nature.com/articles/d41586-020-03348-4

Well, I suppose that we still have the structures of complexes (at the moment). 
I am wondering how the labs will have access to this technology in the future 
(would it be for free coming from the company DeepMind - Google?). It seems 
that they have already published some code. Well, exciting times.

Cheers,

Isabel


Isabel Garcia-Saez PhD
Institut de Biologie Structurale
Viral Infection and Cancer Group (VIC)-Cell Division Team
71, Avenue des Martyrs
CS 10090
38044 Grenoble Cedex 9
France
Tel.: 00 33 (0) 457 42 86 15
e-mail: isabel.gar...@ibs.fr
FAX: 00 33 (0) 476 50 18 90
http://www.ibs.fr/




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Re: [ccp4bb] Fwd: CCP4i2 Export and Deposition task

[Joel Sussman]

Dear Nikolas
I have the exact same problem
Joel


On Nov 26, 2020, at 20:00, Nikolas  wrote:


Hi all,

I am trying to prepare and export the files for a structure solved in CCP4i2 
but so far the only tasks available are the "Prepare and validate" and "Merge 
experimental data .." tasks. I have tried to look for the tutorial but both the 
icon and the input page illustrated are different from the ones I can see in 
the software.

I guess I might be missing the whole part of it since the PDB icon shown in the 
task documentation is missing.

Any suggestions/ideas?

Many thanks,
Nikolas




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Re: [ccp4bb] COVID-19 - help design protease inhibitors - 1st round Thurs midnight

[Joel Sussman]

   27-Mar-2020 Rehovot

Dear Frank

Thanks very much for posting this msg - sounds just terrific and emphasizes 
just how important a role structural biology is playing to aid in the discovery 
of lead compounds for treatment of COVID-19, and how this is being done in a 
collaborative way throughout the world.

We've added a pointer to this initiative to the Proteopedia page on: 
"Coronavirus Disease 2019 (COVID-19)" so as to give additional publicity to 
what you are doing to a wider audience beyond the CCP4 Bulletin board, see 
page, i.e.

http://proteopedia.org/w/Coronavirus_Disease_2019_(COVID-19)

Info on this new initiative is in the text just following the initial work done 
at XChem facility at Diamond, the text reads:

==
* A team of UK & Israeli scientists determined 25 crystal structure of 
SARS-CoV-2 main protease in complex with a series of different inhibitors. All 
the experimental details and results are available online at the Diamond Light 
Source.

* An international group of scientists from academia & industry are trying to 
help combat COVID-19. This effort began when Chinese scientists worked rapidly 
to determine the structure of the novel SARS-CoV-2 main protease (Mpro), which 
triggered a massive crystal-based fragment screen (see text, in the point just 
above) at the XChem facility at UK’s Diamond Light Source. With the same 
urgency, they are now trying to progress these data towards what is desperately 
needed: effective, easy-to-make anti-COVID drugs. They welcome contributions of 
many forms including scientific expertise, experimental capabilities, and 
indeed donations to make this possible, go to PostEra for more information.
===

If you have any suggestions/changes on the text or page in general, please let 
us know.

Best regards
Joel


Prof. Joel L. Sussman.
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309   
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 26 Mar 2020, at 2:36, Frank Von Delft 
mailto:frank.vonde...@sgc.ox.ac.uk>> wrote:

To all you structural biologists locked out of your labs, bored with answering 
emails or writing your non-COVID paper, and itching all your lives to be 
medicinal chemists, here's your chance:

https://covid.postera.ai/covid

And you get to do something directly on COVID too.

It's easy:

  *   stare at the pile of fragments we found bound to the SARS-CoV-2 Main 
Protease in our somewhat epic XChem fragment 
screen
 this month (alluded to by others)
  *   see if you can spot cool ways of (especially) merging those hits - or 
anything else
  *   draw the compound onto that page
  *   hit submit

It's actually a bit harder than it sounds - so we're betting that many brains 
will crack the nut of hitting potency in one go (!).

We will do the rest - well, we'll try, if the Filters Approve and the Funds 
Permit -- and even for that, you can contribute, or tell people that could 
contribute (details on that page).

First collection closes tomorrow (Thurs) midnight Pacific Time (but there will 
be more).


Yes, it is a huge social experiment and a total crapshoot - but we must do 
something!  So thank you for all and any help...

*** Do forward to anybody relevant, especially experienced medicinal chemists.

*** If you know virology labs set up to do SARS-CoV-2 assays, email the address 
on that page.

*** If you have help to offer or wisdom to share, do so on the forums on that 
page

*** If you want to use the data for anything else - PLEASE DO - we were anxious 
to push it out ahead of PDB release cycle or getting preprint written.


Frank


--
Prof Frank von Delft
Professor for Structural Chemical Biology

Principal Beamline Scientist: I04-1 and XChem
Diamond Light Source
+44 1235 778997 (office: M,T,T)
+44 7471 026103 (mobile)

Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583 (office: W,F)





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Re: [ccp4bb] Public resource for the structures, validation and re-modelling of Corona virus macromolecules

[Joel Sussman]

27-Mar-2020 13:40 Rehovot
Dear Andrea,
This looks like a terrific idea,
We’ve just now added a pointer to the Public resource for the structures from 
beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2
at the top of the section on "3D structural studies on Coronavirus COVID-19”
on our Proteopedia page  on "Coronavirus Disease 2019 (COVID-19)” at:

http://proteopedia.org/w/Coronavirus_Disease_2019_(COVID-19)

We’d also be pleased to collaborate with you on this initiative.
Our page is addressed to the Lay Public as well as scientists, so, it has a 
somewhat different emphasis than your resource,
but there is clear synergy.
Best regards
Joel

On 27 Mar 2020, at 13:16, Andrea Thorn 
mailto:andrea.th...@web.de>> wrote:

Dear colleagues,

we are methods developers in structural biology. During this time of
crisis, we decided to put our brains to where our hearts are and have
started a public resource for the structures from beta-coronavirus with
a focus on SARS-CoV and SARS-CoV-2:

https://github.com/thorn-lab/coronavirus_structural_task_force

It can be used to download all relevant structures, look at structural
validation information, diagnostic data for the quality of experimental
data and available re-refinements. We will expand this resource in time,
but as of today, it contains all deposited SARS-CoV and SARS-CoV-2
structures, sorted by protein and virus, PDB-REDO entries, diffraction
data diagnostics from AUSPEX and PHENIX.XTRIAGE, WHATCHECK reports and
Tristan Croll's fantastic manual ISOLDE re-refinements. We will soon add
MOLPROBITY to lighten the traffic on the server at Duke, individual
links to Global Phasing's efforts in re-processing and re-refinement of
individual structures and HARUSPEX map annotations for the Cryo-EM
structures.

We may point out potential improvements in some structures in these
data, but this is not meant as criticism of the achievements of the
researchers who first elucidated these structures! It merely reflects on
recent progress in methods development and the potential to push our
methods to their limit in order to get every last bit of biological
information from a given data set.

We hope this can make a (small) difference for a cure of COVID-19.

If you have any questions or would like to contribute, please let me know!


Andrea Thorn.

The collaborators, as of today, are:
myself, Yunyun Gao, Kristopher Nolte, Ferdinand Kirsten, Sabrina Stäb
(RVZ, University of Würzburg, Germany)
Gianluca Santoni (European Synchrotron Facility, France)
Tristan Croll (CIMR, University of Cambridge, UK)
The Richardson Laboratory (Duke University, USA)

We would also like to thank for their advice: Sameer Velankar, James
Holton, Manfred Weiss, Gerard Bricogne, Clemens Vonrhein and Robbie Joosten.

--
Dr. Andrea Thorn | group leader
andrea.th...@uni-wuerzburg.de
+49 931 31-83677

Rudolf Virchow Center, University of Wuerzburg
Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany
https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/



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Re: [ccp4bb] Covid-19 crowdfighting platform

[Joel Sussman]

23-Mar-2020  11:20 Rehovot
Dear Celia
Your site looks terrific!
We at Proteopedia have, also, begun to set up a web page on structural biology 
(and more) aspects of COVID-19, see:

http://proteopedia.org/w/Coronavirus_Disease_2019_(COVID-19)

Comments/suggestions/criticism - most welcome
thanks
Joel


Prof. Joel L. Sussman.
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309   
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 23 Mar 2020, at 11:02, Claudine MAYER 
mailto:ma...@pasteur.fr>> wrote:




 Message transféré 
Sujet : [RéNaFoBiS.bb] Covid-19 crowdfighting platform:
Date :  Mon, 23 Mar 2020 09:52:54 +0100
De :cont...@renafobis.fr 

Répondre à :cont...@renafobis.fr 

Pour :  renafobis...@services.cnrs.fr


De: "plisson celia" 
Envoyé: Lundi 23 Mars 2020 09:11:42
Objet: Re: [3dem] Covid19 and cryo-EM

Dear all,

I think a lot of us are wondering how to be useful during this crisis; a couple 
of researchers from our institute (and beyond) have set up a Covid-19 
crowdfighting platform: crowdfightcovid19.org; if 
you are interested in joining us, please find informations and contacts below.

best regards to all, stay safe
Celia

--
Dr Célia Plisson-Chastang, PhD, HDR
Laboratoire de Biologie Moléculaire Eucaryote - CBI
UMR CNRS 5099-Université Paul Sabatier Toulouse III
Bâtiment IBCG, 118 Route de Narbonne
31062 Toulouse Cedex, France
Telephone  : +33(0)5 61 33 59 50
Fax : +33(0)5 61 33 58 86



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Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

[Joel Sussman]

  19-Mar-2020
Dear Loes, Peter, Clemens & Gerard,
I concur that it is crucial to preserve the original diffraction data and make 
it available to anyone who would like to use it.
As an example, please see the very recent paper by
Nachon et al (2020). "A second look at the crystal structures of Drosophila 
melanogaster acetylcholinesterase in complex with tacrine derivatives provides 
Insights concerning catalytic intermediates and the design of specific 
insecticides" Molecules 25 pii: E1198
[https://www.ncbi.nlm.nih.gov/pubmed/32155891].
The study reexamines the original data, with modern software tools, the 
original data of a paper we published in 2000 (~20 years ago) and revealed 
features that had not been noticed. Specifically
1) previously unmodeled density in the native active site can be interpreted as 
stable acetylation of the catalytic serine.
2) Similarly, a strong density in the DmAChE/ZA complex, originally attributed 
to a sulfate ion, is better interpreted as a small molecule that is covalently 
bound. The complex is reminiscent of the carboxylate/BChE complexes observed in 
crystal structures of hBChE [Brazzolotto et al, 2012; Nicolet et al, 2003], and 
demonstrates the remarkable ability of ChEs to stabilize covalent complexes 
with carboxylates.
Thus, the study demonstrates that updated processing of older diffraction 
images, and the re-refinement of older diffraction data, can produce valuable 
information that could not be detected in the original analysis, and strongly 
supports the preservation of the diffraction images in public data banks.
Best regards
Joel

Prof. Joel L. Sussman.
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309   
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) 
mailto:l.m.j.kroon-batenb...@uu.nl>> wrote:

Dear Gerard,

This is a great idea. Of course I am very much in favour of making available 
raw diffraction images, and such a virtual workshop could demonstrate the 
usefulness of reprocessing raw diffraction data and structural refinements. I 
am not at all afraid that archiving of raw data that are the basis of a 
scientific paper will have significant environmental effects: this is minor 
compared to our everyday use of cloud services.  And as Graeme mentioned: when 
archiving raw data make sure to add sufficient and correct meta data.

Best wishes,
Loes

___
Dr. Loes Kroon-Batenburg
Dept. of Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht
The Netherlands

E-mail : l.m.j.kroon-batenb...@uu.nl
phone  : +31-30-2532865
fax: +31-30-2533940


Van: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
namens Gerard Bricogne mailto:g...@globalphasing.com>>
Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

Dear colleagues,

Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rather than against the
deposited merged data. This statement should in no way be construed as a
criticism of the remarkable achievements of the research groups concerned,
who have been operating under tremendous time pressure, but as an exciting
opportunity to push methods to their limits on a uniquely significant class
of structures.

Another consideration is that the various logistical problems created by
COVID-19 may soon make it increasingly difficult to collect new diffraction
data on potential drug targets relevant to the fight against SARS-CoV-2,
underlining the importance of ensuring that the best results be obtained
from every dataset actually collected, and that the most useful conclusions
be drawn from the analysis of those datasets towards improving the quality
of subsequent data collections.

On this basis we would like to propose that special efforts be made to grant
public access to the raw image data associated with any SARS-CoV-2 related
structure that is deposited into the PDB. This can be done by (1) archiving
these raw image data using resources such as 
data.sbgrid.org, zenodo.org,

Re: [ccp4bb] Update on cryo-electron microscopy and Instruct

[Joel Sussman]

Dear All,
Msg, below, posted for Instruct-ERIC.
best regards
Joel



Update on cryo-electron microscopy and Instruct


I am writing to make sure everyone is aware of the possibilities of using 
Instruct for access to cryoEM facilities.


Instruct has nine sites offering cryoEM support, from hardware to software and 
from Israel to the Czech republic. The facilities range from Krios microscopes 
with detectors including Gatan K3s and K2s (after energy filters) as well as 
FEI Falcon IIIs, enabling both single particle analysis and tomography, to 200 
kV machines and FIB milling dual beam machines. There is also a specialist 
centre for software support.

All of this is explained on the Instruct-ERIC website:
https://instruct-eric.eu/platform-type/electron-microscopy


Access is essentially free at the point of use following peer review, for 
anyone in any of the currently  13 European countries which are members of 
Instruct (there is a cap on the total funds for any project but this would 
usually cover up to 3 days of access to a high-end microscope). You can make an 
application at any time – if you are not already registered with Instruct you 
will need to register and then simply follow the on-line instructions. The 
criteria for access will be familiar to many of you, so instance for access to 
a high-end 300 kV microscope we would expect evidence such as reasonable 2D 
class averages. However if you go to the web site you will see that you can 
contact experts if you have specific technical questions.


Instruct has been offering access for some time but we are currently trialling 
(currently up to the end of 2019) a new cost model, which we believe will be 
more sustainable for critical but expansive facilities such as high end cryoEM, 
so now is a great time to apply, as we aim to test the new model.

Yours
Dave Stuart
Instruct-ERIC Director





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Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

[Joel Sussman]

Following up what Kay Diederichs recently wrote, each page of Proteopedia that 
contains user added comments have a visible banner on the top,
e.g. see: https://proteopedia.org/w/2bs2
n.b. these user added comments are all signed, i.e. they are NOT anonymous, so 
it is a good location to consider user discussion on structural studies.

Joel


On 22Jul, 2019, at 14:16, Kay Diederichs 
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Proteopedia has this - see 
https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures

Kay

On Fri, 19 Jul 2019 17:42:33 +, Bonsor, Daniel 
mailto:dbon...@som.umaryland.edu>> wrote:

Would it be possible to add a public annotations section to the PDB, to allow 
us to potentially flag/warn whoever downloads that particular structure, there 
could be something wrong with it, such as wrong space group, no/poor density 
fitting for ligand. Something similar to PubPeer maybe?


Daniel A. Bonsor PhD
Institute of Human Virology,
University of Maryland at Baltimore
725 W. Lombard Street N571
Baltimore
MD 21201



From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Patrick Loll mailto:pjl...@gmail.com>>
Sent: Friday, July 19, 2019 1:17 PM
To: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

The idea of contacting the editor (and/or author) is an excellent one, and 
indeed the correct thing to do scientifically. However, I�m disillusioned: I�ve 
been down this path before with a high-profile vanity journal, and while the 
editors paid lip service to the notion that the record should be corrected, in 
reality they led me on for the better part of a year, and got me to write up 
detailed analyses of why the ligand positioning was not justified, before 
eventually saying �no, we don�t see any need to publish a correction.� I 
speculate that the journal prefers not avoid corrections, for fear that too 
many corrections will make the journal a less desirable destination.

On 19 Jul 2019, at 11:23 AM, B�rbel Blaum 
mailto:baerbel.bl...@intherabio.com>> wrote:

Hi Rhys,
the reported B-factors for the �ligands� are all way below the reported 
B-factors for the protein chains, with the worst of the three complexes 
reporting unitless numbers 23.2 and 64.8, respectively, just to highlight *one* 
striking feature of the data collection and refinement table. So even with the 
limited info normally available to reviewers this table should have raised a 
red flag. After the re-refinement suggested by others, i.e. your own proper 
assessment of the crystallographic data, if you do not find noteworthy density 
you may want to contact the article�s editor with your results. If you work in 
this field, i.e. really care about this paper scientifically and you are not 
afraid to confront the authors you could suggest writing a comment/direct 
response article but in my opinion that would only make sense if you can be 
sure beforehand that it will be linked visibly to the actual paper, else it 
will be a waste of time. And don�t forget that just because one or some of the 
authors did a bad job at the crystallographic end other findings of the paper 
might still be solid � in collaborations often one author is unable to 
critically evaluate another author�s contribution and this would not be the 
first case were good synthetic or biological work is presented along with a bad 
crystal structure.
By the way and a bit ironically this protein may have suffered bad 
crystallography/scientific practice before - I think it was one of the fake 
Krishna Murthy structures, right? The associated (now retracted) article I mean 
is here
https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub
[https://ars.els-cdn.com/content/image/S00222836.gif]
RETRACTED: Crystal structure of dengue virus NS3 protease in complex with a 
bowman-birk inhibitor: implications for flaviviral polyprotein processing and 
drug design - ScienceDirect - ScienceDirect.com | 
Science, health and medical journals, full text articles and 
books.
www.sciencedirect.com
COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center 
for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA 
2Department of Biochemistry and Molecular Biology, Kansas University Medical 
Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue viruses 
are members of the Flaviviridae and cause dengue fever Dengue fever and dengue 
hemorrhagic ...

Kind regards, B�rbel
---
B�rbel Blaum, PhD
Inthera Bioscience AG
Einsiedlerstrasse 34
CH-8820 Waedenswil
Switzerland
E-Mail: baerbel.bl...@intherabio.com
Phone: +41 43 477 94 

Re: [ccp4bb] challenges in structural biology

[Joel Sussman]

Dear James
Another key point, which is directly related to the discussion of 'why' one 
does a particular structural study, is:
how one explains the results to others, including even to 'non structural 
biologists’.
This is important and INDEPENDENT of the particular experimental procedure. 
Some examples of possible ways to this can be seen in Proteopedia,
e.g.
* Insulin  - http://proteopedia.org/w/Insulin
* Tutorial:How do we get the oxygen we breathe - 
http://proteopedia.org/w/Tutorial:How_do_we_get_the_oxygen_we_breathe
* Immunodeficiency virus protease - 
http://proteopedia.org/w/Immunodeficiency_virus_protease
* An Interactive 3D Complement to a 'Molecular Cell' paper - 
http://proteopedia.org/w/Journal:Molecular_Cell:1

Joel


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 17Jul, 2019, at 13:00, Susan Lea 
mailto:susan@path.ox.ac.uk>> wrote:

I'll shut up soon

Other than when asked to review, I consider it best to concern myself most with 
how I use the share of the limited resources I have access to and refrain from 
commenting on work by others in fields I have sufficiently little knowledge of 
that my estimate of worth is likely to be flawed.

I certainly do not agree that a structure determined by EM is a priori more 
biologically true than one determined by crystallography - as always the only 
question is exactly what is the structure of, and how has the sample had to be 
compromised to determine it.

If you feel you can prove that this is a flawed statement across the whole of 
biology - publish an article and we can shut the synchrotrons.

Yours - from a mixed-method structural biologist ;-)

Susan

Prof. Susan M. Lea,  FMedSci  tel: +44 1865 275181
--
Director of the Central Oxford Structural Microscopy and Imaging Centre & 
Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ 
WadhamCollege


From: r...@mrc-lmb.cam.ac.uk 
mailto:r...@mrc-lmb.cam.ac.uk>>
Sent: 17 July 2019 10:21:42
To: Susan Lea
Cc: ccp4bb@jiscmail.ac.uk
Subject: Re: [ccp4bb] challenges in structural biology

Hi Susan,

We are not naive if we care about using the limited resources of this planet
responsibly. This has nothing to do with whoever's favourite method. I have
nothing against crystallography, it is a beautiful art and has been a success
historically. I have solved plenty of crystal structures myself and will
probably have to keep doing it for a little while. But it is naive to ignore
that the time to move on has arrived, and that we have to use resources to
develop better technologies which address the real biological questions
instead of keeping dinosaurs on life support.

How many of the structures solved on synchrotrons worldwide and of the
zillions in the PDB are of any use or biological relevance (original
question)? There is an enormous amount of waste, including the nasty chemicals
use to grow crystals and to phase pointless structures, let's be honest.

Best wishes,

Radu



I think we are naive if we care about the method used to obtain the structure
- what matters is getting at the structure.  What is great is that the variety
of ways we can do this has increased meaning more samples become tractable for
high resolution structure determination. I don’t see the point of ridiculous
my method is better than your method arguments - for some samples all methods
are equivalent, for some there is only one method that will yield answers - we
just need to train students and develop methods that allow the broadest
access. Everything else is bias-driven posturing. Let’s just solve some
structures and learn something about biology.


Susan

Sent from my iPhone

On 17 Jul 2019, at 08:43, r...@mrc-lmb.cam.ac.uk 
mailto:r...@mrc-lmb.cam.ac.uk>>
wrote:

Hi Both,

I am not questioning the PDB stats, the issue was whether (crystal)
structures
are sufficiently relevant to address biological questions and justify the
resources. Fragment screening is one example where investment in protein
crystallography can still be justified (for now). But it doesn't really ask
or
answer biological questions... for these, whether we like it or not,
macromolecular crystallography (or NMR, even in cell) cannot be the future.
In
my opinion :-)

Best 

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Disulphide occupancies.

[Joel Sussman]

27-May-2019
Dear Jonathan
A good example to see the actual 'breaking of an S-S bond' can be found in:

Weik, Ravelli, Kryger, McSweeney, Raves, Harel, Gros, Silman, Kroon, & Sussman
"Specific chemical and structural damage to proteins produced by synchrotron 
radiation”
PNAS 97, 623-628 (2000).

See cover illustration of the breaking of one S-S bond as a function of time at:

http://www.weizmann.ac.il/Structural_Biology/Sussman/cover-pages/pnasb

&

http://www.weizmann.ac.il/Structural_Biology/Sussman/radiation-damage-0

best regards,
Joel


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 27May, 2019, at 9:53, 
herman.schreu...@sanofi.com 
mailto:herman.schreu...@sanofi.com>> wrote:

Dear Jonathan,

In these cases, I usually see positive difference density nearby, indicating an 
alternative position for one of the sulfurs, i.e. the disulfide bridge was 
partly broken. I am too lazy to fit these, but if you want to do a perfect job, 
you might want to fit an alternative conformation for this sulfur. You may have 
to create an alternative conformation for the other sulfur as well to have one 
bonded disulfide bridge and one open one.

Considering deposition: you are the depositor. If you believe that the model 
you made is the most faithful representation of the “true” structure, you 
should deposit it and the pdb will have to accept. In the worst case they will 
add some warnings.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Jonathan 
Cooper
Gesendet: Montag, 27. Mai 2019 00:20
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] Disulphide occupancies.


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

When you refine structures with disulphide bridges you often get negative 
difference density for the sulphurs, presumably due to the well-known radiation 
damage effects. The negative difference density often won't disappear with 
usual B-factor refinement. However, it seems to go away if you refine the 
occupancy of the affected sulphur atoms e.g. to 0.9 or thereabouts. Would it be 
acceptable to publish/deposit structures where the sulphur occupancy is less 
than one, given a suitable REMARK in the pdb file? Thank you.



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Re: [ccp4bb] unidentified crescent-shaped electron density

[Joel Sussman]

Please see:

Dym, O., Song, W., Felder, C., Roth, E., Shnyrov, V., Ashani, Y., Xu, Y., 
Joosten, R. P., Weiner, L., Sussman, J. L. & Silman, I. The impact of 
crystallization conditions on structure-based drug design: A case study on the 
methylene blue/acetylcholinesterase complex. Protein Sci. 25, 1096-1114 (2016).


Structure-based drug design utilizes apoprotein or complex structures retrieved 
from the PDB. >57% of crystallographic PDB entries were obtained with 
polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of 
these report presence of individual ethyleneglycol oligomers. We report a case 
in which ethyleneglycol oligomers' presence in a crystal structure markedly 
affected the bound ligand's position. Specifically, we compared the positions 
of methylene blue and decamethonium in acetylcholinesterase complexes obtained 
using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The 
ligands' positions within the active-site gorge in complexes obtained using 
PEG200 are influenced by presence of ethyleneglycol oligomers in both cases 
bound to W84 at the gorge's bottom, preventing interaction of the ligand's 
proximal quaternary group with its indole. Consequently, both ligands are ∼3.0Å 
further up the gorge than in complexes obtained using crystals precipitated 
with ammonium sulfate, in which the quaternary groups make direct π-cation 
interactions with the indole. These findings have implications for 
structure-based drug design, since data for ligand-protein complexes with 
polyethylene glycol as precipitant may not reflect the ligand's position in its 
absence, and could result in selecting incorrect drug discovery leads. Docking 
methylene blue into the structure obtained with PEG200, but omitting the 
ethyleneglycols, yields results agreeing poorly with the crystal structure; 
excellent agreement is obtained if they are included. Many proteins display 
features in which precipitants might lodge. It will be important to investigate 
presence of precipitants in published crystal structures, and whether it has 
resulted in misinterpreting electron density maps, adversely affecting drug 
design.

and the cover image showing the PEG molecules, in blue with their surrounding 
electron density, near the bound ligand,  methylene blue, in pink.

best regards
Joel
[cid:E3F7CC9E-AFE7-47B8-8E92-54FDF7658D14@weizmann.ac.il]


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 2Apr, 2019, at 4:12, Zhen Luo 
mailto:z@imb.uq.edu.au>> wrote:

Hi everyone,

Thank you very much for your help and time. A PEG fragment indeed seems to fit 
into the density. Thanks again!


Best regards,
Zhen
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Zhen Luo mailto:z@imb.uq.edu.au>>
Reply-To: Zhen Luo mailto:z@imb.uq.edu.au>>
Date: Tuesday, 2 April 2019 at 9:01 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] unidentified crescent-shaped electron density

Dear all,

Could you please shed some light on what this crescent-shaped density around 
the lysine side chain might belong to? I now have two unrelated protein 
structures where this kind of density can be found surrounding a lysine side 
chain.




2FOFC maps were contoured at around 1.5 sigma, FOFC map at 3 sigma.


One protein was crystallised in 0.1 M CaCl2 and 20% PEG 3350; the other in 10% 
PEG 2, 20% PEG MME 550, 0.03 M CaCl2/MgCl2, 0.1 M MES/imidazole. Protein 
buffers contained 0.025 M HEPES and 0.15 M NaCl. None of these fitted in well. 
Could it be cleaved PEG?

Any suggestion would be greatly appreciated. Thanks in advance!

Best regards,
Zhen Luo

School of Chemistry and Molecular Biosciences
The University of Queensland, Australia




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Re: [ccp4bb] Seeking Postdoc for the Shifman lab at the Hebrew Univ in Jerusalem

[Joel Sussman]

Msg for Julia Shifman’s Lab at the Hebrew Univ, Jerusalem

The Shifman lab [ http://www.bio.huji.ac.il/Shifman] in the Hebrew University 
of Jerusalem is looking for a postdoctoral scholar in Experimental Protein 
Engineering. In out lab, we engineer inhibitors of protein-protein interactions 
starting from natural binding partners as well as from unrelated small protein 
domains. Such inhibitors could be evolved to selectively target only one family 
member among hundreds of homologs, making them attractive drug candidates. 
Using a combination of computational and directed evolution approaches, we 
convert the natural low-affinity binding partners into high-affinity and 
high-specificity binders. In the particular project, we would like to engineer 
specific inhibitors to various types of Matrix Metalloproteinases, enzymes 
whose activity is related to various diseases including cancer. These molecules 
will be later transformed into drug candidates. We are looking for a highly 
motivated person with a background in Biophysics or Biochemistry to take over 
this exciting project. The candidate should have experience with molecular 
biology and protein expression/purification. Experience in yeast surface 
display is a plus. Our lab is located in the Department of Biological Chemistry 
in the Hebrew University of Jerusalem, Jerusalem, Israel. Please contact Julia 
Shifman: jshif...@mail.huji.ac.il



Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
www.proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-




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Re: [ccp4bb] Open SESAME & Instruct-ERIC Workshop on Remote X-ray Data Collection from European Synchrotrons at the Weizmann Institute of Science on 14-18 May 2018

[Joel Sussman]

I will check again with her tomorrow early morning

Sent from my iPhone

On 8 May 2018, at 22:52, Rikkert Wierenga 
> wrote:



Dear All,

There will be an Open SESAME & Instruct-ERIC Workshop on Remote X-ray Data 
Collection from European Synchrotrons at the Weizmann Institute of Science on 
14-18 May 2018.
For those who are not able to come, the entire workshop will be streamed 
online, password not required, starting on 14-May-2018 at 09:00 CET, at:

https://www.youtube.com/channel/UCs5gSCQJOAQfmxjOqJ8arOQ/live

The program for the workshop can be seen at:

http://www.weizmann.ac.il/conferences/RXDC2018/program-outline

With best regards,
Rik Wierenga & Joel L. Sussman

Re: [ccp4bb] on the resoution of crystal

[Joel Sussman]

6-Feb-2017
Dear Pavel & Tim,
For a very good visualization & description of “Resolution”,
please see the Proteopedia page created primarily by Eric Martz at:
http://www.proteopedia.org/w/Resolution
it includes a pointer to James Holton’s movie showing an Electron Density Map 
vs. Resolution (with model overlay) going from 0.5Å to 5.Å resolution.
best regards
Joel


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
www.proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
-

On 5Feb, 2017, at 23:44, Tim Gruene 
> wrote:

Dear Pavel,

I believe words have a meaning, but they are not defined. This may make
languages a little more demanding than mathematics, since you have to deal
with a variety of a few hundred thousand to millions, depending how popular
the language in question is, but personally I enjoy the challenge.

W.r.t. the thread, 3.8A resolution is poorer than 1.8A. I understand this is
what John meant to clarify.

Best,
Tim

On Sunday, February 5, 2017 11:12:10 AM CET Pavel Afonine wrote:
Hi Tim, hi Natesh,

one expression is mathematically, the other one is technically 'more

correct'.
I favour the terms poor and good resolution to avoid confusion, or
explicitly
list the values.

just out of curiosity.. what's your definition of 'poor' and 'good'
resolutions? I suspect there are as many definitions as many subscribers to
this list are -;)

One way to quantify resolution is that what kind of detail you can see in
the map, like for example:

- deformation density (~0.7A and higher) = ultra-high, sub-atomic,
sub-Angstrom;
- H atoms (~0.9A and higher) = not sure what the name is;
- individual non-H atoms (~1.2A and higher) = atomic;
- hole in rings (~2A and higher?) = high;
- medium;
- still can see side chains (up to 4.5A);
- no side-chains but SS elements (such as tubes of density for helices) =
low
- no SS, molecular envelopes = very low.

Note, resolution alone is not a good measure though. Data completeness is
similarly important, e.g. a map corresponding to 2A resolution may look
like a 3ish A resolution if you miss some low-resolution data or
high-resolution end is severely incomplete (Acta Cryst. (2014). D70,
2593-2606).

Low resolution  --> worse than 2.7 A

Ultra high resolution --> better than 0.95 A

Looking into this in some systematic way one can define low-resolution as
6A and lower, and ultra-high resolution as 0.7A and higher (Page 1291: Acta
Cryst. (2009). D65, 1283–1291).

All the best,
Pavel

--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

Re: [ccp4bb] Absence of contact between layers in a crystal

[Joel Sussman]

6-Feb-2015
Dear Adrian
Maybe a petition could be circulated that many of us could sign requesting 
Nature to retract this paper.
I don’t know if this has ever been tried, but my guess is that Nature would 
take it seriously, especially
due to the overwhelming evidence that the structure was fabricated.
Adrian, would you possibly consider drafting a short msg, with a pointer to a 
file (maybe in the ccp4 archives) with
the evidence, that could serve as the the basis of a petition to Nature???
best regards,
Joel
 
 On 6Feb, 2015, at 14:01, Adrian Goldman adrian.gold...@helsinki.fi wrote:
 
 Well maybe some pressure should be put on Nature to retract the article, so 
 that we can get the publication out of the PDB?  It’s not good that it is 
 there for the unwary.
 
   Adrian
 
 
 On 06 Feb 2015, at 11:44, Folmer Fredslund folm...@gmail.com wrote:
 
 Unfortunately, the structure and associated paper for PDB id 2hr0 has _not_
 been retracted, or marked as invalid.
 
 The University of Alabama had a note about it, but only some of the
 affected PDB entries were removed.
 http://www.uab.edu/reporterarchive/71570-uab-statement-on-protein-data-bank-issues
 
 For 2hr0, the Nature letter (
 http://www.nature.com/nature/journal/v444/n7116/full/nature05258.html)  and
 the associated structure has not been removed from the archives.
 
 
 Best regards,
 
 Folmer Fredslund
 
 Disclosure: I published the structure of native bovine C3 (2b39)
 
 
 
 2015-02-06 12:08 GMT+01:00 David Briggs drdavidcbri...@gmail.com:
 
 Haven'tthat paper and the associated structure been retracted?
 
 http://www.nature.com/news/2009/091222/full/462970a.html
 
 There was a huge scandal when it was discovered that Krishna Murthy had
 falsified data, including the structure you refer to.
 
 See http://en.wikipedia.org/wiki/H.M._Krishna_Murthy
 
 A crystallographer with a wikipedia entry for all the wrong reasons...
 
 Dave
 
 
 On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be wrote:
 
 Hello,
 
 Looking at structure 2HR0 (The structure of complement C3b provides
 insights into complement activation and regulation. »,Abdul Ajees, A.,
 Gunasekaran, K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna
 Murthy, H.M.;  (2006) Nature 444: 221-225), I noticed the absence of
 contacts between layers in the crystal. Is it something that has already
 been observed in other crystals?
 
 Best regards,
 
 Fred
 -
 Frédéric Kerff
 Chercheur qualifié F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège
 17, Allée du 6 Août - Bat B5a
 4000 Liège (Belgium)
 Tel.: +32 (0)4 3663620
 Fax: +32 (0)4 3663772
 
 
 
 Le 6 févr. 2015 à 10:12, Tim Gruene t...@shelx.uni-ac.gwdg.de a écrit :
 
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Dear Smith,
 
 The sca file most likely does not contain flags. pointless can read
 the sca file, standardise it to ccp4 standards and freerflag marks
 random reflections. You should use the maximum of 500 unique
 reflections or 5% of the unique reflections, whichever is larger.
 
 Best,
 Tim
 
 On 02/06/2015 09:49 AM, Smith Lee wrote:
 Dear All, I have a sca file. Will you please tell me by which
 software or how I can know whether the sca file contains R-free
 tags? If not, by which software or how I can add the R-free tags?
 And how much of the reflections I add the R-free tags? I am looking
 forward to getting your reply. Smith
 
 
 - --
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 
 iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
 j0JFZac4kAh8twpov71MG84=
 =XN57
 -END PGP SIGNATURE-
 
 
 
 
 -- 
 Folmer Fredslund
 

Re: [ccp4bb] Young scientist travel awards for Intl Conf. on Structural Genomics 2015 Deep Sequencing Meets Structural Biology

[Joel Sussman]

2-Feb-2015
Dear Colleagues,

We are pleased to announce the availability of young scientist travel 
fellowships to the International Conference on Structural Genomics 2015 Deep 
Sequencing Meets Structural Biology, which will be held on the campus of the 
Weizmann Institute of Science in Rehovot, Israel June 7-11, 2015. This 
conference is intended to foster international collaboration and to provide an 
overview for the most recent developments in Structural Biology and Structural 
Genomics and future impacts on biology, medicine and disease.
Web site: http://www.weizmann.ac.il/conferences/ICSG2015
Poster: https://www.dropbox.com/s/i1s3hsg7a0chqi2/ICSG2015_Poster.pdf?dl=0

There are two types of young scientist travel support available (deadlines are 
both March 31, 2015):

Young scientist travel support of up to $1,000 US will be made available to 
graduate students and post-doctoral researchers to attend ICSG2015. A total of 
5 International Structural Genomics Organization (ISGO) - NIH Protein Structure 
Initiative (PSI) Student Travel Fellowships have kindly been provided by the 
ISGO and the NIH PSI.

Fellowships of €500 for students from Instruct countries will be awarded to 
attend the pre-conference workshop “Technical and Analytical Approaches to the 
Translation of Deep Sequencing Data into Three-Dimensions” (7-June-2014 
09:00-12:00) and to stay on and participate in the full conference. A total of 
8 Fellowships have kindly been provided by Instruct 
(https://www.structuralbiology.eu).

To apply for a student travel fellowship please see 
http://www.weizmann.ac.il/conferences/ICSG2015/young-scientists-travel-support .

The International Conference on Structural Genomics 2015 Deep Sequencing Meets 
Structural Biology” conference

The scientific topics to be covered in ICSG 2015 (see 
http://www.weizmann.ac.il/conferences/ICSG2015) include:

·   Deep sequencing for modeling and refinement of macromolecular structures
·   Membrane protein structure and function using complementary methods
·   Technological advances in XFEL, Cryo-EM, NMR, SAXS, MS, MX and 
macromolecular complexes
·   Combining low and high resolution data and modeling for structural biology
·   Synergistic use of 3D structures and deep sequencing to realize 
personalized medicine
·   Protein design and deep sequencing
·   Cancer, antibiotic resistance and drug discovery

In order to widen the opportunities for younger researchers, we have organized 
satellite workshops before ICSG 2015 (during the day on June 7, 2015). These 
include:

·   Cryo-EM developments for structural biology [Sponsored by FEI]
·   Approaches to the translation of deep sequencing data into three-dimensions 
[Sponsored by Instruct]
·   PHENIX: Automated determination of molecular structures [Tom Terwilliger  
Pavel Afonine]
·   HKL3000: From X-ray diffraction images to structure determination in 
minutes [Wladek Minor]
·   Protein expression and characterization workshop [Tamar Unger  Yoav Peleg]
·   Proteopedia: A Scientific Wiki Bridging the Rift Between 3D Structure  
Function [Jaime Prilusky  Joel L. Sussman]

Five oral presentations will be chosen from the posters, and six poster prizes 
will be awarded, so be sure to submit your abstracts by April 15, 2015!


Speakers include:

Arie Admon (Haifa)
Lucia Banci (Florence)
Pamela J. Bjorkman (Pasadena)
Samir K. Brahmachari (Delhi)
Susan Buchanan (Bethesda)
Martin Caffrey (Dublin)
Mark Gerstein (New Haven)
Wayne Hendrickson (New York)
Yvonne Jones (Oxford)
Roger Kornberg (Stanford)
Luhua Lai (Beijing)
Michael Levitt (Stanford)
Michal Linial (Jerusalem)
Abraham Minsky (Rehovot)
John Moult (Rockville)
Nathan Nelson (Tel Aviv)
Stefan Raunser (Dortmund)
Monica Roth (Piscataway)
Dinakar M. Salunke (Gurgaon)
Eran Segal (Rehovot)
Philip Selenko (Berlin)
Sachdev Sidhu (Toronto)
Rotem Sorek (Rehovot)
Jan Steyaert (Brussels)
Shamil Sunyaev (Boston)
Dan Tawfik (Rehovot)
Janet Thornton (Hinxton) The FEBS National Lecturer
Gunnar von Heijne (Stockholm)
Soichi Wakatsuki (Stanford)
Shigeyuki Yokoyama (Yokohama)
Ada Yonath (Rehovot)
Mingjie Zhang (Hong Kong)


We are looking forward to welcoming you to the Weizmann Institute in the June 
of 2015!

Sincerely yours,

ICSG 2015 Local Organizing Committee
Joel L. Sussman, Gideon Schreiber, Tamar Unger and Israel Silman, Weizmann 
Institute


ICSG 2015 International Organizing Committee
Cheryl Arrowsmith, (Structural Genomics Consortium, Toronto)
Lucia Banci, (University of Florence, Florence)
Jacqui Beckmann, (Swiss Institute of Bioinformatics, Lausanne)
Mark Gerstein, (Yale University, New Haven)
Yvonne Jones, (University of Oxford, Oxford)

--
Prof. Joel L. Sussman
joel.suss...@weizmann.ac.ilmailto:joel.suss...@weizmann.ac.il  
www.weizmann.ac.il/~joelhttp://www.weizmann.ac.il/~joel
Department of Structural Biology tel: +972 (8) 934 4531  

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Joel Sussman]

16-May-2014
Dear Patrick,
Proteopedia [http://proteopedia.org] uses exactly the same style for 
referencing published material.

Proteopedia allows for the easy insertion of Pubmed and DOI references by only 
requesting from the user to enter the Pubmed or DOI ids. We have extended the 
same software used in Wikipedia for the internal Proteopedia engine to, based 
on this reference ID, retrieve, format and insert the correctly formatted 
reference at the bottom of the page.

For example, type refPMID 18673581/ref or refdoi 10.1093/nar/gku213/ref 
in the wikitext box and save the page. If you type the reference in this 
manner, the properly formatted reference will be created automatically at the 
bottom of the page (or wherever you place the necessary wikitext 
references/).

See http://proteopedia.org/w/Help:Editing#Citing_Literature_References and 
Proteopedia pages for actual examples.
best regards,
Jaime  Joel

On 15May, 2014, at 13:48, Patrick Shaw Stewart 
patr...@douglas.co.ukmailto:patr...@douglas.co.uk wrote:


I may be missing something here, but I don't think you have to rebut anything.  
You simply report that someone else has rebutted it.  Along the lines of

Many scientists regard this published structure as unreliable since a 
misconduct investigation by the University of Alabama at Birmingham has 
concluded that it
was, more likely than not, faked [1]

[1] http://www.nature.com/news/2009/091222/full/462970a.html





On 15 May 2014 18:00, Nat Echols 
nathaniel.ech...@gmail.commailto:nathaniel.ech...@gmail.com wrote:
On Thu, May 15, 2014 at 9:53 AM, Patrick Shaw Stewart 
patr...@douglas.co.ukmailto:patr...@douglas.co.uk wrote:
It seems to me that the Wikipedia mechanism works wonderfully well.  One rule 
is that you can't make assertions yourself, only report pre-existing material 
that is attributable to a reliable published source.

This rule would be a little problematic for annotating the PDB.  It requires a 
significant amount of effort to publish a peer-reviewed article or even just a 
letter to the editor, and none of us are being paid to write rebuttals to dodgy 
structures.

-Nat



--
 patr...@douglas.co.ukmailto:patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.ukhttp://www.douglas.co.uk/
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] PDB passes 100,000 structure milestone

[Joel Sussman]

15-May-2014
Dear Martyn
   Proteopedia's (http://proteopedia.org) goal goes well beyond just education 
- it is aimed at Structural Biology and non Structural Biology Community and it 
would be pleased to be a forum for discussion of structures that are 
questionable. There are now over 2,600 registered users, who are contributing 
to Proteopedia, in over 50 different countries.
   Proteopedia has a special area for discussions related to each structure. To 
access it, you go to the structure's page, e.g. http://proteopedia.org/w/2x24 
and click on the 'discussion' tab on the page's upper border. Everyone can read 
the comments there, and it will open a fully editable page for every registered 
user to add their comments on the structure and their full name will be listed 
below their comments.
   If you would like to contribute to this, we’d be pleased to welcome your 
input.
   Best regards,
   Jaime Prilusky  Joel Sussman


On 15May, 2014, at 7:29, MARTYN SYMMONS 
martainn_oshioma...@btinternet.commailto:martainn_oshioma...@btinternet.com 
wrote:

I agree some forum for community annotation and commenting would be a good 
thing for users of structural data.
There was an attempt to do that with the pdbwiki project which was a community 
resource for the bioinformatics community. Unfortunately pdbwiki has now folded 
(see http://pdbwiki.org/) They are now directing people to Proteopedia. However 
Proteopedia has a more educative focus I think - rather than capturing 
technical questions and input.

Pubmed commons (http://www.ncbi.nlm.nih.gov/pubmedcommons/), which is a forum 
for discussing the literature, is currently under testing. Perhaps this is the 
sort of thing that could work for structural data?

cheers
 Martyn


From: Ethan A Merritt 
merr...@u.washington.edumailto:merr...@u.washington.edu
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 14 May 2014, 19:22
Subject: Re: [ccp4bb] PDB passes 100,000 structure milestone

On Wednesday, 14 May, 2014 13:52:02 Phil Jeffrey wrote:
 As long as it's just a Technical Comments section - an obvious concern
 would be the signal/noise in the comments themselves.  I'm sure PDB
 would not relish having to moderate that lot.

 Alternatively PDB can overtly link to papers that discuss technical
 issues that reference the particular structure - wrong or fraudulent
 structures are often associated with refereed publications that point
 that out, and structures with significant errors often show up in that
 way too.  I once did a journal club on Muller (2013) Acta Cryst
 F69:1071-1076 and wish that could be associated with the relevant PDB
 file(s).

Perhaps some combination of those two ideas?

The PDB could associate with each deposited structure  a crowd-sourced
list of published articles citing it.They already make an effort to
attach the primary citation, but so far as I know there is currently
no effort to track subsequent citations.

While spam comments in a free-format forum are probably inevitable,
spam submission of citing papers seems less likely to be a problem.

- Ethan

  On Wed, May 14, 2014 at 12:32 PM, Zachary Wood 
  z...@bmb.uga.edumailto:z...@bmb.uga.edu
  mailto:z...@bmb.uga.edumailto:z...@bmb.uga.edu wrote:
 
 Hello All,
 
 Instead of placing the additional burden of policing on the good
 people at the PDB, perhaps the entry page for each structure could
 contain a comments section. Then the community could point out
 serious concerns for the less informed users. At least that will
 give users some warning in the case of particularly worrisome
 structures. The authors of course could still reply to defend their
 structure, and it may encourage some people to even correct their
 errors.
 
--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,  University of Washington, Seattle 98195-7742

Re: [ccp4bb] Comparison of Water Positions across PDBs

[Joel Sussman]

For detailed examination of this topic, see:

Koellner, G., Kryger, G., Millard, C. B., Silman, I., Sussman, J. L.  Steiner, 
T. (2000).
Active-site gorge and buried water molecules in crystal structures of 
acetylcholinesterase from Torpedo californica. Journal of Molecular Biology 
296, 713-735.

http://www.ncbi.nlm.nih.gov/pubmed/10669619

best regards,
Joel

On 30 Oct 2013, at 01:35, Ed Pozharski 
epozh...@umaryland.edumailto:epozh...@umaryland.edu wrote:

http://www.ccp4.ac.uk/html/watertidy.html


On 10/29/2013 04:43 PM, Elise B wrote:
Hello,

I am working on a project with several (separate) structures of the same 
protein. I would like to be able to compare the solvent molecules between the 
structures, and it would be best if the waters that exist in roughly the same 
position in each PDB share the same residue number. Basically, I want to 
compare solvent molecule coordinates and assign similar locations the same name 
in each structure.

What would be the best strategy for re-numbering the water molecules such that 
those with similar coordinates in all the structures receive the same residue 
number? I'd appreciate any suggestions.

Elise Blankenship



--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
   Julian, King of Lemurs

Re: [ccp4bb] Post-Doc Position Available at the Weizmann Institute of Science

[Joel Sussman]

Post-Doc Position: Structure-aided redesigning of an enzyme: molecular biology, 
protein expression/purification  crystallography

Immediate opening, in the Sussman lab at the Weizmann Institute of Science,  
for a postdoctoral fellow with experience in cloning and in protein expression, 
purification and characterization. Interest or experience in protein 
crystallography would be an advantage. The appointment will be for 2-3 years, 
and the project, which will focus on structure-aided redesigning of an enzyme, 
will be implemented in close collaboration with Prof Dan Tawfik (Dept of 
Biological Chemistry) and the Israel Structural Proteomics Center (ISPC).

-
Prof. Joel L. Sussman 
joel.suss...@weizmann.ac.ilmailto:joel.suss...@weizmann.ac.il
Pickman Prof. of Structural Biology   +972 (8) 934 4531 - tel
Head, The Israel Structural Proteomics Center (ISPC)  +972 (8) 934 6312 - fax
Department of Structural Biology  
www.weizmann.ac.il/~joelhttp://www.weizmann.ac.il/~joel
Weizmann Institute of Science 
www.weizmann.ac.il/ISPChttp://www.weizmann.ac.il/ISPC
Rehovot 76100 ISRAEL  
proteopedia.orghttp://www.proteopedia.org/
-

Re: [ccp4bb] 3D printing structures?

[Joel Sussman]

Output should be in VRML formal
RasMol, PyMol  Jmol all have options to write out VRML format files.
Sometimes you need add additional 'struts' to give additional structural 
support, Jmol has option of adding these struts.
best regards,
Joel

On 23 Aug 2013, at 21:33, Edward A. Berry 
ber...@upstate.edumailto:ber...@upstate.edu wrote:

Along the same lines, does anyone have a program for converting Raster-3D format
such as Molscript puts out, into one of the formats readable by a 3D printer?
eab

Ronnie wrote:
An off-topic question-now that 3D printing is becoming more common, has anyone 
tried to print protein structures other than just the surface representation 
like in this tutorial? 
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/

Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

Re: [ccp4bb] About NCS and inhibitors

[Joel Sussman]

Dear All,
Something like what Felix wrote is seen in the crystal structure of recombinant 
human acetylcholinesterase (rhAChE) (PDB-ID: 3lii), with two molecules are seen 
in the asymmetric unit.
* In one molecule, the active-site gorge (where inhibitors normally lie) is 
occupied with part of a peptide loop from a symmetrically related rhAChE.
* While the corresponding region of the other copy of rhAChE is void of this 
peptide.
See figs 15-16 in:
Dvir, H., Silman, I., Harel, M., Rosenberry, T. L.  Sussman, J. L. (2010). 
Acetylcholinesterase: From 3D structure to function Chemico-Biological 
Interactions 187, 10-22.
* So, in essence, no reason to ever assume that two copies in asymmetric unit 
will be identical, or have identical inhibitors bound, or 'surrogate 
inhibitors' (like in this case) bound. Sometimes differences are due to 
difference in crystal packing
Best regards,
Joel


On 7 Jan 2013, at 11:58, Felix Frolow wrote:

I apologise for typing blinbly:
 if one is in, the second can't be
FF
Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jan 7, 2013, at 11:48 , Felix Frolow 
mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il wrote:

Why not? They can be mutually excluding! If one is in, the second can be. This 
phenomenon brakes a local symmetry.
FF

Dr Felix Frolow
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.ilmailto:mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Jan 7, 2013, at 11:28 , Xiaopeng Hu 
huxp...@mail.sysu.edu.cnmailto:huxp...@mail.sysu.edu.cn wrote:

Dear All,

We recently resolved an enzyme/inhibitor complex structure. The enzyme contains 
two NCS related active site and we did find extra density in both of 
them.However we observed that the two inhbitor moleculors are not NCS related, 
but partly overlaped if make a NCS moleculor. Has anyone else observed this 
before? Thanks for any help and suggestion!


Best,

Xiaopeng Hu

Re: [ccp4bb] Nobel Prizes for 3D Molecular Structure

[Joel Sussman]

Just want to make sure anyone interested in Nobel Prizes knows about this 
existing page:
http://proteopedia.org/wiki/index.php/Nobel_Prizes_for_3D_Molecular_Structure
best regards,
Joel Sussman

Re: [ccp4bb] electrostatic potential and charged residues

[Joel Sussman]

14-Sep-2012   21:50 Rehovot
Dear Qiang
A good example of just such a case is acetylcholinesterase,
where homologous proteins have very similar electrostatic motifs,
with an very large electric dipole, ~1,700.
see three representative papers on this,

1. Ripoll, D. R., Faerman, C. H., Axelsen, P. H., Silman, I.  Sussman, J. L. 
(1993). An electrostatic mechanism for substrate guidance down the aromatic 
gorge of acetylcholinesterase. The Proceedings of the National Academy of 
Sciences U.S.A. 90, 5128-5132.

2. Felder, C. E., Botti, S. A., Lifson, S., Silman, I.  Sussman, J. L. (1997). 
External and internal electrostatic potentials of cholinesterase models. 
Journal of Molecular Graphics and Modelling 15, 318-327.

3. Botti, S. A., Felder, C., Sussman, J. L.  Silman, I. (1998). Electrostatic 
homology modelling of a set of ChE-like neural adhesion proteins identifies a 
shared 'annular' motif with ChEs. Structural implications for a 
cell-recognition role of ChEs. Journal of Physiology (Paris) 92, 414-416.

best regards,
Joel
-
Prof. Joel L. Sussman 
joel.suss...@weizmann.ac.ilmailto:joel.suss...@weizmann.ac.il
Pickman Prof. of Structural Biology   +972 (8) 934 4531 - tel
Head, The Israel Structural Proteomics Center (ISPC)  +972 (8) 934 6312 - fax
Department of Structural Biology  
www.weizmann.ac.il/~joelhttp://www.weizmann.ac.il/~joel
Weizmann Institute of Science 
www.weizmann.ac.il/ISPChttp://www.weizmann.ac.il/ISPC
Rehovot 76100 ISRAEL  
www.proteopedia.orghttp://www.proteopedia.org/
-

On 14 Sep 2012, at 21:37, Qiang Chen wrote:

Hi all,

I'm working on a protein structure which showed a special electrostatic
potential on its surface: positive on one end and negative on the other
end. I wonder to what extent I can say this pattern is determined by the
charged residues? If the residues are conserved, could I make a conclusion
that its homologues also have such pattern?

Thanks!


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Re: [ccp4bb] dumb software question

[Joel Sussman]

7-Aug-2012 20:30
Dear Paul,
Pls see Virtual nanoscopy: Like 'Google Earth' for cell biologists
http://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/?et_cid=2784615et_rid=54732139linkid=http%3a%2f%2fwww.rdmag.com%2fNews%2f2012%2f08%2fLife-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists%2fhttp://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/?et_cid=2784615et_rid=54732139linkid=http://www.rdmag.com/News/2012/08/Life-Science-Biology-Microscopy-Virtual-nanoscop-Like-Google-Earth-for-cell-biologists/
Is this what you were looking for?
best regards,
Joel

On 7 Aug 2012, at 18:24, Paul Kraft wrote:


Hi guys,
is there a program similar to ccp4/coot that allows one to visuallize an ideal 
cell (either prokaryote or eukaryote) in 3D with semi accurate distances. One 
that is windows based (as much as I detest) that would be good for teaching 
biochem 380 students emphasising distance, diffusion, etc measurements with 
links to the pdb? Thanks in advance.
Paul

Dr. Paul Kraft
Structural Biologist
cell 586-596-2770
email: haresea...@yahoo.commailto:haresea...@yahoo.com

Re: [ccp4bb] nmr blog

[Joel Sussman]

See also in Proteopedia:

http://proteopedia.org/w/NMR_Ensembles_of_Models

best regards,
Joel

On 23 Mar 2012, at 09:42, Daniel Picot wrote:

You can find here several links concerning NMR

http://www.drorlist.com/nmr.html

with a discussion list:

https://listes.sc.univ-paris-diderot.fr/sympa/info/nmr

Daniel


Le 22/03/2012 19:35, Luthra,Amit a écrit :
Is any NMR blog available for discussion?


Amit Luthra, Ph.D.
Post-Doctoral Fellow
The Radolf Laboratory
Department of Medicine
University of Connecticut Health Center

[e]   aut...@uchc.edumailto:aut...@uchc.edu
[p]   860/ 679 - 8390
[w]   http://spirocheteresearch.uchc.edu/

Re: [ccp4bb] Crystal Structures as Snapshots

[Joel Sussman]

2012_02_11
Dear All,
Two really striking examples of Intrinsically Flexible Proteins are:

(1) Adenylate kinase: Vonrhein, Schlauderer  Schulz (1995) Structure 3, 483
“Movie of the structural changes during a catalytic cycle of nucleoside 
monophosphate kinases”
http://portal.uni-freiburg.de/structbio/structuregallery/ak_folder/mpeg
in particular look at:
video as MPEG white background, closing  opening enzyme (707kb)
Each black dot [upper left, in the morph] indicates an observed crystal 
structure.

(2) Lac repressor: see Proteopedia page on lac repressor,
morphing from the structure bound to its cognate DNA, to that of the structure 
bound to its the non-cognate DNA,
at: http://proteopedia.org/w/Lac_repressor

best regards,
Joel


On 10 Feb 2012, at 22:51, Jacob Keller wrote:

Interesting to juxtapose these two responses:

James Stroud:
How could they not be snapshots of conformations adopted in solution?

David Schuller:
How could that possibly be the case when any structure is an average of all
the unit cells of the crystal over the timespan of the diffraction
experiment?

JPK



***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu
***

Re: [ccp4bb] protein structure for high schoolers

[Joel Sussman]

6-Feb-2012
Dear Marilyn
Have you looked at Proteopedia 
[www.proteopedia.orghttp://www.proteopedia.org], see e.g.
http://proteopedia.org/w/DNA
http://proteopedia.org/w/Forms_of_DNA
http://www.proteopedia.org/w/HIV-1_protease
http://www.proteopedia.org/w/Proton_Channels
and many more.
n.b. How the green links cause the 3D Jmol images to change so as to reflect 
what the test says.
Pls let me know what you think of these pages.
best regards,
Joel

On 21 Jan 2012, at 00:11, Yoder, Marilyn wrote:

Hi,

I’ve given a couple talks/demos to HS students.  As much as I love enzymes, I 
found it more effective to show structures of proteins binding to other 
biological molecules (not just other proteins).  I typically show 
phosphatidylinositol binding protein (PITP) bound to phosphatidylcholine, 
simply because that is a structure I solved and am comfortable with.  I think 
DNA binding proteins would also be effective.  p53 might be a good candidate, 
especially because of its association with cancer – that will get their 
attention.

I used pymol, it was easy to install on the teachers computer, then they could 
easily use it after I left.

Regards,
Marilyn

Marilyn D. Yoder
Division of Cell Biology  Biophysics
School of Biological Sciences
University of Missouri-Kansas City
5007 Rockhill Rd.
Kansas City, MO 64110
Phone: 816-235-1986

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Whittle
Sent: Friday, January 20, 2012 3:41 PM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] protein structure for high schoolers

Hi-

I am trying to help my former chemistry teacher set up a demonstration of 
protein structure for her class. I'd like to include electron density maps, and 
maybe show an enzyme active site. Are there suggestions from the BB on the 
easiest way to do this? Would pymol be the program of choice, or is there a 
simpler program that could show electron density? Has anyone already created 
such a demonstration they could and have advice on it?

James

Re: [ccp4bb] Efficient way of showing residue conservation

[Joel Sussman]

8-Dec-2011   10:40am
Dear Bostjan
Consurf is also interfaced to Proteopedia, http://www.proteopedia.org,  i.e. 
for all structures that have at least several sequences, one can automatically 
see an evolutionarily colored 3D Jmol image of the structures by just pushing 
the ConSurf button.
See, e.g. http://proteopedia.org/wiki/index.php/1hho
the STRUCTURE OF HUMAN OXYHAEMOGLOBIN AT 2.1 ANGSTROMS RESOLUTION by Boaz 
Shaanan
and click on button Evolutionary conservation:  [show]
best regards,
Joel
On 8 Dec 2011, at 07:39, Bostjan Kobe wrote:

Consurf will do this for you.

Bostjan

---
Bostjan Kobe
NHMRC Research Fellow
Professor of Structural Biology
School of Chemistry and Molecular Biosciences

and Institute for Molecular Bioscience (Division of Chemistry and
Structural Biology) and Centre for Infectious Disease Research


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On 8/12/11 3:26 PM, Yuri Pompeu 
yuri.pom...@ufl.edumailto:yuri.pom...@ufl.edu wrote:

I once saw a figure showing the protein as surface, but instead of having
it coloured by atom type
or potential, it was shown by percent conservation in the family.
Something like red highly conserved, all the way to white, not conserved
at all...
Now, I assume the figure was done by uploading aligned sequnces of
several members of a family, and the colouring
the generated surface accordingly.
Does anyone know a way to do this more elegantly than what I tried doing?
ps. I quit colouring them manually after I remebered my protein was 407
aa long...