Re: [ccp4bb] Mac M2 chip

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

Re: [ccp4bb] sequence search

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>

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

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,

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

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

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

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

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

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

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

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

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

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

Re: [ccp4bb] Covid-19 crowdfighting platform

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

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

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

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

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

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

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

Re: [ccp4bb] challenges in structural biology

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

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

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).

Re: [ccp4bb] unidentified crescent-shaped electron density

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.

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

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

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

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

Re: [ccp4bb] on the resoution of crystal

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

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

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

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

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,

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

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

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

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

Re: [ccp4bb] Comparison of Water Positions across PDBs

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.

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

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,

Re: [ccp4bb] 3D printing structures?

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

Re: [ccp4bb] About NCS and inhibitors

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

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

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

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.

Re: [ccp4bb] dumb software question

7-Aug-2012 20:30 Dear Paul, Pls see Virtual nanoscopy: Like 'Google Earth' for cell biologists

Re: [ccp4bb] nmr blog

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:

Re: [ccp4bb] Crystal Structures as Snapshots

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”

Re: [ccp4bb] protein structure for high schoolers

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

Re: [ccp4bb] Efficient way of showing residue conservation

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,