Hi Kevin, Pavel and others, Since it seems that so far nobody answered the primary question: “Is there any sever available to create electron density maps for cryo-em structures?” So I will do it. The answer is very simple: They do not need to be created, they are available from the pdb!
To give an example: On the RCSB pdb web-site, I searched for entry 5vai. Then under the button “Download Files” I selected “Download EM Map” and downloaded emd_8653.map.gz. As the name suggests, this file needs to be unzipped, but this is trivial. Then in Coot in the “File” pull-down menu, I select “Open Map” to load the map. Next, you may not see anything since to contour level might be too high (when I load the map, the contour level is around 6 rmsd) so you have to scroll down the contour level to see anything. As Marin and Ian pointed out, the maps are very similar to regular electron density maps, probably with the exception that the EM “electron density” maps are influenced by the local charge density. However in coot they behave 100% identical and you can scroll up and down the contour level as you like. Of course, if the authors did not deposit their EM-map, you cannot download it, but the same is true for X-ray structure factors. Happy viewing! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Ian Tickle Gesendet: Montag, 10. September 2018 12:58 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures. Hi Marin I was about to comment on that too but then I realised that Pavel is referring to the map _contours_ (which is what most people using a map visualisation program like Coot actually see). So the contoured map does represent an iso-potential surface. I'm sure Pavel is aware that the original cryo-EM maps are 3-dimensional objects. Cheers -- Ian On Mon, 10 Sep 2018 at 10:49, Marin van Heel <0000057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:0000057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>> wrote: Unfortunately, The problem here lies primarily in the answer given, not so much in the question asked by a newcomer: "1) In cryo-EM maps are not electron density maps but surfaces representing electric potential. " The answer appears to reflect the widespread misunderstanding that EM images (and hence cryo-EM maps) only show the surfaces not the internal density of the complexes we study. In my Imperial College/Leiden University lecture notes, I have always used the below slide to illustrate this point. Cheers, Marin [cid:part1.5DA80E33.F02E5B7D@googlemail.com] On 10/09/2018 01:38, Pavel Afonine wrote: Hi, Is there any sever available to create electron density maps for cryo-em structures? The questions are nonsensical. Here is why: 1) In cryo-EM maps are not electron density maps but surfaces representing electric potential. 2) Creating such a map is essentially carrying on from cryo-EM experiment and obtaining the 3D reconstruction. Are you really sure about what you are asking for? Or, we should create the maps from mmCIF. mmCIF is a file format. It may contain representations of rabbits, boysenberries or some diffraction data. So.. how you think it may be related to cryo-EM, in your particular case? I am particularly interested in those cryo-em structures with high resolution, like 2.6~2.8A. Sure, all are excited about high-res cryo-EM!!! Please give me an education. Sure. One of available universities can do this. Cheers, Pavel ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0P6iRXbkPPZFs&e=> -- ============================================================== Prof Dr Ir Marin van Heel Laboratório Nacional de Nanotecnologia - LNNano CNPEM/LNNano, Campinas, Brazil Skype: Marin.van.Heel email: marin.vanheel(A_T)gmail.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g&e=> marin.vanheel(A_T)lnnano.cnpem.br<https://urldefense.proofpoint.com/v2/url?u=http-3A__lnnano.cnpem.br&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=yJ2hAZdRJw5ICBpLLolSUKM1Dp8cAemaHi6pNIR5Ua4&e=> and: mvh.office(A_T)gmail.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g&e=> -------------------------------------------------- Emeritus Professor of Cryo-EM Data Processing Leiden University -------------------------------------------------- Emeritus Professor of Structural Biology Imperial College London Faculty of Natural Sciences email: m.vanheel(A_T)imperial.ac.uk<https://urldefense.proofpoint.com/v2/url?u=http-3A__imperial.ac.uk&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=MtApOPqE5MmHLkxoyVe7L2FShxxiDiX3rT_V0VZ-CQA&e=> -------------------------------------------------- I receive many emails per day and, although I try, there is no guarantee that I will actually read each incoming email. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0P6iRXbkPPZFs&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg&s=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0P6iRXbkPPZFs&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
