Dear Herman and all ccp4ers, Many thanks for the helps and education from all of you.
I am a fresh beginner in Cryo-EM, and have no access to those resource, like Chimera, Phenix, Rosetta and papers, etc. For me, any answer will be valuable. Please forgive me for asking such a naive question. I highly appreciate your comments and education. Kevin On Mon, Sep 10, 2018 at 5:28 AM <herman.schreu...@sanofi.com> wrote: > 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> 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 > > > > > > 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 > -- Kevin Jin Sharing knowledge each other is always very joyful...... 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