Dear Garib, Thank you! I will definitely check the website immediately.
Sorry, I forgot to mention that I have been a user for CCP4 since 1998. CCP4 is a great tool and reliable for crystallography, love it! Cheers, Kevin On Mon, Sep 10, 2018 at 10:09 AM Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> wrote: > Dear Kevin, > > You can have access to all these resources (And ccpem, ccp4). They are > free for non-commercial users. > > (You can also have access to any papers you want via https://sci-hub.tw/ > <http://scihub.tw>, it is also free but …) > > If you want to see some of the maps then you can go to emdb at > https://www.ebi.ac.uk/pdbe/emdb/, they have many cryoEM maps and tools to > visualise them. > > If you want to generate maps from coordinates then refmac from ccp4 and > ccpem has an option to generate 3D electrostatic potential from > coordinates. I can send a script for that. > > Regards > Garib > > P.S. In spite of some unusual answers you should not be afraid asking > questions on ccp4 bb. This bulletin board is exactly for this type of > questions. > > > On 10 Sep 2018, at 18:01, Kevin Jin <kevin...@gmail.com> wrote: > > 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...... > > Website: http://www.jinkai.org/ > > > ------------------------------ > > 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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