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/ <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 > <mailto: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 > <mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Ian Tickle > Gesendet: Montag, 10. September 2018 12:58 > An: CCP4BB@JISCMAIL.AC.UK <mailto: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 > > > > > > 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 > <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/ <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 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
