Hi
If you only want to view the EM volume for a PDB entry then you can do this directly from the PDB entry pages at PDBe. For example: http://pdbe.org/6a5p then click “3D visualisation” on the right hand side. It gets a compressed model and EM volume so will also work on your mobile phone… John From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Zhijie Li Sent: 10 September 2018 20:42 To: [email protected] Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures. Hi Kevin, a) If your goal is merely to display EM maps, then UCSF Chimera, COOT, pymol, etc. should all do. The EM maps are saved in the MRC format (.mrc or .mrcs). Despite a different extension and some minor differences in the headers, the MRC format is essentially the same format as our electron density maps (.ccp4 .map, etc.). Your favorite software for displaying crystallographic maps should work just fine. You will later find that owing to the fact that images are just 2D pixels, movies are series of 2D pixels, maps are (saved as) 3D voxels, the single MRC/CCP4 format can hold many different types of data, including images, stacks of images, movies, maps, masks, etc.. That is why there is often also a .star file (similar to CIF files) that holds information on what is inside one or more MRC files. So be aware of what type of data you are opening. b) To get an idea how cryo-EM single particle data processing works, the minimum you need would be RELION/EMAN2+UCSF Chimera (best for this job), which are all free to everyone. These will get you from the raw EM movies to the EM maps. If you have a computer with enough memory (16GB minimum, the more the better) and an Nvidia 1080TI card (~USD 800? a $150 1050TI can also get you started) you can already solve some EM structures! To do this, you need to get RELION and/or EMAN2 (ideally both): https://www2.mrc-lmb.cam.ac.uk/relion/index.php?title=Download_%26_install http://blake.bcm.edu/emanwiki/EMAN2/Install The reason for the 1080TI card is that it allows the programs to use its 300+ GPU cores to accelerate computations. This capability is provided by Nvidia's CUDA library. You need to download the CUDA 8.0 library from Nvidia. CUDA 8.0 needs to be installed before you compile RELION if you are going to compile it yourself (not quite necessary). At present, EMAN2 only uses GPU at the particle picking step so it is not essential to have a GPU card just for running EMAN2. But classifications and refinements will be very slow (days and weeks) without a GPU. Ideally you should install everything in Linux, such as Ubuntu 16.04 mate. You will also need softwares such as Motioncor2, GCTF, CTFFind, for some jobs in the workflow. Certain settings need to be put as environmental variables in the Linux system. Please figure them out yourself. It will take days to succeed for first-timers. You can start playing by following the tutorials of either RELION or EMAN2 with their own tutorial datasets. These datasets are not really raw data though: they are particle "stacks" that contain the particles picked from the raw micrographs. But starting from there would be the easiest way to learn the essentials. BTW, following the EMAN2 tutorial does not involve using a GPU at all. This might be true for the non-GPU version of RELION too. If you want to start from the very beginning, you can download the 396GB proteasome movie dataset from EMPIAR: https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10025/ On youtube, Grant Jensen has a great series on cryoEM basics. I strongly suggest you to watch at least the part1, especially those having to do with CTF. https://www.youtube.com/watch?v=gDgFbAqdM_c <https://www.youtube.com/watch?v=gDgFbAqdM_c&list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8> &list=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8- Zhijie On 10/09/2018 1:01 PM, Kevin Jin 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 <[email protected] <mailto:[email protected]> > 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:[email protected] <mailto:[email protected]> ] Im Auftrag von Ian Tickle Gesendet: Montag, 10. September 2018 12:58 An: [email protected] <mailto:[email protected]> 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 <[email protected] <mailto:[email protected]> > 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 <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=> &A=1 -- ============================================================== 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 <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=> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <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=> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
