Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li Sent: 10 September 2018 20:42 To: CCP4BB@JISCMAIL.AC.UK 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=PL8_xPU5epJdctoHdQjpfHmd_z9WvGxK8> =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 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 tri
Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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 <057a89ab08a1-dmarc-requ...@jiscmail.ac.uk <mailto:057a89ab08a1-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=1 <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0P6iRXbkPPZFs=> -- == 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=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g=> marin.vanheel(A_T)lnnano.cnpem.br <https://urldefense.proofpoint.com/v2/url?u=http-3A__lnnano.cnpem.br=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=yJ2hAZdRJw5ICBpLLolSUKM1Dp8cAemaHi6pNIR5Ua4=> and: mvh.office(A_T)gmail.com <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g=> -- Emeritus Professor of Cryo-EM Data Processing Leiden University -- Emeritus Professor of Structural Biology
Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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 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 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 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 < >> 057a89ab08a1-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 il
Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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 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 <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 > <057a89ab08a1-dmarc-requ...@jiscmail.ac.uk > <mailto:057a89ab08a1-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. > >
Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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 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 < > 057a89ab08a1-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=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8
Re: [ccp4bb] Electron density maps for Cryo-EM structures.
Dear Kevin, Are you referring to "generating a map" from the model (PDB coordinates) generated from tracing the chain in the ab-initio EM map? Best wishes, Natesh On Mon, 10 Sep 2018 at 09:58, Kevin Jin wrote: > Dear All, > > Is there any sever available to create electron density maps for cryo-em > structures? Or, we should create the maps from mmCIF. I am particularly > interested in those cryo-em structures with high resolution, like 2.6~2.8A. > > Please give me an education. > > Thanks, > > Kevin > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- -- "Live Simply and do Serious Things .. " - Dorothy Mary Crowfoot Hodgkin OM, FRS "In Science truth always wins" - Max Ferdinand Perutz OM FRS -- Dr. Ramanathan Natesh Assistant Professor, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram (IISER-TVM), Maruthamala P.O., Vithura, Thiruvananthapuram, 695551, Kerala, India nat...@iisertvm.ac.in http://www.researcherid.com/rid/C-4488-2008 ORCID: http://orcid.org/-0002-1145-5962 https://publons.com/author/1520837/ramanathan-natesh#profile http://faculty.iisertvm.ac.in/natesh Office Ph. 0091- 471-2778087 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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 <057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:057a89ab08a1-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=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=A66BPdK7455wfEqkW7nlTOFIrLwyiZ0P6iRXbkPPZFs=> -- == 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=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=dS2VEfbgNj0-C_rK4Gz-4eXTJsZj7sQEp5cuMvr1i5g=> marin.vanheel(A_T)lnnano.cnpem.br<https://urldefense.proofpoint.com/v2/url?u=http-3A__lnnano.cnpem.br=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=oyq4_tjHvYKRzK3yN_rOpIQo6sflk9725vR5aINqpHg=yJ2hAZdRJw5ICBpLLolSUKM1Dp8cAemaHi6pNIR5Ua4=> and: mvh.office(A_T)gmail.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__gmail.com=DwMFaQ=Dbf
[ccp4bb] AW: [ccp4bb] Electron density maps for Cryo-EM structures.
yes, but irrespective of how much one knows or thinks one knows, one should avoid being gratuitously offensive. cheers jon 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: 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 <057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:057a89ab08a1-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=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<http://gmail.com> marin.vanheel(A_T)lnnano.cnpem.br<http://lnnano.cnpem.br> and:mvh.office(A_T)gmail.com<http://gmail.com> -- 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<http://imperial.ac.uk> -- 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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Electron density maps for Cryo-EM structures.
Great, thanks! On Sun, Sep 9, 2018 at 9:49 PM Pavel Afonine wrote: > P.S.: all questions are welcome of course, no labeling. It's just some of > them are so orthogonal to common sense that answers my be such as well. > Best, > Pavel > > On Sun, Sep 9, 2018 at 9:38 PM 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 >> >> -- 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=1
Re: [ccp4bb] Electron density maps for Cryo-EM structures.
P.S.: all questions are welcome of course, no labeling. It's just some of them are so orthogonal to common sense that answers my be such as well. Best, Pavel On Sun, Sep 9, 2018 at 9:38 PM 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=1
Re: [ccp4bb] Electron density maps for Cryo-EM structures.
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=1
[ccp4bb] Electron density maps for Cryo-EM structures.
Dear All, Is there any sever available to create electron density maps for cryo-em structures? Or, we should create the maps from mmCIF. I am particularly interested in those cryo-em structures with high resolution, like 2.6~2.8A. Please give me an education. Thanks, Kevin To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Electron Density Maps
Dear Pascal, 2009/8/10 Pascal Egea pas...@msg.ucsf.edu: Dear All, I am currently carrying the refinement of a structure and comparing the results obtained in Refmac, Phenix and CNS. While Phenix and Refmac write maps and their corresponding coefficients in mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the corresponding Fo-Fc map as written by CNS does not show positive and negatives peaks. There is density but it does not look like why I would expect for a Fo-Fc map. Why is that? Is your map read as an Fo-Fc map? I guess not... I believe there is a way to tell COOT that you want to load you CNS map as a difference map. This section http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC160 of the user manual might explain better. Hope this helps, Folmer Fredslund
Re: [ccp4bb] Electron Density Maps
If you want to display CNS maps in Coot and have them on the right scale, then you need to do one of two things. Either: 1. Don't use the map file, use the reflection file containing the map coefficients, or 2. Change the setting in CNS which controls the extent of the output map. Instead of outputting a map covering a single molecule, you need to output a map covering a whole asymmetric unit (or if you prefer a whole unit cell). The Xplor maps output by CNS are output in O mode, not Coot mode, by default. This is due to a fundamental difference in understanding what a map is between programs which work crystal space (e.g. Coot, Quanta, XtalView) and those which don't. Kevin Pascal Egea wrote: Dear All, I am currently carrying the refinement of a structure and comparing the results obtained in Refmac, Phenix and CNS. While Phenix and Refmac write maps and their corresponding coefficients in mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the corresponding Fo-Fc map as written by CNS does not show positive and negatives peaks. There is density but it does not look like why I would expect for a Fo-Fc map. Why is that? I am also surprised by the differences between maps and their contouring levels between Refmac/Phenix and CNS. Is the way to scale ED maps different between those programs? Can differences in the way to perform bulk solvent correction account for those differences? Thanks in advance for your suggestions. Pascal Egea
Re: [ccp4bb] electron density maps in Coot vs O / Pymol
I use this to get the same maps: http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcover http://xanana.ucsc.edu/Library/init/zsh/local-functions/xtal/mapcoverdiff I used zsh but I think it should work with current versions of bash. mac minista wrote: Dear all, I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. I have used the following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT. The .o map file was generated using FFT, MAPMASK and MAPMAN. I want to know why I am not getting identical maps, and if there is a solution to avoid this problem then I would really appreciate your help. With regards Mac - Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains.
Re: [ccp4bb] electron density maps in Coot vs O / Pymol
On Wed, 2007-02-14 at 07:59 -0800, mac minista wrote: Dear all, I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. I have used the following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT. The .o map file was generated using FFT, MAPMASK and MAPMAN. I want to know why I am not getting identical maps, and if there is a solution to avoid this problem then I would really appreciate your help. Well, the devil is in the detail. a MAPMAN map in O vs a REFMAC MTZ in Coot. Somewhat apples and oranges. Stating the obvious: the griding and contour level may well be different. The contouring algorithms certainly are. How about a Coot/Refmac + Mapman map in O or a MAPMAN map in Coot? Then the differences will be more clear? What do you get if you overlapmap ADD 1 -1 and look at differences there?
Re: [ccp4bb] electron density maps in Coot vs O / Pymol
Hi Mac, I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. I have used the following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT. The .o map file was generated using FFT, MAPMASK and MAPMAN. I want to know why I am not getting identical maps, and if there is a solution to avoid this problem then I would really appreciate your help. There could be any number of reasons; which is more likely would depend on the level of differences between the maps. In (rough) level of significance, the ones I can think of are: 1. inputs - are your scripts using the same columns as coot (if I'm understanding correctly that coot is calculating the maps on the fly for you)? 2. FFT specific stuff - are both maps being calculated using the same gridpoints and FFT algorithm? 3. contouring issues - the graphics programs may be using different contouring algorithms; if you're contouring by sigma/rms deviation, then this can be affected by the size of the region used for rms determination (are the maps the same size?). Map normalization may also be an issue. 4. Computational noise - I've been able to get non-identical maps just by changing the variable precision (identical input files) used by the programs. The differences are minimal, but observable. I'm assuming that you're using a single system for both maps, otherwise there could be additional issues (although these should also be relatively minor). One thing that shouldn't make a difference - O can directly read ccp4 formatted maps, so using FFT with xyzlim asu and reading in O with qmap or fmap should let you skip over the mapmask/mapman steps. As far as your specific case, run down the list of things that could have an effect (there may be other issues that I'm forgetting), and eventually you should find where the differences are. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [ccp4bb] electron density maps in Coot vs O / Pymol
I am guessing it is a difference in normalization, but I would love to hear a definitive answer from someone. Steve -Original Message- From: CCP4 bulletin board on behalf of mac minista Sent: Wed 2/14/2007 10:59 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] electron density maps in Coot vs O / Pymol Dear all, I have noticed that going from refmac 5 (script) to generate fo-fc and 2fo-fc maps in O / Pymol once and Coot in the other, the outcome is not exactly the same electron density maps-I mean some differences are seen. I have used the following columns in Coot (latest version): FOFCWT, PHFOFCWT and 2FOFCWT, PH2FOFCWT. The .o map file was generated using FFT, MAPMASK and MAPMAN. I want to know why I am not getting identical maps, and if there is a solution to avoid this problem then I would really appreciate your help. With regards Mac Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites http://farechase.yahoo.com/promo-generic-14795097;_ylc=X3oDMTFtNW45amVpBF9TAzk3NDA3NTg5BF9zAzI3MTk0ODEEcG9zAzEEc2VjA21haWx0YWdsaW5lBHNsawNxMS0wNw-- to find flight and hotel bargains. -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. --
Re: [ccp4bb] electron density maps in Coot vs O / Pymol
Hi, thank you for your suggestions, the difference I am seeing in the maps is mainly with the Fo-Fc maps i.e. what appears in coot does not always appear in O/Pymol. Here are the scripts for FFT and MAPMASK: FFT #!/bin/sh set -e fft hklin model.mtz mapout fofc_f.map eof title fofc map labin F1=FOFCWT PHI=PHFOFCWT end eof # fft hklin model.mtz mapout 2fofc_f.map eof title 2fofc map labin F1=2FOFCWT PHI=PH2FOFCWT end eof MAPMASK #!/bin/sh set -e # Run mapmask after fft to extend the map mapmask mapin fofc_f.map mapout fofc_fext.map \ xyzin model.pdb eof border 2.0 eof # mapmask mapin 2fofc_f.map mapout 2fofc_fext.map \ xyzin model.pdb eof border 2.0 eof I will try and get some figures. Regards Mac Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html
