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&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
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Sharing knowledge each other is always very joyful......
Website: http://www.jinkai.org/
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