[ccp4bb] Postdoctoral position on Circadian Clock in Prof. Andy LiWang’s lab at UCMerced
Dear crystallography community, The laboratory of Prof. Andy LiWang at UC Merced is now recruiting a postdoctoral research associate. Please circulate the link to the ad below. His lab has made a series of groundbreaking contributions in our understanding of molecular circadian clocks using structural biology, and of course has published many high profile papers. I interacted with several alumni from his lab; they all highly recommended the lab. I also enjoyed talking with him twice in person, including once in his lab. Postdoctoral Research Associate in the Structural Biology of a Circadian Clock https://jobs.sciencecareers.org/job/576638/postdoctoral-research-associate-in-the-structural-biology-of-a-circadian-clock/?LinkSource=PremiumListing Many thanks, Steven -- Steven Chou To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] displyaing cryo-EM map in pymol
Hi George, The following commands use to work for me. = # on computer terminal gzip ~/Desktop/pore_loops/myProt.mrc # compress .mrc file into .gz file; it will generate a file named myProt.mrc.gz load the pdb into PyMOL # on PyMOL terminal hide all show cartoon set cartoon_oval_length, 1 # make helices slimmer load ~/Desktop/pore_loops/myProt.mrc.gz, vvv_map, format=ccp4 isomesh vvv_mesh, vvv_map, 0.1 color blue, vvv_mesh = Steve On Thu, Mar 19, 2020 at 4:02 PM George Lountos wrote: > I wanted to ask if anyone has a good reference or tutorial link for > displaying and working with cryo-EM map files in pymol. > > Thanks, > George > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Steve Chou To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Looking at an EM map..
EM maps are electron potential maps, fundamentally different from electron density maps in X-ray crystallography. You might also want to check the Protein Science paper by Jimin Wang & Peter Moore, 2017 http://onlinelibrary.wiley.com/doi/10.1002/pro.3060/abstract EM maps are electron potential maps, fundamentally different from electron density maps in X-ray crystallography. All the best, Steve On Thu, Mar 15, 2018 at 12:09 PM Pavel Afonine <pafon...@gmail.com> wrote: > This is discussed, for example, here: > http://www.pnas.org/content/114/12/3103 > > Also, here I calculated the distribution of map values (scaled in r.m.s.) > for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP > and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of ARG > and LYS (positively charged NH1, NH2, NZ), and all other side-chain atoms. > Clearly side-chain oxygen atoms of ASP and GLU have indeed systematically > weaker density: > > http://cci.lbl.gov/~afonine/tmp/fig.png > > First picture: all maps from EMDB of resolution 3A or better. Second > picture: all maps from EMDB of resolution 3-4A. > > All the best, > Pavel > > On Thu, Mar 15, 2018 at 7:17 AM, Eleanor Dodson < > 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >> I am pig-ignorant about these ,, but this example has negative values as >> well as positive.. >> >> What does this mean? I thought a well phased map would be pretty well all >> positive.. >> >> Eleanor >> > > -- Steve Chou
[ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?
Dear Coot developers and CCP4 list subscribers, The density of my map is not perfect. However, I know where a specific atom should be located. Every time I did real space fitting, the atom and the associated chemical groups in the whole ligand ran away. Is there a way to fix the position of this atom, and let the force field drive the fitting of the rest of the atoms in the ligand? Many thanks in advance! Steve -- Steve Chou
