Hi Tim, sorry maybe I did not explain myself well. What I am saying is that I have run dock_in_map and real_space_refienement in phenix with the map without having any problems, and for some reason coot thinks that the same map is full of zeros. To me sounds like the map is not full of zeros but coot is not able to read it properly.
Best, Igor El mié., 12 feb. 2020 a las 14:59, Tim Gruene (<tim.gru...@univie.ac.at>) escribió: > Dear Igor, > > you are saying that you used a map full of zeros in phenix. Sounds like a > serious bug in phenix, at least in case phenix produced some non-zero > numbers. > > You may want to report this to the phenix mailing list. > > Best, > Tim > > On Wednesday, February 12, 2020 2:45:35 PM CET Igor > Tasc=?UTF-8?Q?=C3=B3n?= > wrote: > > Hi Paul, > > > > thanks for the quick response. > > I have used the map density histogram and you are right looks like the > map > > is full of zeros, but I honestly don't get why I could use the map in > > phenix... > > > > Igor > > > > On Wed, 12 Feb 2020 12:18:17 +0000, Paul Emsley < > pems...@mrc-lmb.cam.ac.uk> > wrote: > > >On 12/02/2020 11:46, igor tascon wrote: > > >> I am having some problems to open a mrc cryoEM map in coot. I received > > >> the map as a spi volume file and I converted it into a mrc file using > > >> xmipp_image_convert command in scipion to perform some > > >> real_space_refienement, that worked fine. However, when I open in coot > > >> the mrc file the map is loaded (I can see it in the display manager) > but > > >> I can not visualise it. Besides, if I try to change the map counter > > >> level I don't see any number: > > >> map 0 level: nanV ( nanrmsd) > > > > > >It seems as if you have a map full of zeros, sadly. To diagnose, you can > > >use the map density histogram in Coot: Calculate -> Map Tools -> Map > > >Density Histogram > > > > > >Also, you can try mapdump > > > > > >$ mapdump MAPIN converted.mrc > > >END > > > > > >Paul. > > > > > >######################################################################## > > > > > >To unsubscribe from the COOT list, click the following link: > > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 > > > > ######################################################################## > > > > To unsubscribe from the COOT list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
