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
signature.asc
Description: This is a digitally signed message part.
