Different contour level of map shown by chimera

3 posts / 0 new

Sat, 08/10/2019 - 19:59

jinru

Hi All,

Anyone has experience on contour level confliction between cisTEM refined map and other software refined maps. For example, two refined maps opened in chimera (they are refined from the same original map just refined seperately by cisTEM or CryoSparc), which were brought to the same sacle by eyes to overlap with each other, but they show very different contour level, say map from CryoSparc show as level 0.01 while map from CisTEM show as level 2. Is that normal? Or what Can I do to make them into same scale.

Thanks!

Jinru

Sun, 08/11/2019 - 20:35

timgrant

Hi Jinru,

The scaling is somewhat arbritrary in EM data. You should be able to normalize both maps to the same value, which will give you similar scaling. You can do that, for example in Chimera by entering the following in the chimera command line :-

"vop scale vol-spec rms 0.03"

Where vol-spec is the number of your model (e.g. #0 if there is only one model).

Thanks,

Tim

Mon, 08/12/2019 - 20:15

(Reply to #2) #3

jinru

Thanka Tim, Super fast reply.

Thanka Tim, Super fast reply. The vop scale command do help to bring back the rms to the same level. Thanks again!

Jinru