[Chimera-users] resmap

R.I.Koning at lumc.nl R.I.Koning at lumc.nl
Thu Nov 5 12:56:42 PST 2015

Dear Tom,

Thanks for the tip. Deleting the optional part of the script and rerunning it solves the problem!

Best regards,


From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Date: Friday 30 October 2015 18:23
To: Roman Koning <r.i.koning at lumc.nl<mailto:r.i.koning at lumc.nl>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] resmap

Hi Roman,

  I tried ResMap and it produced a Chimera command script for my map emd_1007.map with file name


That script tries to do both the surface coloring and the plane slicing animation.  First it does the surface coloring, then it immediately shows only a single plane of the map so you can’t see the surface.  So the script is messed up.  If you make a copy of the script, delete all the lines below the one that says OPTIONAL: ResMap Slice Animation, then start Chimera (with no data open) and open the new edited script it will show the colored surface.  You would have to talk to the author of ResMap, Alp Kucukelbir to get this fixed.


Here is what the Chimera script produced by ResMap looks like for reference:

# Color a map by local resolution computed by ResMap
#   Initial version of script courtesy of Tom Goddard, UCSF.

# Open both volumes and hide the ResMap volume.
set bg_color white
open #0 emd_1007.map
open #1 emd_1007_resmap.map
volume #1 hide

# Color the original map with the values from the ResMap output.
scolor #0 volume #1 cmap 12.40,blue:14.42,cyan:16.44,green:18.46,yellow:20.48,orange:22.50,red:22.51,gray

# OPTIONAL: ResMap Slice Animation.

# Show midway slice of the original map with contour level below the minimum map value.
volume #0 planes z,65 step 1 level -1 style surface

# Show a smooth transparent contour surface indicating the structure boundaries.
vop gaussian #0 sDev 5 model #2
volume #2 level 0.02 step 1 color .9,.7,.7,.5

# Zoom out a bit and tilt to a nice viewing angle.
turn x -45
turn y -30
turn z -30
scale 0.5

# Cycle through planes from N/2 to 4N/5 up to N/5 and back to N/2.
volume #0 planes z,65,104,0.25
wait 156
volume #0 planes z,104,26,0.25
wait 312
volume #0 planes z,26,65,0.25

On Oct 30, 2015, at 8:24 AM,  wrote:

I want to use the colors representing resolution in Resmap to color the surface of my map. From what I understand from the documentation the script that automatically runs after Resmap is finished and “… color the surface of your input map with the results of ResMap…”. This last thing does not happen.  Though this script seems to run (I see a slice depicting the remap (in 2D) moving back and forth in chimera somehow only a map with 1 slice opens in Chimera afterwards and I cannot use the resolution color coding for my surface. Should some sort of 3D file be generated that can be used to do this via Surface color or should the coloring be on the surface map by default? Both is not possible now.

Best regards,

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