Hi Enrico, The fact that ChimeraX loses the surface transparency when you play the trajectory is a bug. I'll look at whether that is easy to fix. But for now you can set the transparency each frame using command the perframe command. Here's the example from Elaine's email using perframe. open 1plx coordset true perframe "coord #1 $1 ; surf close ; surf update false ; transparency :TYR 75" frames 80 The perfame command runs the sequence of commands separated by semicolons. So it first sets which time point of the trajectory is shown. The $1 is replaced with the frame number 1, then 2, then 3, up to 80 in this example. Then the commands close the previous surface and create a new one with "update false" which means don't recompute the surface when the atoms move. And the last command sets the transparency. This sequence is run 80 times, before each frame is drawn. The two surface commands are needed because of an obscure technical issue. The molecular surface normally gets recomputed when the atoms move just before the frame is drawn, which would be after the transparency command and that would undo the transparency. So we need the "surface update false" to prevent that from happening, and since we are no longer updating the surface we need the "surface close" to remove the old non-updating surface. Here is the bug report I made for this problem https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10282 Tom
On Dec 4, 2023, at 3:32 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users !
I am working on molecular visualization of membrane system from the md trajectory loaded in the Chimera-x using the open coordset true command.
The issue is with the surface representation of the membrane: transparency :OL,PA,PE,PC 80 target s which are applied only on the current frame (not on the whole trajectory).
Also when I try to make a movie of the system the presence of the surface does slow down everything. Which options could be useful e.g. to decrease the quality of the surface representation ?
Many thanks in advance
Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/