VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Mar 26 2018 - 13:59:16 CDT

Hi Miguel,

My preferred method would be to abuse the "user" field, and color by user.

set center [list 0 0 0]
set sel [atomselect top "protein"]
for { set f 0 } { $f < [molinfo top get numframes] } { incr f } {
    $sel frame $f
    set userlist [list ]
    foreach v [$sel get {x y z}] {
       lappend userlist [vecdist $v $center]
    }
    $sel set user $userlist
}

Basically, this approach works whenever the default VMD colorings do not do what you want them to, since you can specify the user field per-frame.

-Josh

On 03/26/2018 11:31 AM, Miguel Caro wrote:

Hello,

I would like to use the radial coloring method using as center a position chosen by me. By default, VMD uses the center of mass of the atoms. How could I use, e.g., the center of my box as the origin?

Regards,

Miguel 

--
Dr. Miguel Caro
Academy of Finland Postdoctoral Researcher
Department of Electrical Engineering and Automation,
and Department of Applied Physics
Aalto University, Finland
Personal email: mcaroba_at_gmail.com<mailto:mcaroba_at_gmail.com>
Work: miguel.caro_at_aalto.fi<mailto:miguel.caro_at_aalto.fi>
Websites: http://mcaroba.dyndns.orglGJ2ANxoi8s0%26m%3DWB-l19X1hIwaBbzGMpBK9AP4_exyXoPAEQ9i2yn9yrU%26s%3Dd__KGmw872P93XXXCS88HhffiTZIi9If4CqdQqba5xU%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C8757e8f5c7134186e55608d5933f5735%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636576822623769903&sdata=%2Bn0aHCtxutyRJWRKAFa6XSBVbSmxldIDfpGwxHMNMo4%3D&reserved=0> http://dospt.orgDWB-l19X1hIwaBbzGMpBK9AP4_exyXoPAEQ9i2yn9yrU%26s%3DMCSH7F7SoVwZSd9k_P9Vngtmrgk5dqGuxbhm0Kdt6lw%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C8757e8f5c7134186e55608d5933f5735%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636576822623769903&sdata=Y%2FOaxtBfTNF%2BWlodrYW29yjam2nsbcEnteIWGPK1yIw%3D&reserved=0>