VMD-L Mailing List

From: Miguel Caro (miguel.caro_at_aalto.fi)
Date: Tue Mar 27 2018 - 02:32:59 CDT

Hi Josh,

Many thanks, this is a very powerful approach.

Miguel

On 2018-03-26 21:59, Vermaas, Joshua wrote:
> 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>
> 

-- 
*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*
Work: *miguel.caro_at_aalto.fi*
Websites: http://mcaroba.dyndns.org http://dospt.org