VMD-L Mailing List

From: ROPÓN-PALACIOS G. G. (groponp_at_gmail.com)
Date: Sat Sep 23 2023 - 09:16:15 CDT

Thanks Diego,

For help !

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________________________________
De: Diego Gomes <diego.enry_at_gmail.com>
Enviado: Friday, September 22, 2023 1:07:32 PM
Para: Ropón-Palacios G. <groponp_at_gmail.com>
Cc: vmd-l <vmd-l_at_ks.uiuc.edu>
Assunto: Re: vmd-l: <<measure command>>

Adding "-withradii" to "measure minmax" will calculate the bounding box that encloses the entire extents of the molecule, rather than just the atom centers.

For solvating in general you can keep using the standard "measure minmax", that is because "solvate" uses a 2.4A boundary by default.

Friendly,
Diego.

On Thu, Sep 21, 2023 at 5:04 PM Ropón-Palacios G. <groponp_at_gmail.com<mailto:groponp_at_gmail.com>> wrote:
Dear All,

I am trying to measure the exact size that I need to solvate a protein inserted in a membrane, then I came across the simple charmm-gui solution that measures the cross section and adds a padding (according to the user's need), that is, if I measure in the xy e minmax plane of the protein, choose the largest value and add pad (i.e. if it were pad/2 on each side), now when I was looking at the vmd commands, I have the option of using [measure minmax $sel] and [measure minmax $sel -withradii], what is the difference and which of them would be more appropriate when calculating this value for solvating in general.

best,

Geo. 

--
Diego Enry B. Gomes, PhD
Department of Physics
Leach Science Center
Auburn University
dgomes_at_auburn.edu<mailto:dgomes_at_auburn.edu>
+1 (334) 559-4016