VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Mar 19 2018 - 06:41:46 CDT

Volutil is typically included in the VMD plug-ins. Unless you must compile
VMD for some reasons, you have already a copy of volutil inside VMD. I did
give you the Tcl command to load it as well.

Giacomo

On Mon, Mar 19, 2018 at 3:47 AM, Lizelle Lubbe <LBBLIZ002_at_myuct.ac.za>
wrote:

> Hi Giacomo,
>
> Thanks for the response earlier.
> I have contacted the authors and they used their own in-house programs for
> this analysis.
>
> To try your suggestion, I have downloaded VMD volutil and have been trying
> to compile it but have no experience with this.
> I am using Linux Mint and ran the following to get g++ and gnumake:
>
> sudo apt-get update
> sudo apt-get install g++
> sudo apt-get install build-essential
> gcc -v
> make -v
> sudo ln -s /usr/bin/make /usr/bin/gmake
>
> A test shows that the compiler is working. After the last command it
> finds gmake when typing gmake in the volutil-src directory but then gives
> warnings and errors of which the first and last are included here:
>
> Compiling volmap.C
> volmap.C: In member function ‘virtual char* RegOpType::name()’:
> volmap.C:29:25: warning: deprecated conversion from string constant to
> ‘char*’ [-Wwrite-strings]
> char *name() {return "regular";}
> ^
> volmap.C: In member function ‘virtual char* PMFOpType::name()’:
> volmap.C:36:25: warning: deprecated conversion from string constant to
> ‘char*’ [-Wwrite-strings]
> char *name() {return "PMF";}
> ^
> volmap.C: At global scope:
> volmap.C:46:19: error: ‘NULL’ was not declared in this scope
> Operation *RegOps=NULL;
> ^
>
> Makefile:19: recipe for target 'volmap.o' failed
> gmake: *** [volmap.o] Error 1
>
> Do you know how I can fix this please?
>
> I also haven't been able to find any detailed documentation on VMD
> Volutil. Where can I read up on usage of the -clamp and -binmask options
> you mentioned?
>
> Kind regards
>
> Lizelle Lubbe
>
> PhD (Medical biochemistry) candidate
> Department of Integrative Biomedical Sciences
> University of Cape Town
>
> ________________________________________
> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> Sent: 16 March 2018 05:10:31 PM
> To: Lizelle Lubbe
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Occupancy volume quantitation
>
> There isn't a mathematically unique solution, because you have a 3D
> density map that gradually goes to zero.
>
> But to could probably use the volutil command in VMD (package require
> volutil):
> 1. use the -clamp option to set to zero all the values of the map that are
> below a certain threshold;
> 2. use the -binmask option to generate a binary mask of the resulting map--001a114e72b26140af0567c27142--