VMD-L Mailing List

From: Lizelle Lubbe (LBBLIZ002_at_myuct.ac.za)
Date: Mon Mar 19 2018 - 07:06:41 CDT

Okay thanks, I appreciate your help
It’s not in the gui plugins so I’ll use the tcl command.

As mentioned earlier, I haven’t been able to find documentation on the use of this plugin.
Would you mind please explaining how I would proceed after loading the structure and .dx map?

Kry Outlook vir iOS<https://aka.ms/o0ukef>
________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Monday, March 19, 2018 1:41:46 PM
To: Lizelle Lubbe
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Occupancy volume quantitation

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<mailto: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<mailto:giacomo.fiorin_at_gmail.com>>
Sent: 16 March 2018 05:10:31 PM
To: Lizelle Lubbe
Cc: vmd-l_at_ks.uiuc.edu<mailto: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.

volutil doesn't seem to have an option to compute the integral of a map, but it shouldn't be difficult to open the masked map in another script (a .dx is a text file with comments at the top) and just count the 1's and 0's.

You should also contact the corresponding author of the paper to ask how to reproduce their results. They are not required to give you step-by-step instructions, but they must tell you what they used.

Giacomo

On Fri, Mar 16, 2018 at 10:31 AM, Lizelle Lubbe <LBBLIZ002_at_myuct.ac.za<mailto:LBBLIZ002_at_myuct.ac.za><mailto:LBBLIZ002_at_myuct.ac.za<mailto:LBBLIZ002_at_myuct.ac.za>>> wrote:
Hi

I have simulated the behaviour of 2 glycoproteins (homologs) and would like to compare the volume occupied by sugars at each glycan site between the two proteins. This would identify changes in the glycans' dynamic range due to unique protein interactions etc.

I’ve used VMD's Volmap extension to produce and visualize .dx occupancy volmaps and visually observed differences.
Is there any way in which I can calculate exact volume values per glycan in cubic angstroms to quantitatively compare? Haven’t been able to figure out a way to do this.

I would like an output like fig 2 in Yang et al 2017 (doi:10.1038/s41598-017-04532-9) but they don't mention the software used in calculating the volume

Kind regards

Lizelle Lubbe
PhD Chemical Biology
University of Cape Town
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Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin
Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111<tel:%2B27%2021%20650%209111>. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.
--
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin
Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/page/report-an-incident.php.