VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Mar 19 2018 - 07:12:06 CDT

The command invoked without arguments gives you a list of options.

On Mon, Mar 19, 2018 at 8:06 AM, Lizelle Lubbe <LBBLIZ002_at_myuct.ac.za>
wrote:

> 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>
> 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.
>>
>> 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>> 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
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>> the sender in an individual capacity. Please report security incidents or
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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 <+27%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