VMD-L Mailing List

From: Jesper Sørensen (lists_at_jsx.dk)
Date: Tue May 03 2011 - 08:38:29 CDT

Hi Alex,

Thanks for the suggestions and clarifying the problems.
I can see there are a lot of issues to deal with. I'll try to think, whether
there is a better way to express the information that I want from the
simulations.

Best regards,
Jesper

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
Sent: 3. maj 2011 15:32
To: Jesper Sørensen
Subject: Re: vmd-l: SASA calculation using periodic images?

jesper,

please always cc: the list when replying. thanks.

2011/5/3 Jesper Sørensen <lists_at_jsx.dk>:
> Hi Alex,
>
> Thanks for the reply. Sorry about pasting the wrong old-post in. It
> was an old message from John Stone, who hinted that he would perhaps
> make some changes to the code to handle these periodic images in SASA
calculations.
>
> Perhaps you can tell me if I understand this correctly.
> SASA is defined in AtomSel.py, which means the calculation is tied in
> with

AtomSel.py is just a wrapper for the internal VMD code.

> the way selections in vmd is handled. Since there is no way (that I
> know of) to select atoms in the periodic images without also selecting
> them in the "original" image, that is where the problem arises to begin
with?

there are a number of issues here.

- you have to identify and define individual clusters with PBC
- you have to make the SASA calculations work with PBC
- you have to figure out, whether the SASA is a good measure
  at all for clusters that are self-assembling. what about radius
  of gyration, for example?
- you have to figure out a good way to summarize your results
  and hand it back the VMD script level.

all of that requires some effort and this gets more complicated by the fact
that VMD in its original conceptions assumes to be processing one huge
protein immersed in a block of small water molecules and perhaps a few ions.

> So, as you said, I will have to re-write the way atoms are selected in
> vmd to be able to calculate what I am aiming for?

i don't know exactly what you have to do. this is a complex problem and i am
not even convinced that VMD is the best tool to do this unless you are
comfortable hacking complex legacy c++ code.
i would recommend before going full throttle to first perhaps construct a
test system that has no PBC issues and test if the kind of analysis that you
want to do will be giving you meaningful answers and try to see if there are
alternate ways to get something equivalent more easily.

cheers,
    axel.

>
> Best regards,
> Jesper
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of Axel Kohlmeyer
> Sent: 3. maj 2011 14:11
> To: Jesper Sørensen
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: SASA calculation using periodic images?
>
> 2011/5/3 Jesper Sørensen <lists_at_jsx.dk>:
>> Hello all,
>>
>>
>>
>> I want to calculate the solvent accessible surface area in a system
>> with many monomers that aggregate. The aggregation occurs across the
>> periodic images and therefore the wrapping of the system gets a
>> little
> complicated.
>>
>>
>>
>> Is there a way to make the SASA script/plugin in vmd take the
>> periodic images into account when calculating the SASA of certain
surfaces?
>
> no. at least not without significant modification of the VMD source code.
>
>>
>> I found the below post on the VMD list from March of 2010, but I
>> haven’t seen any changes to the SASA script since. Does anybody have
>> an updated version that includes the periodic images?
>
> i don't understand. the quoted post is from yesterday and has nothing
> to do with SASA.
>
>> I am more than willing to make the code change myself – but I am not
>> sure how complicated it would be…
>
> anything with PBC inside VMD is somewhat complicated.
>
> cheers,
>    axel.
>
>
> From: John Stone (johns_at_ks.uiuc.edu)
> Date: Thu Mar 04 2010 - 10:50:11 CST
> Next message: Filippo Federici: "Re: CUDA issues"
> Previous message: John Stone: "Re: CUDA issues"
> In reply to: Edward Lyman: "Re: 2 questions about "measure sasa""
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
> attachment ]
>
> Hi,
>  If you're getting surface area due to periodic boundaries, the
> easiest solution (at present) would be to replicate the structure
> across the boundary before doing the calculation, or use the PBC tools
> plugins to unwrap the parts of the structure crossing the boundary. I
> hope to implement
>
> handling of periodic cells in the SASA calculation, but it I haven't
> started
>
> working on it yet.
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Fri, Feb 26, 2010 at 12:44:59PM -0700, Edward Lyman wrote:
>> Hi again,
>>
>> The -restrict option is working very well, except that I have
>> contributions coming from the boundaries of the box that the sasa
>> algorithm thinks are exposed to the solvent. Is there some simple way
>> to eliminate those contributions? The only way that comes to mind is
>> to include an extra layer of lipids around the edges from the
>> periodic image,
>
>> and then use restrict to eliminate that layer. maybe there is a
>> clever atom selection taht will do the trick...
>>
>> any ideas are greatly appreciated!
>>
>> Ed
>>
>> On Thu, Feb 25, 2010 at 4:00 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>>
>> Hi,
>> Sorry for being slow to reply, I've been swamped finishing papers and
>> getting some new code up and running...
>>
>> For 1) you would feed the list of points into 'draw' commands to draw
>> them however you like.
>>
>> For 2) yes, the -restrict command can be used to prevent part of the
>> structure from contributing. You can visualize the points to help you
>> figure that out.
>>
>> Let us know if you need more help.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>> On Wed, Feb 17, 2010 at 01:40:53PM -0700, Edward Lyman wrote:
>> > Hi all,
>> >
>> > 2 questions about vmd's built in sasa calculator:
>> >
>> > (1) how do i visualize the surface data after i store it using the
>> -points
>> > option?
>> > (2) will the following command measure for me the sasa for $subsel,
>> > excluding the surface area of $subsel that is occluded by $sel?
>> >
>> > measure sasa [atomselect top "$sel"] -restrict [atomselect top
>> "$subsel"]
>> >
>> > Thanks!
>> > Ed
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
>> Institute for Advanced Science and Technology University of Illinois,
>> 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
> Institute for Advanced Science and Technology University of Illinois,
> 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>
> 

--
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science Temple University,
Philadelphia PA, USA.