VMD-L Mailing List

From: Jesper Sørensen (lists_at_jsx.dk)
Date: Tue May 03 2011 - 06:50:35 CDT

Hi again,

 

The post i was referring to (below) was the wrong one. The correct one is there now.

 

Best,

Jesper

 

From: Jesper Sørensen [mailto:lists_at_jsx.dk]
Sent: 3. maj 2011 13:15
To: 'vmd-l_at_ks.uiuc.edu'
Subject: SASA calculation using periodic images?

 

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?

 

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 am more than willing to make the code change myself – but I am not sure how complicated it would be…

 

Best regards,

Jesper

  

--
Jesper Soerensen
Ph.D. student
Dept. Chemistry
Aarhus University, Denmark
 
 
From: John Stone ( <mailto:johns_at_ks.uiuc.edu?Subject=Re:%20%202%20questions%20about%20%22measure%20sasa%22> johns_at_ks.uiuc.edu)
Date: Thu Mar 04 2010 - 10:50:11 CST 
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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 
   <mailto:vmd_at_ks.uiuc.edu?Subject=Re:%20%202%20questions%20about%20%22measure%20sasa%22> 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 < <mailto:johns_at_ks.uiuc.edu?Subject=Re:%20%202%20questions%20about%20%22measure%20sasa%22> 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 
>  <mailto:vmd_at_ks.uiuc.edu?Subject=Re:%20%202%20questions%20about%20%22measure%20sasa%22> 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:  <mailto:johns_at_ks.uiuc.edu?Subject=Re:%20%202%20questions%20about%20%22measure%20sasa%22> johns_at_ks.uiuc.edu Phone: 217-244-3349 
> WWW:  <http://www.ks.uiuc.edu/~johns/> 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:  <mailto:johns_at_ks.uiuc.edu?Subject=Re:%20%202%20questions%20about%20%22measure%20sasa%22> johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW:  <http://www.ks.uiuc.edu/~johns/> http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078