From samuelfloresc at gmail.com  Wed Mar  6 04:01:11 2013
From: samuelfloresc at gmail.com (Samuel Flores)
Date: Wed Mar  6 04:01:14 2013
Subject: [RNABuilder-help] MMB 2.11 released
Message-ID: <97040865-AFCE-4026-9DAA-C33E87AB2880@gmail.com>

Dear MMB Users,

I have now posted MMB 2.11 for OSX, Windows, and Linux.  The following is from the "What's New" section of the Reference Guide:
In release 2.11 the length units are ?ngstr?ms rather than nanometers, consistent with molmodel?s conventions.  This makes it easier to relate various stiffnesses, energies, and other physical quantities. I have created the rootMobilizer command, which for the first time allows you to connect a chain to ground using a Weld mobilizer (rather than the default Free) ? this reduces the degrees of freedom of the system and saves compute time, for the often-found situation in which one or more chains are fixed to ground. There is also now a constrainChainRigidSegments command, which constrains all rigid segments in a chain either to ground or to a specified residue in the same chain (permitting center of mass motions).  One application of this is to flexibilize an interface and allow (or not allow) center of mass motions, e.g. to equilibrate clashes on that interface. 

I welcome comments on the release.

Happy modeling!

Sam



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From samuelfloresc at gmail.com  Fri Mar  8 08:31:14 2013
From: samuelfloresc at gmail.com (Samuel Flores)
Date: Fri Mar  8 08:31:12 2013
Subject: [RNABuilder-help] Re: pdb write bug in MMB 2.11
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Message-ID: <45433585-7E97-40E8-8D78-AA9396DED2D2@gmail.com>


On Mar 7, 2013, at 11:45 PM, Michael Kuiper wrote:

> Greetings Samuel!
> 
> Please feel free to use any movies I send you any way you like.  I hope to have some more later. 
> 
> I think I've found a bug in 2.11 with regards to writing out large pdb files.  (I'm not quite sure the official way to report this) 
> 

I'm not sure i like how the fora work .. so for now writing to rnatoolbox-help@simtk.org is best

> It seems to me that if there are more than 100000 atoms, we will see a shift in the x,y,z coordinates due to the limitations in the  
> pdb format in the atom number column.   I've written a small python script that corrects these errors for myself but it is easier to do it in the source! 


If your molecules are big you should just see a reduction in the precision.  Can you send me your commands.dat and input structure file?

> 
> The error means that the large molecule trajectories are not displayed properly in vmd and also restarting from a 
> 'last.x.pdb' file also seems corrupted. 
> 
> For large atom numbers I use hexadecimal notation in pdb files. 
> 
> Have to run to a meeting,  
> chat soon! 
> 
> Mike
>