From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Jul 20 2010 - 07:58:01 CDT
Try with VegaZZ
there you can define reference frame and calculate rmsd in respect to
On 7/20/2010 4:03 AM, Axel Kohlmeyer wrote:
> On Mon, 2010-07-19 at 21:06 -0400, Ian Stokes-Rees wrote:
> hi ian,
>>> You should also try to figure out what structural changes are giving
>>> rise to the RMSD changes; clustering analysis would be a good way to
>> Does VMD provide tools to cluster conformations? I have done a very
>> rudimentary study of the two primary domains with RMSD relative to about
>> half a dozen points (after aligning all frames around the most static
> our group is currently working on that.
> a first minimal implementation is in the current
> VMD development cvs. the implementation is particularly
> optimized for long (many frames) trajectories.
> i'd be happy to help you get started using it
> and giving us feedback.
> there also is an external plugin that allows to
> visualize the results from other clustering packages.
>> I don't understand why the RMSD isn't reported as exactly zero for the
>> reference frame, and it is unfortunate that the built-in plotter can't
>> have the RMSD range fixed, to make successive plots easily comparable.
> like many of the VMD plugins, it is implemented by somebody
> to satisfy a particular personal need and programmed to the
> taste and capability of the author. typically, people writing
> these plugins are not formally trained as programmers, and
> sometimes not even very experienced (everybody has to start
> somewhere). as you already experienced, keeping the status of
> a plugin in sync with the currently available molecules is
> a particularly difficult to program item. several plugins
> have problems with that, and it took my quite some time and
> feedback from users to program it without (apparent) failures
> for the GUI plugins that i have written.
> feedback is always appreciate, code even more. in general, it
> is a good idea to look up the original author and make direct
> contact, but for some of the older plugins, that might be difficult.
> people move on quite quickly in our business.
>> I can, of course, save the data, import it into another program
>> bit-by-bit, and then plot these with a fixed Y-axis (RMSD, starting from
>> zero), but it would be so much easier if this had the y-axis fixed to
>> start at zero, and the option of auto-scaling the maximum, or fixing the
>> maximum RMSD value.
>> Thanks for your input.
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