[Chimera-users] lines thinner in images; trajectory clustering method and visualization

[Elaine Meng]

Hi Natesh,
(A) This is a common issue discussed in previous posts, for example 
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-October/008025.html>

...and in the “Tips for Saving Images"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#sstip>

Basically, your system can only draw a line up to a certain pixel width.  When you save a high-res image (more pixels than shown in the Chimera window), especially with supersampling (which makes the initial image NxN times larger than the final image), what you get in the final image  may be proportionally thinner than in the Chimera window.

You can see what final width is possible by choosing menu: File… Save Image. The resulting dialog will report (near the bottom) the maximum attainable linewidth in the final image given the requested image dimensions and the supersampling level. Decreasing the supersampling level and/or image dimensions will increase the linewidth in the final saved result.  Generally supersampling is nice because it smooths edges (pixel stairsteps less visible), so I would first see if 2x2 supersampling solves the problem before turning it off (setting it to 1x1).

The movie-saving dialog from MD Movie also has this supersampling option, but it does not report what the final linewidth will be… that’s why I suggest looking at the main save-image dialog to decide what level to use, even though you won’t be using that dialog directly.

(B) the clustering methodology is described in the paper cited in the Ensemble Cluster manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html>

An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Kelley LA, Gardner SP, Sutcliffe MJ. Protein Eng. 1996 Nov;9(11):1063-5.
<http://peds.oxfordjournals.org/content/9/11/1063.long>  (free full text)

I agree it could be useful if the clusters and the inter-cluster distances could be written out to the Log or a text file, or even exported to Cytoscape for network visualization, but we have not implemented any of those, sorry.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 28, 2016, at 6:36 AM, Natesh Singh <a1468984 at unet.univie.ac.at> wrote:
> 
> Dear Elaine,
> Thanks for help. The script worked out fine.
> 
> I have another two queries:
> A. When I run the per frame script and record the movie, then I could not see the original h-bond width in the movie which I had changed from pseudobondgroup panel (line width: 5.0 from 1.0), though line style from bold to dashed could be seen in the movie.
> The new width is properly displayed in the chimera window but not reflecting in the movie.
> 
> B. I would like to know how chimera is clustering the trajectory.., on what basis the number of clusters are obtained and what cut off is used during the process. I think based on pairwise rmsd matrix it's doing the clustering and cut off is used to identify the unique clusters. I could not find the same in the documentation so it would be nice if could shade some light on this. I was thinking if chimera could also give cluster map of the trajectory, where we could see different clusters and distances between them.
> 
> Best regards,
> Natesh
> Uni. Wien