Hi Chen, > could anybody suggest me an easy way to generate the spectrum bar for the > color-coded residue-wise scores? Generating a spectrum bar in Pymol seems > nontrivial to me…
There are some HTML/javascript files that will allow you to reproduce the horizontal and vertical legends seen in the ProSMART publications. I've made them available from our website, but here's a direct link: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/prosmart/docs/prosmart_legends.tar.gz You can open the "legend.html" file in a web browser, then zoom in and/or export to whatever format you want. You can edit the "legend.css" file if you want to adjust the text font. You can edit the values in the top of the "legend.js" file in order to change the legend scale and colours so that they correspond to your ProSMART run (if you have adjusted these parameters). I hope this is an acceptable solution for you. Let me know if you need further help with this. > BTW, here is a rather unrelated question. what does the white color represent > (in default color setting)? Does it mean the residues that are not included > in the analysis? You are correct. The white colour represents residues that were not included in the analysis - these were not matched to any residues in the other model. > I might be careless, but I failed to find a documentation for this. I'd say that the best resource for providing practical usage info is the tutorial that's available from our website (see part 2 of the tutorial): http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ I'll try to update and expand on the documentation soon to help clarify such issues. Best regards, Rob -- Dr Robert A Nicholls Career Development Fellow MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH 07729 202999 On 13 Dec 2014, at 23:55, Chen Zhao wrote: > Hi all, > > Sorry for bothering you with this small technical question. I just got to > know PROSMART as a handy local structural alignment tool. But could anybody > suggest me an easy way to generate the spectrum bar for the color-coded > residue-wise scores? Generating a spectrum bar in Pymol seems nontrivial to > me... > > BTW, here is a rather unrelated question. what does the white color represent > (in default color setting)? Does it mean the residues that are not included > in the analysis? I might be careless, but I failed to find a documentation > for this. > > Thank you so much in advance! > > Best, > Chen
