Dear Robert, These are great and all I want! Thank you for your PROSMART and it is really a nice tool.
Best, Chen On Sun, Dec 14, 2014 at 5:05 AM, Robert Nicholls <[email protected] > wrote: > > 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 > > >
