Re: [ccp4bb] STRAP secondary structure
Dear John you can try Promal3D..it will work hopefully.. bye and take care On Sat, Apr 27, 2013 at 6:27 AM, Mike John perturb-w...@hotmail.com wrote: Hello, Every one, I am preparing a ppt presentation in an emergency style. What I want is a graph of sequence alignment with secondary structure on the top. Using STRAP i can got alignment nicely, but did not know the tips to add secondary structure on top. Anybody of experienced can give me a hand? Tutorial-like instruction would be much helpful. Your kindness is greatly appreciated. Thanks Mike -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] STRAP secondary structure
Dear John, You can you the Prosmart http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/prosmart/documentation.html and also pdbsum can give what you asking for. Thanks Appu On 27 April 2013 02:57, Mike John perturb-w...@hotmail.com wrote: Hello, Every one, I am preparing a ppt presentation in an emergency style. What I want is a graph of sequence alignment with secondary structure on the top. Using STRAP i can got alignment nicely, but did not know the tips to add secondary structure on top. Anybody of experienced can give me a hand? Tutorial-like instruction would be much helpful. Your kindness is greatly appreciated. Thanks Mike
Re: [ccp4bb] STRAP secondary structure
Hope you already finished your presentation, but if not here is anther way. You don't mention whether you have predicted secondary structure or you want to base it on actual structure for one or more of the sequences. If the latter, CCP4's procheck makes such a cartoon in its postscript pages, you can open them in Adobe Illustrator, un-group, select the bits that make up the cartoon, group them, copy and paste into powerpoint. At least I did something like that a long time ago. You can see the graphic style at pdbsum or starting about page 9 of this pdf: http://sb20.lbl.gov/cytbc1/procheck-3h1h.pdf Its the blue/yellow ribbon near the middle of each page. Blue shading indicates surface accessibility, i think. Of couse whie its in illustrator you can change the color sheme and shrink or expand in case your font-size is different. Mike John wrote: Hello, Every one, I am preparing a ppt presentation in an emergency style. What I want is a graph of sequence alignment with secondary structure on the top. Using STRAP i can got alignment nicely, but did not know the tips to add secondary structure on top. Anybody of experienced can give me a hand? Tutorial-like instruction would be much helpful. Your kindness is greatly appreciated. Thanks Mike
Re: [ccp4bb] STRAP secondary structure
Hi john i like espript to do this for instant. here is the link http://espript.ibcp.fr/ESPript/ESPript/ On Fri, Apr 26, 2013 at 7:57 PM, Mike John perturb-w...@hotmail.com wrote: Hello, Every one, I am preparing a ppt presentation in an emergency style. What I want is a graph of sequence alignment with secondary structure on the top. Using STRAP i can got alignment nicely, but did not know the tips to add secondary structure on top. Anybody of experienced can give me a hand? Tutorial-like instruction would be much helpful. Your kindness is greatly appreciated. Thanks Mike -- Vandna Kukshal Postdoctral Research Associate Dept. Biochemistry and Molecular Biophysics Washington University School of Medicine 660 S. Euclid, Campus Box 8231 St. Louis, MO 63110
[ccp4bb] STRAP secondary structure
Hello, Every one, I am preparing a ppt presentation in an emergency style. What I want is a graph of sequence alignment with secondary structure on the top. Using STRAP i can got alignment nicely, but did not know the tips to add secondary structure on top. Anybody of experienced can give me a hand? Tutorial-like instruction would be much helpful. Your kindness is greatly appreciated. Thanks Mike
