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Re: [PyMOL] displaying cartoon helix and sheet in multiple identical chains
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From: Sampson, J. <Jar...@ny...> - 2012-07-11 20:09:48
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Hi Hena - If you're not seeing the effects of the "alter" statement, try issuing the command "rebuild" afterward and see if that helps. Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Jul 10, 2012, at 2:09 PM, Hena Dutta wrote: Hi Jared, As I have only C-alpha coordinates. I used set cartoon_trace, 1 Then I can see a connected smooth ribbon like diagram. I can change the color as follows: color blue resi 10-23 and this working for all identical chains simultaneously. But, the problem is when I am using alter resi 10-23, ss='H' is not working at all. Hena On Tue, Jul 10, 2012 at 1:50 PM, Sampson, Jared <Jar...@ny...<mailto:Jar...@ny...>> wrote: Hi Hena - You can type the following commands in the command line of the pymol graphics window, one at a time. color red, ss h color yellow, ss s color white, ss l+'' If you don't mind the loops being green, you could also use the first preset under the Color menu for your object. [C] > by ss > helix sheet loop (choose the colors you want) Hope that helps, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center 550 First Ave MSB 398 New York, NY 10016 212-263-7898<tel:212-263-7898> http://kong.med.nyu.edu/ On Jul 10, 2012, at 1:39 PM, Hena Dutta wrote: Hi, Sorry, I forgot to mention that, I have only C-alpha coordinates of 60 chains in one pdb file. I have 60 identical chains. Each chain is about 140 residues. Residues from 10-36 is helix and residues from 50-56 is beta sheet. I want to prepare a cartoon diagram displaying helix and sheet in red and yellow color respectively and the rest part(loop) in white. I need to do this for all 60 chains in diagram. Can someone help me? what commands I can use for this? Regards... ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
