Hi Weifei - The first image looks like it was drawn using a vector drawing program like Adobe Illustrator or Inkscape. If you're looking for something automatically generated, two of the first hits from a Google search for "protein interaction diagram" are LigPlot+ (http://pubs.acs.org/doi/abs/10.1021/ci200227u) and LeView (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765711/).
For your second question, to show the residues on chain A within a cutoff distance (e.g. 3.5Å) of chain E, you could use two PyMOL commands like this: show sticks, br. (chain A and donors) within 3.5 of (chain E and acceptors) show sticks, br. (chain A and acceptors) within 3.5 of (chain E and donors) Check out http://www.pymolwiki.org/index.php/Selection_algebra and http://www.pymolwiki.org/index.php/Single-word_Selectors for more info. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On May 17, 2015, at 7:08 AM, weifei <weife...@outlook.com<mailto:weife...@outlook.com>> wrote: Dear all, I am sorry to disturb you. I have two question to ask. The first one is how to draw a residue-DNA interaction picture looks like this one? <Mail Attachment.png> The second question is how to use pymol to select all the residues of a complex that interact with other protein or DNA by polar contacts? 1.I select chain E (DNA) and choose polar contacts --to other atoms in object. <Mail Attachment.png> 2.I can see polar contacts between ChainA(protein) and ChainE(DNA) but I want to show all the connected residue in ChainA. How to choose all the residues that have polar contacts in the Protein. <Mail Attachment.png> <Mail Attachment.png> Thank you so much for your answear. Best, Weifei
