The problem with your gray/green carbons is that when you create the near901A object, you include residue 901 in that object. Since that residue exists in both objects its just a matter of chance which version pymol chooses to display on top. You can see this by turnig off and back on the display of your 901 object.
unfortunately, you can't simply not pick residue 901 because to exclude it would exclude bonds between residues to either side, I think to get the effect you want here you should create your near901A object then select residue 901 in that object and recolor only the carbons in that selection. hope this helps, -Tzuni Garcia -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net on behalf of Sabuj Pattanayek Sent: Fri 3/11/2005 6:12 PM To: PyMOL-users@lists.sourceforge.net Cc: Subject: Re: [PyMOL] setting a ray resolution then outputting a png doesn't always work Hi, bug 1) I think the problem is with what is saved in the pse. The pse which is giving me these problems does not display the message "I can't display an oversized image". So I decided to recreate the scene from my .pml command file. bug 2) Now this leads to another possible bug. I setup my scene with the .pml file, and do ray 1200,1200 I get the "I can't display an oversized image" message. Then I do png file.png while the message is still on the display window and I get the ray-traced image. But when you open file.png some of the carbon bonds/atoms in stick mode that should be gray (as seen in the display window) are green in the file.png (I tried looking at the image using eog, gimp, & konqueror and all show the same problem). bug 3) using movie -> render frames no longer shows a rendered frame in the display window. Is this the normal behavior, because it used to work? Tried restarted several times and used only the .pml command file and not the "buggy" pse, but no luck. bug 4) When movie -> render frames used to work, I believe it displayed all the colors properly, but the same thing happens as with bug 2 when you output the png (some carbon atoms that are gray in the display window become green in the png file). Here are the contents of the pml file causing all the bugs: load file.pdb hide all bg_color white create 901, (resi 901 and chain a) show sticks, (901) color gray, (elem c) color red, (elem o) color yellow, (elem p,pa,pb,pg) color cyan, (elem s) create near901A, (byres (901 around 3 and chain a)) show sticks, (near901A) color green, (near901A and elem c) create near901B, (byres (901 around 3 and chain b)) show sticks, (near901B) color cyan, (near901B and elem c) set orthoscopic=1 set antialias=1.0 Now here is a very similar .pml file which does not cause all these bugs, the only difference is that in the buggy pml I use the byres and around commands while in this one I explicitly identify which residues I want displayed. load file.pdb hide all bg_color white create 903, (resi 903 and chain a) show sticks, (903) color gray, (elem c) color red, (elem o) color yellow, (elem p,pa,pb,pg) color cyan, (elem s) create near903A, (resi 218,241,89 and chain a) show sticks, (near903A) color green, (near903A and elem c) create near903B, (resi 230,232 and chain b) show sticks, (near903B) color cyan, (near903B and elem c) set orthoscopic=1 set antialias=1.0 The only explanation I can give for the green carbons being outputted rather than gray is that the byres around commands are also coloring the 901 carbon atoms green (since it is itself within 3 angstroms), but in the display window I see it as gray ..strange. Sorry if this is really confusing, but I hope it's some error in the pml and not in pymol. Thanks, Sabuj Pattanayek Matt Franklin wrote: > Sabuj Pattanayek wrote: > >> Hi, >> >> I set smooth lines from the menu, then I did: >> >> set orthoscopic=1 >> set antialias=1 >> ray 1200,1200 >> png file.png >> >> and file.png was the same size as the display window (less than >> 1200x1200), and I could still see jagged lines, as if it outputted >> exactly the quality seen in the display window. I got this to work >> once with a different pse file, tried restarting pymol but I can't get >> it to work anymore. I'm using 0_98beta27 on linux. >> >> Thanks, >> Sabuj Pattanayek >> > > This could be a genuine bug, but did you do anything between the ray > command and the png command? If you click in the graphics window, the > raytraced image goes away and you get the OpenGL image again. Was the > message "I can't display an oversized image" still in the window when > you did the png command? > > - Matt > ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
