Hi Adiphol, It would have been better to state "several questions" as subjcts, but ok...
1. I would like to show side chain one colour by stick and its backbone by cartoon another colour. So I tried to create to same molecules. One with normal backbone (no1) and the other with backbone and a sidechain stick (no2). And it seem fine the no1 can cover no2 backbone so I have no problem with the unwanted backbone colour on the sidechain that I want but when I tried to ray and png them the colour was change it show only no2 molecule so I have backbone as the sidechain. Does anyone have suggestion on how can I let the no1 shows on no2? Or if you have easier suggestion please don't hesitate to tell.
What about "set cartoon_color" to control the color of the cartoon to show for the backbone? This is completely separated from the atom colors. Alternatively, you may colour everything the way you want for the atoms and then color the c-alpha atoms otherwise (which control the cartoon color). The difference with the first approach is that in the latter the bond with the side chain will be partially coloured as the backbone.
2. How to show hydrogen bond and other interactions?
You can create distance objects to show these things... have a look at the command "dist". Particularly useful with the selection statement "x within r of y".
3. What different between normal 'aline' and 'optAlign'?
optAlign uses a different algorithm and I believe that it can do several molecules at the same time (though I'm not completely sure on this one; Isn't this explained on the Wiki?).
4. How to fix the molecule (lock or make it not move).
You can "disable" an object (which also hides it from view) or you can "mask" a selection, which makes atoms "unpickable". There's also the command "protect". Have a look at the help files for these.
5. Does pymol have any build in procheck or Ramachandran plot?
No.
6. Do you know any website for pymol beginner tutorial? Esp. how to create movie. I tried to read from pymol manual but I'm quite confuse.
No. There must be a "movie.py" around somewhere, written by Kristian Rother and edited by myself, which contains handy movie-making functions.
Thank you cery much. Adiphol
You're cery welcome :p Tsjerk
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-- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
