From: Yoder, M. <Yo...@um...> - 2006-02-15 22:37:07
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Hi all, =20 There is a beautiful ball-and-stick image on pymol-wiki that I am trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick). =20 The wiki image has grey bonds and light blue balls for carbon, dark blue for nitrogen, and red balls for oxygen. My problem is that all my bonds and balls are the same color, and I can't figure out how to make the bonds a grey color, distinct from the atom ball colors. And I'm trying to script this. =20 Part of my current script is below. I'm superimposing three molecules, and showing sidechain atoms for three residues (which are Args). The carbons from each molecule I want to be distinct colors, but I want the bonds in all to be grey. The ball-and-stick is displaying nicely, I just don't know how to color the thing. I suspect my problem is from earlier commands in coloring the whole molecule, and the selections below are showing these same colors. =20 --------------- what I'm currently doing ------------ =20 select ec_RR, resi 191-192+208 and eccdtb select hd_RR, resi 249-250+232 and 1sr4b select aa_RR, resi 249-250+232 and aacdtb =20 cmd.show("sticks","ec_RR+hd_RR+aa_RR") cmd.show("spheres","ec_RR+hd_RR+aa_RR") set stick_radius=3D0.2 set sphere_scale=3D0.25 ----------------end----------------- =20 Hope this is clear, Marilyn =20 Marilyn D. Yoder Division of Cell Biology and Biophysics University of Missouri-Kansas City 5007 Rockhill Rd. Kansas City, MO 64110-2499 phone: 816-235-1986 fax: 816-235-1503 =20 |
From: <Mat...@im...> - 2006-02-15 23:30:09
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pym...@li... wrote on 02/15/2006 05:36:51 PM: > Hi all, > > There is a beautiful ball-and-stick image on pymol-wiki that I am > trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick). > > The wiki image has grey bonds and light blue balls for carbon, dark > blue for nitrogen, and red balls for oxygen. My problem is that all > my bonds and balls are the same color, and I can't figure out how to > make the bonds a grey color, distinct from the atom ball colors. > And I'm trying to script this. > Hi Marilyn - You probably can't do it all with one object. Create another object which is a duplicate of the one you're working with, then show spheres on object #1 and sticks on object #2. You can then color the balls and the sticks separately, since each object gets its own set of colors. For example: PyMOL>create obj1, 1FLT and chain w Selector: found 797 atoms. Executive: object "obj1" created. PyMOL>create obj2, 1FLT and chain w Selector: found 797 atoms. Executive: object "obj2" created. PyMOL>color gray, obj2 Executive: Colored 797 atoms and 1 object. PyMOL>color green, obj1 Executive: Colored 797 atoms and 1 object. PyMOL>show spheres, obj1 PyMOL>show sticks, obj2 PyMOL>set stick_radius, 0.1 Setting: stick_radius set to 0.10000. PyMOL>set sphere_scale, 0.25 Setting: sphere_scale set to 0.25000. This gives a ball-and-stick of one chain where the balls are all green and the sticks are all gray. Modify as needed.... - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you. |
From: Michael G. L. <ml...@um...> - 2006-02-20 17:23:31
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set stick_color, grey the image looks a little more like set stick_color, grey90 but I can't quite tell. -michael -- www.umich.edu/~mlerner | _ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bring It On| / \ | mlerner@umich On Wed, 15 Feb 2006, Mat...@im... wrote: > pym...@li... wrote on 02/15/2006 05:36:51 PM: > >> Hi all, >> >> There is a beautiful ball-and-stick image on pymol-wiki that I am >> trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick). >> >> The wiki image has grey bonds and light blue balls for carbon, dark >> blue for nitrogen, and red balls for oxygen. My problem is that all >> my bonds and balls are the same color, and I can't figure out how to >> make the bonds a grey color, distinct from the atom ball colors. >> And I'm trying to script this. >> > > > > Hi Marilyn - > > You probably can't do it all with one object. Create another object which > is a duplicate of the one you're working with, then show spheres on object > #1 and sticks on object #2. You can then color the balls and the sticks > separately, since each object gets its own set of colors. > > For example: > > PyMOL>create obj1, 1FLT and chain w > Selector: found 797 atoms. > Executive: object "obj1" created. > PyMOL>create obj2, 1FLT and chain w > Selector: found 797 atoms. > Executive: object "obj2" created. > PyMOL>color gray, obj2 > Executive: Colored 797 atoms and 1 object. > PyMOL>color green, obj1 > Executive: Colored 797 atoms and 1 object. > PyMOL>show spheres, obj1 > PyMOL>show sticks, obj2 > PyMOL>set stick_radius, 0.1 > Setting: stick_radius set to 0.10000. > PyMOL>set sphere_scale, 0.25 > Setting: sphere_scale set to 0.25000. > > > This gives a ball-and-stick of one chain where the balls are all green and > the sticks are all gray. Modify as needed.... > > - Matt > > > -- > Matthew Franklin phone:(917)606-4116 > Senior Scientist, ImClone Systems fax:(212)645-2054 > 180 Varick Street, 6th floor > New York, NY 10014 > > > > Confidentiality Note: This e-mail, and any attachment to it, contains > privileged and confidential information intended only for the use of the > individual(s) or entity named on the e-mail. If the reader of this e-mail > is not the intended recipient, or the employee or agent responsible for > delivering it to the intended recipient, you are hereby notified that > reading it is strictly prohibited. If you have received this e-mail in > error, please immediately return it to the sender and delete it from your > system. Thank you. > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |