From: Kristian R. <k_r...@ya...> - 2004-07-23 10:10:58
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Dear PyMOL users, One of our students and i have written a plugin that colors proteins by the amino acid scales on www.Expasy.ch. It is available at http://www.rubor.de/bioinf Also, i have updated the PyMOL tips pages to reflect some topics discussed here in recent months. Yours, Kristian Rother |
From: Alex W. S. <ale...@as...> - 2004-09-08 21:19:04
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Is there a way to set the size of non-bonded spheres to two different sizes within the same residue? For example, I have a metal ion with a bound water and have both in the same residue but I want the metal ion to be bigger than the water. I have check the list archives and googled "PyMol non-bonded sphere size" and have had no luck. Suggestions? Best regards, Alex |
From: Scott C. <cl...@uc...> - 2004-09-08 21:43:21
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Alex, You need to create two separate objects one for your metal and another for your water create MG, (chain M) create WAT, (chain W) then you can change the properties of each object individually set sphere_scale, 1.2, MG set sphere_scale, 0.8, WAT good luck, Scott On Sep 8, 2004, at 2:19 PM, Alex W. Smith wrote: > Is there a way to set the size of non-bonded spheres to two different > sizes within the same residue? For example, I have a metal ion with a > bound water and have both in the same residue but I want the metal ion > to be bigger than the water. > > I have check the list archives and googled "PyMol non-bonded sphere > size" and have had no luck. > > Suggestions? > > Best regards, > > Alex ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. ACS Postdoctoral Fellow Department of Molecular & Cell Biology University of California, Berkeley 237 Hildebrand Hall #3206 Berkeley, CA 94720-3206 LAB 510.643.9491 FAX 510.643.9290 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
From: Alex W. S. <ale...@as...> - 2004-09-08 22:33:13
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Thanks Scott. I keep trying to mess with the non-bonded size instead of the regular sphere size. Alex On Sep 8, 2004, at 2:38 PM, Scott Classen wrote: > Alex, > You need to create two separate objects one for your metal and another > for your water > > create MG, (chain M) > create WAT, (chain W) > > then you can change the properties of each object individually > > set sphere_scale, 1.2, MG > set sphere_scale, 0.8, WAT > > good luck, > Scott > > > On Sep 8, 2004, at 2:19 PM, Alex W. Smith wrote: > >> Is there a way to set the size of non-bonded spheres to two different >> sizes within the same residue? For example, I have a metal ion with >> a bound water and have both in the same residue but I want the metal >> ion to be bigger than the water. >> >> I have check the list archives and googled "PyMol non-bonded sphere >> size" and have had no luck. >> >> Suggestions? >> >> Best regards, >> >> Alex > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > ACS Postdoctoral Fellow > Department of Molecular & Cell Biology > University of California, Berkeley > 237 Hildebrand Hall #3206 > Berkeley, CA 94720-3206 > LAB 510.643.9491 > FAX 510.643.9290 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop > FREE Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=5047&alloc_id=10808&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |