From: Ann M. <am...@tu...> - 2003-12-16 23:05:46
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Hello, I have been using PyMol for a few months now, and I am wondering if I can adjust the radius about which the surface is calculated. I have a very large protein (28,000 atoms) to model, and I would like to be able to create a more evenly rounded surface. Not "realistic" perhaps, but easier for students to see the larger view than marveling at all the nooks and crannies. All suggestions greatly appreciated. Ann Ann Mullin Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) am...@tu... |
From: Scott C. <cl...@uc...> - 2003-12-17 17:39:15
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Hi Ann, you can set the radius of the "water" probe used to construct the surface by setting solvent_radius to something smaller than 1.4. You can either look in the pulldown menus for the settings panel to adjust the value in a GUI or type: set solvent_radius, 1.2 in the text window. Good Luck Scott On Dec 16, 2003, at 3:05 PM, Ann Mullin wrote: > Hello, > > I have been using PyMol for a few months now, and I am wondering if I > can adjust the radius about which the surface is calculated. I have > a very large protein (28,000 atoms) to model, and I would like to be > able to create a more evenly rounded surface. Not "realistic" > perhaps, but easier for students to see the larger view than marveling > at all the nooks and crannies. All suggestions greatly appreciated. > > Ann > > > Ann Mullin > Cell and Molecular Biology Dept. > Tulane University > New Orleans, LA 70118-5698 > 504-865-6742 (Ph) > 504-865-6785 (FAX) > am...@tu... ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: Paulo M. <pm...@ua...> - 2003-12-17 18:12:23
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On Wed, 2003-12-17 at 17:39, Scott Classen wrote: > Hi Ann, > you can set the radius of the "water" probe used to construct the=20 > surface by setting solvent_radius to something smaller than 1.4. You=20 > can either look in the pulldown menus for the settings panel to adjust=20 > the value in a GUI or type: >=20 Scott, I think that Ann wants a sphere radius larger than 1.4, since she is looking for a less detailed surface... reducing the probe radius will increase the amount of detail, or roughness (tending towards the vdw surface, for radius=3D0.0) Cheers, Paulo > set solvent_radius, 1.2 in the text window. >=20 > Good Luck > Scott >=20 > On Dec 16, 2003, at 3:05 PM, Ann Mullin wrote: >=20 > > Hello, > > > > I have been using PyMol for a few months now, and I am wondering if I=20 > > can adjust the radius about which the surface is calculated. I have=20 > > a very large protein (28,000 atoms) to model, and I would like to be=20 > > able to create a more evenly rounded surface. Not "realistic"=20 > > perhaps, but easier for students to see the larger view than marveling=20 > > at all the nooks and crannies. All suggestions greatly appreciated. > > > > Ann > > > > > > Ann Mullin > > Cell and Molecular Biology Dept. > > Tulane University > > New Orleans, LA 70118-5698 > > 504-865-6742 (Ph) > > 504-865-6785 (FAX) > > am...@tu... > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > 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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ --=20 Paulo Martel Dept. de Qu=EDmica e Bioqu=EDmica Faculdade de Ci=EAncias e Tecnologia Universidade do Algarve Campus de Gambelas, 8000-117 FARO Tel: 289800900 Ext.7402 |