From: Warren D. <wa...@de...> - 2006-03-06 15:06:59
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Wulf, The easiest thing would be to convert your small molecule to an SDF, = MOL, or MOL2 format before loading it into PyMOL. Short of that, you'd have to select each bond independently = (ctrl-right-click while in editing mode) and use Ctrl-W to set the = valences. Cheers, Warren -----Original Message----- From: pym...@li... on behalf of Wulf = Blankenfeldt Sent: Mon 3/6/2006 6:22 AM To: pym...@li... Subject: [PyMOL] Displaying/defining double bonds in a ligand molecule =20 Hello pymolers, I'd like to display double bonds in a small molecule ligand bound to the = active centre of a protein. Of course, the ligand is non-standard, i.e.=20 pymol doesn't know about its chemical nature. Googling a bit, I found=20 that I can set valence, 0.1 but this only display double bonds in the protein, which I don't want. How do I teach pymol to display double bonds in my ligand? Thanks for your help, Wulf ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting = language that extends applications into web and mobile media. Attend the live = webcast and join the prime developer group breaking into this new coding = territory! http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D= 121642 _______________________________________________ PyMOL-users mailing list PyM...@li... https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: Warren D. <wa...@de...> - 2006-03-06 15:34:14
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Wulf, Unfortunately, the lighting model has changed...I am assuming that you = are having problems with existing session files or scripts? =20 It may be necessary to reoptimize the lighting settings. The new = defaults are: set ambient, 0.14 set gamma, 1.0 set direct, 0.45 set reflect, 0.45 set specular_intensity, 0.5 set light_count, 2=20 set light, [ -0.40000, -0.40000, -1.00000 ]=20 set spec_reflect, -1 set spec_power, -1 set shininess, 55 Perhaps you can simply paste those commands into your scripts? If you want pre-0.99-like lighting model (it has an extra dot product = that shouldn't be there). use=20 set ray_legacy_lighting, 1 with the above settings Cheers, Warren -----Original Message----- From: Wulf Blankenfeldt [mailto:wul...@mp...] Sent: Mon 3/6/2006 7:23 AM To: Warren DeLano Subject: Re: [PyMOL] Displaying/defining double bonds in a ligand = molecule =20 Ah, bingo! Thanks for that, Warren. BTW: we have a little difficulty with the 0.99 version under windows:=20 colours have become very glary in raytracing, like an overexposed=20 photograph. Is this a feature, a non-optimised colour scheme or simply=20 my mistake? Best, Wulf Warren DeLano schrieb: > > Wulf, > > The easiest thing would be to convert your small molecule to an SDF,=20 > MOL, or MOL2 format before loading it into PyMOL. > > Short of that, you'd have to select each bond independently=20 > (ctrl-right-click while in editing mode) and use Ctrl-W to set the=20 > valences. > |
From: Mark A S. <sa...@um...> - 2006-03-07 05:33:15
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Wulf et al, I've had similar results to what you report even with a session file created with the latest version of PyMol. You should first try what Warren suggests. Then, if the specular highlights still look too contrasty, you can try reducing the specular_intensity to about 0.2 and also adjust the shininess value. -Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@um... (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html |
From: Wulf B. <wul...@mp...> - 2006-03-07 13:55:47
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Warren, Mark; thanks for these suggestions concerning "overexposed" images. We have dumped Warren's settings into our pymolrc file and are now getting much better results... Best, Wulf Mark A Saper schrieb: > Wulf et al, > > I've had similar results to what you report even with a session file > created with the latest version of PyMol. You should first try what > Warren suggests. Then, if the specular highlights still look too > contrasty, you can try reducing the specular_intensity to about 0.2 > and also adjust the shininess value. > Wulf. BTW: we have a little difficulty with the 0.99 version under windows: colours have become very glary in raytracing, like an overexposed photograph. Is this a feature, a non-optimised colour scheme or simply my mistake? Warren: It may be necessary to reoptimize the lighting settings. The new defaults are: set ambient, 0.14 set gamma, 1.0 set direct, 0.45 set reflect, 0.45 set specular_intensity, 0.5 set light_count, 2 set light, [ -0.40000, -0.40000, -1.00000 ] set spec_reflect, -1 set spec_power, -1 set shininess, 55 |