From: <tan...@st...> - 2005-08-12 12:59:39
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Hi everybody, i've just created many CGOs, which show up solid surfaces like spheres and ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 and leave the others solid? I've checked out the reference and the manual, and found something like: set transparency=0.5, object But this actually does not work for CGO's. Any ideas.... Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann-Wolfgang-Goethe Univerity Frankfurt Siesmayerstrasse 70 60326 Frankfurt am Main - Germany - tan...@bi... |
From: Mikko H. <mhu...@ab...> - 2005-08-17 08:38:00
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> i've just created many CGOs, which show up solid surfaces like spheres and > ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 > and leave the others solid? > I've checked out the reference and the manual, and found something like: The CGO support in Pymol does not quite seem to be all there; I had CGOs appear correctly in raytracing some of the time, other times they just would not render at all. I needed transparency, too, so I ended up exporting everything to Povray and rendering the image there. This requires some familiarity with Povray, because the material definition for the transparent surfaces needs to be written manually and the CGOs must be found in the Povray input that Pymol spews out (80 MB of text in my case...). One way to do this is to write out the CGOs in one Povray file and the molecules in another. With Povray you can get shadows on CGOs and molecules inside transparent CGOs to render correctly, which is not really possible in 2D (Photoshopping or such). Mikko |
From: Lari L. <lar...@he...> - 2005-09-02 15:42:03
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Hello, I'm in a process of making a whole bunch of figures for a paper and I have = an=20 irritating problem. Some of the figures just do _not_ get ray traced. It=20 processes the image, but the image stays normal (=3Dugly). I'm running 0.98 on an amd64 box with gentoo and I've tried the binary=20 distribution as well as compiled pymol from the source. If I start from=20 scratch and make similar objects, it works fine again.=20 Has anyone else seen this kind of behaviour?=20 ~Lari~ _______________________________________ Lari Lehti=F6 University of Helsinki Institute of Biotechnology Macromolecular X-ray crystallography P.O.Box 65 00014 HY =46inland http://www.biocenter.helsinki.fi/~lehtio/ _______________________________________ |
From: Akanksha N. <gt...@ma...> - 2005-09-02 18:23:57
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Dear PyMol Users: Does anyone knows how to move labels to the desired position using PyMol? Any suggestions are appreciated. Thanks, Akanksha -- Akanksha Nagpal, Ph.D. School of Chemistry and Biochemistry Georgia Institute of Technology Atlanta, GA 30332 |
From: Lari L. <lar...@he...> - 2005-09-02 21:52:25
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Thank you Warren and Jacob, I pressed stop and then ray tracing went fine. I don't know who pressed tha= t=20 play-button, but it wasn't me... ~Lari~=20 On Friday 02 September 2005 18:41, Lari Lehtio wrote: > Hello, > > I'm in a process of making a whole bunch of figures for a paper and I have > an irritating problem. Some of the figures just do _not_ get ray traced. = It > processes the image, but the image stays normal (=3Dugly). > > I'm running 0.98 on an amd64 box with gentoo and I've tried the binary > distribution as well as compiled pymol from the source. If I start from > scratch and make similar objects, it works fine again. > > Has anyone else seen this kind of behaviour? > > ~Lari~ > > _______________________________________ > Lari Lehti=F6 > University of Helsinki > Institute of Biotechnology > Macromolecular X-ray crystallography > P.O.Box 65 > 00014 HY > Finland > http://www.biocenter.helsinki.fi/~lehtio/ > _______________________________________ > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic= es > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |