From: Lari <lar...@he...> - 2005-08-12 13:26:54
|
Hi, I've done this by rendering two images (actually 4 to get stereo). One wi= thout the CGOs and one with them. Then I overlaid them with photoshop and chang= ed the trasnparency of the CGO containing layer. I just used triangles and it lo= oked rather nice. ~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/ _______________________________________ Quoting tan...@st...: # Hi everybody, #=20 # 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= : #=20 # set transparency=3D0.5, object #=20 # But this actually does not work for CGO's. # Any ideas.... #=20 # Yusuf #=20 #=20 # -- # Yusuf Tanrikulu # Bioinformatics Diploma Student # Department of Biosciences # Johann-Wolfgang-Goethe Univerity Frankfurt # Siesmayerstrasse 70 # 60326 Frankfurt am Main # - Germany - # tan...@bi... #=20 #=20 # ------------------------------------------------------- # SF.Net email is Sponsored by the Better Software Conference & EXPO # September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices # Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA # Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf # _______________________________________________ # PyMOL-users mailing list # PyM...@li... # https://lists.sourceforge.net/lists/listinfo/pymol-users #=20 |
From: <tan...@st...> - 2005-08-15 10:04:50
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Lari, the way you've described is a nice workaround for images and presentations, which I had in mind, too. But it is not applicable while I am working with PyMOL online and want to make my CGO's transparent to see what is in them (including ability to rotate and zomm in/out the scene (which is not very doable in static pictures ;-)). I'm familiar with scripting in PyMOL. Probably I can change any transparenc= y variable while creating my triangles, which result in my CGO's? Isn't there= a implemented command in PyMOL, which does what I need? Cheers, Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann-Wolfgang-Goethe Univerity Frankfurt Siesmayerstrasse 70 60326 Frankfurt am Main - Germany - tan...@bi... Quoting Lari Lehti=F6 <lar...@he...>: > Hi, > > I've done this by rendering two images (actually 4 to get stereo). > One without > the CGOs and one with them. Then I overlaid them with photoshop and > changed the > trasnparency of the CGO containing layer. I just used triangles and it lo= oked > rather nice. > > ~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/ > _______________________________________ > > > Quoting tan...@st...: > > # 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=3D0.5, 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... > # > # > # ------------------------------------------------------- > # SF.Net email is Sponsored by the Better Software Conference & EXPO > # September 19-22, 2005 * San Francisco, CA * Development Lifecycle Pract= ices > # Agile & Plan-Driven Development * Managing Projects & Teams * Testing &= QA > # Security * Process Improvement & Measurement * http://www.sqe.com/bsce5= sf > # _______________________________________________ > # PyMOL-users mailing list > # PyM...@li... > # https://lists.sourceforge.net/lists/listinfo/pymol-users > # > > > ------------------------------------------------------- > 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 & Q= A > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Michael G. L. <ml...@um...> - 2005-08-15 14:38:09
|
>> Quoting tan...@st...: >> >> # 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 The last time I looked at this, it seemed like the easiest (only?) way to do this was to tweak the transparency at creation time. So, I typically have functions that look like this: def makeSphere(name,x,y,z,r,transparency=0,...): ... obj = [] ... obj.extend([cgo.ALPHA,1-transparency]) obj.extend([cgo.SPHERE,x,y,z,r]) ... cmd.load_cgo(obj,name,1) I don't know how to change it later, though. Hope that helps, -michael >> # >> # >> # -- >> # Yusuf Tanrikulu >> # Bioinformatics Diploma Student >> # Department of Biosciences >> # Johann-Wolfgang-Goethe Univerity Frankfurt >> # Siesmayerstrasse 70 >> # 60326 Frankfurt am Main >> # - Germany - >> # tan...@bi... >> # >> # |
From: <tan...@st...> - 2005-08-16 11:36:25
|
Michael, thanks for your reply, this works fine for me. However, I thought there is a nicer solution on setting the transparency for cgo's after creation. Regards, Yusuf -- Yusuf Tanrikulu Bioinformatics Diploma Student Department of Biosciences Johann-Wolfgang-Goethe Univerity Frankfurt Siesmayerstrasse 70 60323 Frankfurt am Main - Germany - tan...@bi... Quoting Michael George Lerner <ml...@um...>: >>> Quoting tan...@st...: >>> >>> # 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 > > The last time I looked at this, it seemed like the easiest (only?) > way to do this was to tweak the transparency at creation time. So, I > typically have functions that look like this: > > def makeSphere(name,x,y,z,r,transparency=0,...): > ... > obj = [] > ... > obj.extend([cgo.ALPHA,1-transparency]) > obj.extend([cgo.SPHERE,x,y,z,r]) > ... > cmd.load_cgo(obj,name,1) > > I don't know how to change it later, though. > > Hope that helps, > > -michael > >>> # >>> # >>> # -- >>> # Yusuf Tanrikulu >>> # Bioinformatics Diploma Student >>> # Department of Biosciences >>> # Johann-Wolfgang-Goethe Univerity Frankfurt >>> # Siesmayerstrasse 70 >>> # 60326 Frankfurt am Main >>> # - Germany - >>> # tan...@bi... >>> # >>> # > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > 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 > |