Re: [PyMOL] Font problem
On 11/03/14 07:52, Justin Lecher wrote: > On 10/03/14 21:52, Thomas Holder wrote: >> Hi Justin, >> >> this is fixed in SVN rev 4070, sorry that it took so long. >> >> Cheers, >> Thomas >> > > Hi Thomas, > > Thanks a bunch. I will try it out tomorrow on my 3D machine. > > Cheers, > Justin > Looks beautiful now. Thanks a lot Thomas, Justin -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117 smime.p7s Description: S/MIME Cryptographic Signature -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] ALPHA cgo causes COLOR to be ignored
Dear PyMOL users, I'm wondering about coloring CGO objects in PyMOL. In the recent version 1.7. If ALPHA is specified for a cgo object, all the colors are neglected. In version 1.6 and previous everything works just fine. Is this a bug, an intension or am I missing a point somewhere? Let's take a following piece of code. It provides correct colorful triangle, only in the case 'ALPHA' line is omitted for version of PyMOL 1.7+ (I'm running Windows). data = [ BEGIN,TRIANGLES, ALPHA,1.0, COLOR,1.00,0.30,0.30, NORMAL,-0.997,-0.057,-0.051, VERTEX,52.083,62.446,50.739, COLOR,0.6,0.60,0.10, NORMAL,-0.999,-0.009,-0.044, VERTEX,52.048,63.219,50.739, COLOR,1.000,0.567,0.567, NORMAL,-0.998,-0.059,0.024, VERTEX,52.076,62.446,51.498, COLOR,0.600,0.2,0.2, END ] cmd.load_cgo(data,'triangle') Thank you for your answer Lukas -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] ALPHA cgo causes COLOR to be ignored
Hi Lukas, this was a bug which is fixed in SVN revision 4072. Cheers, Thomas On 12 Mar 2014, at 05:07, Lukáš Pravda wrote: > Dear PyMOL users, > > I’m wondering about coloring CGO objects in PyMOL. In the recent version 1.7. > If ALPHA is specified for a cgo object, all the colors are neglected. In > version 1.6 and previous everything works just fine. Is this a bug, an > intension or am I missing a point somewhere? Let’s take a following piece of > code. It provides correct colorful triangle, only in the case ‘ALPHA’ line is > omitted for version of PyMOL 1.7+ (I’m running Windows). > > data = [ > BEGIN,TRIANGLES, > ALPHA,1.0, > COLOR,1.00,0.30,0.30, > NORMAL,-0.997,-0.057,-0.051, > VERTEX,52.083,62.446,50.739, > COLOR,0.6,0.60,0.10, > NORMAL,-0.999,-0.009,-0.044, > VERTEX,52.048,63.219,50.739, > COLOR,1.000,0.567,0.567, > NORMAL,-0.998,-0.059,0.024, > VERTEX,52.076,62.446,51.498, > COLOR,0.600,0.2,0.2, > END > ] > cmd.load_cgo(data,'triangle') > > Thank you for your answer > > Lukas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Volume API and panel improvements
Dear all, I like to announce some significant changes to the volume user interface and API, as of SVN revision 4072. This is considered a beta feature and we welcome any kind of feedback. Changes include: * new commands: volume_color, volume_ramp_new * volume presets * custom volume ramps/presets * resizable volume panel * real-time volume update while dragging color dots in the panel * any click operation in the panel operates on three color dots if holding CTRL (adding, deleting, dragging, changing color), this is useful for isosurface-like peaks. Volume rendering requires OpenGL Shaders, and the more powerful your hardware, the better your volume experience will be. The changes affect PyMOL session files, volumes which are saved with this new version will not load in older versions of PyMOL. This also breaks scripts which use the old non-official API to create volumes. However, these should be easy to migrate. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] color each polymer chain differently
Dear PyMOL users, I build 100 chains of polymer in a box. Residue number is different for every chain. Chain 1 has residue no. 1, chain 2 has residue no. 2 and so on. I want to color each chain differently. So, I wrote a script which generates a pml file, and opening this pml file with PyMOL should color each chain differently. ##color.pml load 128md_c.pdb select 1, i. 1 color 1, i. 1 select 2, i. 2 color 2, i. 2 select 3, i. 3 color 3, i. 3 select 4, i. 4 color 4, i. 4 select 5, i. 5 color 5, i. 5 select 6, i. 6 color 6, i. 6 select 7, i. 7 ... ... color 125, i. 125 select 126, i. 126 color 126, i. 126 select 127, i. 127 color 127, i. 127 select 128, i. 128 color 128, i. 128 I have 128 chains. What I find that mostly green or black dominates the coloring. While displaying color by the numeric code, what is the maximum no, after which the color repeats? Chandan -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] color each polymer chain differently
I think... What is happening is that the color command should take in a name like “color yellow, i. 1" or a CMYK color vector. When you are saying “color 1” it is just starting at the first index of CMYK which is black. There is a command for your problem though. Just say util.color_chains() and it will color all individual chains a different color. On Mar 12, 2014, at 11:15 PM, Chandan Choudhury wrote: > > Dear PyMOL users, > > I build 100 chains of polymer in a box. Residue number is different for every > chain. Chain 1 has residue no. 1, chain 2 has residue no. 2 and so on. I want > to color each chain differently. > So, I wrote a script which generates a pml file, and opening this pml file > with PyMOL should color each chain differently. > > ##color.pml > load 128md_c.pdb > select 1, i. 1 > color 1, i. 1 > select 2, i. 2 > color 2, i. 2 > select 3, i. 3 > color 3, i. 3 > select 4, i. 4 > color 4, i. 4 > select 5, i. 5 > color 5, i. 5 > select 6, i. 6 > color 6, i. 6 > select 7, i. 7 > ... > ... > color 125, i. 125 > select 126, i. 126 > color 126, i. 126 > select 127, i. 127 > color 127, i. 127 > select 128, i. 128 > color 128, i. 128 > > I have 128 chains. > > What I find that mostly green or black dominates the coloring. > While displaying color by the numeric code, what is the maximum no, after > which the color repeats? > > Chandan > > -- > Chandan Kumar Choudhury > National Chemical Laboratory, Pune > India > > -- > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/13534_NeoTech___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
