[PyMOL] Transparency in residues
Dear all, I am new to this list, and new to PyMOL, so I appologise if this is an old question. Is it possible to alter the transparency of a stick/cartoon model? I have searched the manual, but have only been able to find how to change transparency of a surface and that is not what I want to show. Thank you, Mads Gabrielsen -- -- Mads Gabrielsen, MSc Research Assistant / PhD Student WNH-group Phone:(0044) 01382 345 746 MSIWTB, School of Life Sciences Fax: (0044) 01382 345 764 University of DundeeE-mail: m.gabriel...@dundee.ac.uk Scotland
RE: [PyMOL] Transparency in residues
Mads, That feature didn't make it into the 0.86 release, but it is in the current development version. Look for it in the next release. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Mads Gabrielsen Sent: Tuesday, April 22, 2003 11:42 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Transparency in residues Dear all, I am new to this list, and new to PyMOL, so I appologise if this is an old question. Is it possible to alter the transparency of a stick/cartoon model? I have searched the manual, but have only been able to find how to change transparency of a surface and that is not what I want to show. Thank you, Mads Gabrielsen -- -- Mads Gabrielsen, MSc Research Assistant / PhD Student WNH-group Phone:(0044) 01382 345 746 MSIWTB, School of Life Sciences Fax: (0044) 01382 345 764 University of DundeeE-mail: m.gabriel...@dundee.ac.uk Scotland --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] surface charge?
Hi Warren, I'm using PyMol to make the figures in a paper I am currently writing. I know that pymol can generate surfaces at the moment but not charge. Is there any way to colour a surface by charge in pymol using charges calculated in grasp? ...or can I import a grasp surface? I heard that this sort of thing was in the pipe-line, do you have a rough estimate of when it will be available? Camille p.s. I'm working on os x with npymol.
[PyMOL] RGB2CMYK
Hi, can anyone direct me to a url with RGB colours (in the format below) and their CMYK equivalents? At the moment I'm messing around with the following kind of thing set_color cyan2=[0.7, 1.0, 1.0] I need to use a cyan color in a figure but unfortunately this becomes very dark when the resulting ray traced image file is viewed in CMYK mode in illustrator. Greens, especially, seem to suffer in conversion. Help! cheers, Camille MRC-LMB Cambridge University UK
Re: [PyMOL] RGB2CMYK
On Wednesday, April 23, 2003, at 06:30 AM, cami...@mrc-lmb.cam.ac.uk wrote: can anyone direct me to a url with RGB colours (in the format below) and their CMYK equivalents? At the moment I'm messing around with the following kind of thing Hi Camille, One free utility I found very useful for this kind of things is ColorWrite (http://www.adaptiveview.com/cw); it's a Java application, so you can run it under OS X, Linux, Solaris and Windows. Good luck, Luca Luca Jovine, Ph.D. Brookdale Department of Molecular, Cell Developmental Biology Mount Sinai School of Medicine Annenberg Building, Room 25-18 One Gustave L. Levy Place, New York, NY 10029-6574, USA Voice: +1.212.241-8620 FAX: +1.509.356-2832 E-Mail: lucajov...@mac.com - luca.jov...@mssm.edu W3: http://www.mssm.edu/students/jovinl02
RE: [PyMOL] RGB2CMYK
Camille, Gil Prive posted a set of CMYK colors before: http://sourceforge.net/mailarchive/message.php?msg_id=2299470 My only comment was that you don't need to add a preceeding underscore to his color names -- you can simply redefine the ones which already exist. set_color _green= [0.00 , 0.53 , 0.22] can be set_color green=[0.00,0.53,0.22] etc. One thing you can do with existing images is use Photoshop's Image-Mode-Convert To Profile option to adjust how the conversion is performed (at least I think that is what it does). I'm not sure Illustrator allow you to control RGB to CMYK conversions as well as Photoshop. The thing to understand is that CMYK is a subset of RGB color space. Many RGB colors simply don't exist in it. Bright green is one of them. RGB to CMYK is lossy, nonlinear, and dependent on the assumptions which are made about the ink colors, blending, and about the paper stock. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk Sent: Wednesday, April 23, 2003 3:31 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] RGB2CMYK Hi, can anyone direct me to a url with RGB colours (in the format below) and their CMYK equivalents? At the moment I'm messing around with the following kind of thing set_color cyan2=[0.7, 1.0, 1.0] I need to use a cyan color in a figure but unfortunately this becomes very dark when the resulting ray traced image file is viewed in CMYK mode in illustrator. Greens, especially, seem to suffer in conversion. Help! cheers, Camille MRC-LMB Cambridge University UK --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] surface charge?
Camille, This capability exists in the development version, but isn't ready for prime-time yet. Look for it in the next release. In the meantime, you might try using raster3d to render your grasp surface, via its ungrasp tool. http://www.bmsc.washington.edu/raster3d/html/r3d_filters.html#grasp Or you can load the converted grasp surface into PyMOL as a .r3d file and render it there. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of cami...@mrc-lmb.cam.ac.uk Sent: Wednesday, April 23, 2003 3:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface charge? Hi Warren, I'm using PyMol to make the figures in a paper I am currently writing. I know that pymol can generate surfaces at the moment but not charge. Is there any way to colour a surface by charge in pymol using charges calculated in grasp? ...or can I import a grasp surface? I heard that this sort of thing was in the pipe-line, do you have a rough estimate of when it will be available? Camille p.s. I'm working on os x with npymol. --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] Stereo pictures, light vector and shadows
Yow, good point! I'm surprise none of us realized this before : ) You need to change the direction of the light 6 degrees as well. Try using this sequence to create your stereo pair: set light=[-0.348,-0.348,-0.870] ray png image1.png turn y,6 set light=[-0.437,-0.348,-0.902] ray png image2.png turn y,-6 Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Anthony Duff Sent: Tuesday, April 22, 2003 9:03 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Stereo pictures, light vector and shadows I make stereo pictures by making two pictures, with the command turn y, 6 in between. Now that I am looking into a crevice, I have discovered a problem with this simple method. When the view is rotated, the light vector moves with the view. This results in the two pictures having different shadows, thus ruining the stereo picture. I don't want to give up on having shadows. Has anybody solved this problem? I am attempting to solve the problem by specifying the light setting (set light = [-0.4, -0.4, -1.0]). What are the definitions of the light parameters? Anthony -- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 -- --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] how to make molecule B move around molecule A
Dear Pymolers, I started to use Pymol(0.86) from last week and am still new to it. A complex at my hand contains mol A + B. MolA is hexamer (A1-A6) and B a monomer. Mol B modifies mol A one by one (please see the diagram below). when making a movie, is there any easy way to move B around A(fixed) in Pymol? Any suggestions would be greatly appreciated. Kindest regards yibin image001.jpg
