[PyMOL] rgb to cmyk woes
Hi all, I'm trying to prepare some figures for publication and of course the journal requires them in cmyk format. I have produced the images in pymol using the cmyk color space and saved them as png files. However, the png files themselves are in 24 bit rgb format if I'm correct. Trying to subsequently convert them to cmyk format tiff files in photoshop or coreldraw results in all the colors being mangled (becoming duller and darker). Is there some trick to converting to the cmyk color space without altering the colors - I assumed working in the cmyk mode in PyMOL would ensure this didn't occur? Thanks in advance for any help Roger Dodd
RE: [PyMOL] rgb to cmyk woes
Roger, CMYK and RGB are non-equivalent, and there will always be some mangling like what you describe. The CMYK color mode in PyMOL is an attempt to constrain PyMOL to using the a subset of RGB values that can be mapped reliably into the CMYK color space, at least via Photoshop. It's not a perfect solution, but it usually gives better results than trying to convert normal RGB images. The best advice I can offer is to try changing the PyMOL colors slightly, and to then use the color adjustments in Photoshop to fix the image as best you can. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist 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 Roger Dodd Sent: Thursday, September 16, 2004 4:23 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] rgb to cmyk woes Hi all, I'm trying to prepare some figures for publication and of course the journal requires them in cmyk format. I have produced the images in pymol using the cmyk color space and saved them as png files. However, the png files themselves are in 24 bit rgb format if I'm correct. Trying to subsequently convert them to cmyk format tiff files in photoshop or coreldraw results in all the colors being mangled (becoming duller and darker). Is there some trick to converting to the cmyk color space without altering the colors - I assumed working in the cmyk mode in PyMOL would ensure this didn't occur? Thanks in advance for any help Roger Dodd --- This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 Project Admins to receive an Apple iPod Mini FREE for your judgement on who ports your project to Linux PPC the best. Sponsored by IBM. Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Two maps subtraction?
Dear pymol-users, It is possble to subtract the values written in two diffrent maps in Pymol. Maps of electrostatic potential are in AVS format (generated by MEAD). Best regards, Votyakov Kirill Center of Biophysics MIPT
RE: [PyMOL] ATI Mobility Radeon 9000 Problems (?)
Hi All, The crash problem with some rate combinations of Radeon hardware and drivers has been identified and eliminated. Thanks to everyone who responded. This turned out to be an issue of the driver not completely flushing the OpenGL pipeline before returning pixels from the display buffer. The driver got confused and was bringing down the whole system as a result. The problem goes away if we manually flush the pipeline before issuing any glReadPixels calls. Thus, it is one again safe to buy Mobility Radeon 9000 hardware for use with PyMOL! (the latest beta has the patch http://delsci.com/beta ). Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren DeLano Sent: Monday, September 13, 2004 8:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] ATI Mobility Radeon 9000 Problems (?) PyMOL Users, A major PyMOL sponsor is having problems with the Mobility Radeon 9000 chip on their Dell laptops under Windows XP. I am curious to know whether others have seen or are encountering similar problems with this chipset. The issue is as follows: When attempting to choose atoms using the mouse, either picking or selecting, the system experiences a hard system freeze and total loss of responsiveness, no blue-screen, no mouse movement, no nothing. The only recovery is a power-off system reboot. Has anyone else experienced this behavior on identical or related hardware? And if so, has anyone found a solution? such as a particular driver upgrade or downgrade? Or on the contrary, are there plenty of people out there with Radeon 9000-based PCs running PyMOL just fine? Any information about experiences with Radeon 8500-to-9200-based cards under Windows could be helpful. However, please send feedback to me directly mailto:war...@delsci.com in order to avoid unnecessary technical traffic on the mailing list. I will of course summarize once the situation becomes clear. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 --- This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 Project Admins to receive an Apple iPod Mini FREE for your judgement on who ports your project to Linux PPC the best. Sponsored by IBM. Deadline: Sept. 13. Go here: http://sf.net/ppc_contest.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] PDB to DXF
A quick Google for pdb dxf suggests that there are a couple: http://www.okino.com/conv/imp_pdb.htm http://www.danforthcenter.org/smith/MolView/Writeup/file.htm ... although this article http://www.sciencemag.org/cgi/content/full/281/5384/1814a suggests that MolView's DXF output is poor. hth, Gareth On Thu, 2004-09-16 at 16:16, andRe ambrosio wrote: Hi, Is it possible to convert a .pdb in a .dxf (AUTOCAD) file? Does anyone know how? Thanks in advance, andre ambrosio PhD student cbme/ifsc/usp - brazil --- This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170 Project Admins to receive an Apple iPod Mini FREE for your judgement on who ports your project to Linux PPC the best. Sponsored by IBM. Deadline: Sept. 24. Go here: http://sf.net/ppc_contest.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Gareth Stockwell gar...@ebi.ac.uk European Bioinformatics Institute
Re: [PyMOL] rgb to cmyk woes
On Thu, 16 Sep 2004 12:23:01 +0100, Roger Dodd wrote [snip] correct. Trying to subsequently convert them to cmyk format tiff files in photoshop or coreldraw results in all the colors being mangled (becoming duller and darker). This may be a result of an inappropriate colour-space profile being used in PS and/or the wrong choice for the cmyk conversion profile. It's actually a little odd that the journal expects to have files in cmyk. Most professional print houses would prefer to do the conversion from rgb to cmyk themselves so they can control the process for their printers (cmyk colour space is tied to the actual output device). If the journal is serious about demanding cmyk originals they should be more than willing to provide you with a profile for converting from an rgb space to their printing conditions (approximately). Rich
[PyMOL] building pymol on sgi irix 6.2 gcc 2.95.2
Hi Warren and all, I'm trying building pymol on sgi irix 6.2 gcc 2.95.2 (I got root access to that old sgi indigo2 extreme irix 6.2, and got a 13W3 to VGA cable to connect it to my sony g520 monitor, and it works great.) I installed gcc2.95.2, and am building the external dependencies for pymol but on running build.com I got an error about previous declaration of memchr and sure enough there is a file on my system called /usr/include/string.h and line 69 has memchr is there a way around this? I edited build.com : setenv SGI_ABI -n32 setenv MAKE make setenv CXX /usr/freeware/bin/c++ are these ok? will the hardware stereo work with pymol? this is really all I need this machine for, good for students (unless I can get a new licensed version of insightII on it ... from the csc here in finland) cheers Dan Dr. Daniel James White BSc. (Hons.) PhD Cell Biology, Ambiotica C242 Department of biological and environmental science PO Box 35 University of Jyväskylä Jyväskylä FIN 40014 Finland +358 14 260 4183 (work) +358 468102840 (mobile) http://www.chalkie.org.uk d...@chalkie.org.uk wh...@cc.jyu.fi
Re: [PyMOL] rgb to cmyk woes
Dr Charles S. BondUniversity of Dundee Tel: +44-1382-348325 Honorary Lecturer Dow St, Dundee Fax: +44-1382-345764 BBSRC David Phillips Fellow DD1 5EH, Scotland c.s.b...@dundee.ac.uk School of Life Sciences http://stein.bioch.dundee.ac.uk/~charlie Richard Ball r...@ellerbach.com 09/16/04 5:23 PM On Thu, 16 Sep 2004 12:23:01 +0100, Roger Dodd wrote It's actually a little odd that the journal expects to have files in cmyk. Hi Richard, Pretty much all of the journals I submit to prefer cmyk. In my experience, if I submit cmyk, the final printed colours look better than if I leave it to them. On linux the two methods I've found for doing this are: Imagemagick: e.g. convert -colorspace cmyk -gamma 0.5 a.png a.tiff The Imagemagick conversion tends to result in a fairly drab, dark image, hence the gamma correction (try a few different values). GIMP: The is a cymk conversion plugin for gimp which, in my hands, does a better job of producing a vivid cmyk tiff. The program uses the Adobe ICC profiles. (see http://www.blackfiveservices.co.uk/separate.shtml) Cheers, Charlie
