[PyMOL] effect of number of pixels on ray image quality
Hi everyone, I would like some confirmation or explanation about the differences I see, and the way I understand it. I was comparing the quality of images with different numbers of pixels along the length and width, e.g. ray 1000,750 I used the above command initially, because the highest display option on my Mac G3 is apparently 1024 x 768 I also decided to try higher numbers like 1200,1000 and 1500,1200. I also did the default option of just typing 'ray' without specifying pixels. The default ray command gives the the poorest quality image by visual comparison. The 1024 x 768 gave quite acceptable quality. But I was surprised that I could create and save images with higher pixel values than the apparent display limits. There was a small improvement in quality in these too, but the image size was much bigger. Furthermore, in one case, the image was slightly magnified/'zoomed in' when compared to the default, and the right and left edges were 'cropped'. But the quality was still better than the 1000x750 image. I suppose I could have kept increasing the numbers of pixels, but the tradeoff would be unacceptably large images. And the reason for all this is ... ... is a *.png image created with ray 1000,750 going to be good enough for publication standards? Is there much benefit in going higher? what causes the limits, if any? Yvonne
[PyMOL] how do I color specific residues
Hello, I am trying to learn PyMOL and doesn't know any programming. I am working with a file from pdb (1HPV). I would like to color specific residues. Basically I have trouble picking residues (there are two chains and a ligand in the asymmetric unit). How do I choose a specific residue/atom? Please help me. Thanks in advance, Madhavi
Re: [PyMOL] effect of number of pixels on ray image quality
yvonne leduc wrote: I would like some confirmation or explanation about the differences I see, and the way I understand it. Hello Yvonne, The command ray does not care about the size of your display, it may even be used in batch mode on a computer that does not have a monitor attached to it at all. To prevent the cropping or zooming on images created by the ray command you have to make sure that the aspect ratio of the width and height of the ray command are the same as the aspect ratio of your current viewport. Example 1) if you will be rendering (thats what the command ray does) figures of 2000 x 2000 you should choose a viewport of say 700x700, then: 2000 / 2000 = 1 = 700 / 700 - so you should execute the command: viewport 700, 700 - and then fine tune your figure and then run the ray command: ray 2000, 2000 Exmaple 2) - you want images at 3000 Width x 2000 Height 3000 / 2000 = 1.5 - your limiting display size is your height so try for instance height = 768 width = height * 1.5 = 768 * 1.5 = 1152 - but 1152 is wider than your display (1024) so lets try height = 500 width = 500 * 1.5 = 750 (which is good now, or at least it fits) - so you would issue the command viewport 750, 500 - then ray 3000, 2000 And the reason for all this is ... ... is a *.png image created with ray 1000,750 going to be good enough for publication standards? Is there much benefit in going higher? what causes the limits, if any? The journal usually specifies the resolution at which the images will be printed. If the journal says images print at 300 dpi (Dots Per Inch) and your figure will have a final printed width of 3 inches then you want to render images with a width of 900. The publisher will usually scale the picture with a very good software so even if it has to be enlarged by a few pixels the result will be good. But if it has to be shrinked you may run into trouble with labels, thin lines etc. Hope this helped a bit. Zac -- Ezequiel PANEPUCCI, Ph.D. - Institut Pasteur Plate-Forme 6 - Cristallogénèse et Diffraction des Rayons X Telephone: +33 (0)1 44 38 94 57 Portable: +33 (0)6 13 14 39 06
Re: [PyMOL] effect of number of pixels on ray image quality
On Thursday 20 January 2005 15:37, yvonne leduc wrote: [snip] And the reason for all this is ... ... is a *.png image created with ray 1000,750 going to be good enough for publication standards? Is there much benefit in going higher? what causes the limits, if any? Journals typically demand at least 600 dpi (dots per inch) resolution for figures. So if you want a figure 1 inch (2.54 cm) to a side, it will have to be 600 pixels to a side. A typical figure is about five by five centimeters, so that would call for a 1200x1200 pixel image. I have never run into any practical limitations using the PyMOL raytracer, which produces images of the requested size independent of the screen or window size, even if the image becomes so large it cannot be displayed in the PyMOL window (using ray sizex,sizey and png filename). Hope this helps, -- Lieven Buts Ultrastructure Laboratory Vrije Universiteit Brussel
[PyMOL] Monitors
I can highly recommend the price awarded Iiyama HM204DT 22 140KHz TCO99 Vision Master Pro 514. It has the same specs as the NEC monitor with a similar price tag. The Dell P1130 is also not bad at all with 130KHz (Iiyama technology!?) Also, the Nuvision glases are certenly not low cost and offer nowadays an excellent quality and comfort. The stereographics glasses are just way too expensive (My last quotation 1000 dollar including emitter) whereas the Nuvision glasses including emitter are 650 Euro including emitter. These actually work with the stereoglasses emitter too and are certenly more rigid with respect to the frame. J. -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: mest...@biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
[PyMOL] electrostatics in MacPyMol
Thanks to all for the help on recent topics. I'm now making beautiful movies (my eye being that of the beholder), and learning a lot more about the protein I study. I'm using MacPyMol and can't find a replacement for the Windows generate vacuum electrostatics command. Apparently I can't install the APBS tool on the Aqua version? Is there a suitable way to render electrostatics using MacPyMOL? Thanks again, Jeff
Re: [PyMOL] selection help + align question
Thanks for that one; it works as advertised. Another question: if I have 10 different structures read into PyMOL, what is the best (most accurate) method for aligning the structures as an ensemble? Currently, I'm aligning all to the first structure read in (i.e. 21, 31, etc.) using a for loop and the 'align' command. Since the structures have different sequences, I cannot use 'intra_fit', etc., is that right? Are there any other commands or methods of aligning that might be easy to script? Thanks, Doug On Jan 20, 2005, at 2:12 PM, Warren DeLano wrote: Doug, Setwise logical ANDs and ORs are tricky at first. In this case, you want to create a new set that contains atoms in a1 *or* a2. There aren't any atoms that are in both a1 and a2 which is why you're ending up with an empty object. create one, a1 or a2 -Original Message- I'm having some problems with selection syntax w/ multiple objects. I've loaded four different PDB files (in sequence structure): load 1.pdb, a1 load 2.pdb, a2 load 3.pdb, b1 load 4.pdb, b2 I wanted to create two new selections: one = a1 a2 two = b1 b2 I've tried many different combinations of PyMOL selection syntax, but I cannot get the objects to add to the same selection (using 'create' or 'select'): create one, a1 + a2 create one, a1 and a2 create one, object a1 + object a2 create one, a* From what I've read in the manual, I think these commands are not working because they actually work to select atoms that are the same between a1 a2. The manual says it 'selects atoms included in both s1 and s2'. Any clues or hints? Thanks, Doug
