Re: [PyMOL] spectrum and the default minimum and maximum values
Hi Emily, No, it takes them from the selection. Cheers, Tsjerk On Jul 7, 2015 4:09 PM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: To be extra clear/redundant: The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the list of values, ...do you mean that it takes the minimum/maximum values from the list of b-values from within that pdb file? So that for each pdb file, blue vs. white vs. red (on a blue_white_red palette) could have very different values from one file to the next (if the structures are different in that respect)? Emily. otherwise it will take the value provided. The interpolation is indeed linear. Hope it helps, Tsjerk On Tue, Jul 7, 2015 at 4:11 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: Hello All. Can anyone tell me what values are assigned by default to the minimum and maximum arguments of the spectrum command? To be clear, I know how to change the value of these arguments, but what does PyMOL assign to these values if one calls the spectrum tool using the pull-down menus to color by b-factor (or does not include values for the minimum and maximum arguments at the command line)? Does it assign the smallest b-factor found in that file to 'minimum', and the highest b-value found to 'maximum', and then spreads the values linearly according to the number of colors in the chosen palette? I'd like for it to do that, and I'm sure it can be coded, but first I'd like to find out the default approach. I am using a PyMOL incentive package on my Mac. Regards, Emily. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ 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] spectrum and the default minimum and maximum values
Hi Emily, The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the list of values, otherwise it will take the value provided. The interpolation is indeed linear. Hope it helps, Tsjerk On Tue, Jul 7, 2015 at 4:11 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: Hello All. Can anyone tell me what values are assigned by default to the minimum and maximum arguments of the spectrum command? To be clear, I know how to change the value of these arguments, but what does PyMOL assign to these values if one calls the spectrum tool using the pull-down menus to color by b-factor (or does not include values for the minimum and maximum arguments at the command line)? Does it assign the smallest b-factor found in that file to 'minimum', and the highest b-value found to 'maximum', and then spreads the values linearly according to the number of colors in the chosen palette? I'd like for it to do that, and I'm sure it can be coded, but first I'd like to find out the default approach. I am using a PyMOL incentive package on my Mac. Regards, Emily. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ 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] spectrum and the default minimum and maximum values
To be extra clear/redundant: The default value passed is None. If Pymol finds that the argument is None, it takes the minimum/maximum value from the list of values, ...do you mean that it takes the minimum/maximum values from the list of b-values from within that pdb file? So that for each pdb file, blue vs. white vs. red (on a blue_white_red palette) could have very different values from one file to the next (if the structures are different in that respect)? Emily. otherwise it will take the value provided. The interpolation is indeed linear. Hope it helps, Tsjerk On Tue, Jul 7, 2015 at 4:11 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: Hello All. Can anyone tell me what values are assigned by default to the minimum and maximum arguments of the spectrum command? To be clear, I know how to change the value of these arguments, but what does PyMOL assign to these values if one calls the spectrum tool using the pull-down menus to color by b-factor (or does not include values for the minimum and maximum arguments at the command line)? Does it assign the smallest b-factor found in that file to 'minimum', and the highest b-value found to 'maximum', and then spreads the values linearly according to the number of colors in the chosen palette? I'd like for it to do that, and I'm sure it can be coded, but first I'd like to find out the default approach. I am using a PyMOL incentive package on my Mac. Regards, Emily. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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] spectrum and the default minimum and maximum values
Hello All. Can anyone tell me what values are assigned by default to the minimum and maximum arguments of the spectrum command? To be clear, I know how to change the value of these arguments, but what does PyMOL assign to these values if one calls the spectrum tool using the pull-down menus to color by b-factor (or does not include values for the minimum and maximum arguments at the command line)? Does it assign the smallest b-factor found in that file to 'minimum', and the highest b-value found to 'maximum', and then spreads the values linearly according to the number of colors in the chosen palette? I'd like for it to do that, and I'm sure it can be coded, but first I'd like to find out the default approach. I am using a PyMOL incentive package on my Mac. Regards, Emily. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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] spectrum
Hi Mark and Sean, On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law magic...@hotmail.com wrote: Sorry for the earlier confusion. I think I found a hackish way of getting a gray spectrum: snip Sean's extensive explanation I know I'm biased, since I wrote the color_b.py script, but I fail to see what is difficult about typing: color_b selectionname, gradient=user, user_rgb=[.2,.2,.2,.5,.5,.5,.8,.8,.8] In order to colour selectionname in a gray spectrum that goes from 20% gray, has a midpoint of 50% gray and ends at 80% gray (where 20% gray is the same as the colour called gray20, i.e. close to black and 80% gray is almost white). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Spectrum
Hi Sean, On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law magic...@hotmail.com wrote: Robert, I would have to agree with you. I've used many of your scripts and have also learned a lot from them and think that the color B script is pretty robust and helpful. Thanks. I could be wrong but I remember the original poster commenting about using the min max settings from the spectrum command and I wonder if that is used to control the min/max of B-factor values to color (so that any values outside of the range of min and max will be colored the extreme min/max color values). Of course, I'm sure it's just as easy to add a couple of lines of extra code into your script to account for that (if it isn't already there). The color_b.py script has options called minimum and maximum just like the spectrum command. These are used to select the range of B-values to colour. So (using PDB code 1dvi as an example) if your actual B-values are between 2 and 55.98 and you set the minimum to 10 and maximum to 50, then use 8 bins (just to get nice numbers here!), by typing: color_b minimum=10, maximum=50, nbins=8 You'll see the following output from the color_b.py script: Minimum and Maximum B-values: 2.0 55.975422 Color select: n. ca and (b15 or b = 15) Color select: n. ca and b15 Color select: n. ca and b20 Color select: n. ca and b25 Color select: n. ca and b30 Color select: n. ca and b35 Color select: n. ca and b40 Color select: n. ca and b45 So yes, anything within the lowest range and below will be in colour 1 and anything within the highest range and above will be in colour 8. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
