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
[PyMOL] spectrum colouring for dashes?
Dear Pymol Users, I'm creating dashes between atoms via the distance command. So far I have always indicated the size of the distance simply by the label that pops up automatically with the distance command. I was wondering however whether it is actually possible to also colour dashes according to their distance size. I'm looking for something similar to the cmd.spectrum command for colouring atoms according to their b-factor or occupancy value. Big thanks for your help in advance. Abdullah ---@ Dr. Abdullah Kahraman PostDoc Aebersold - Malmstroem Group Institute of Molecular Systems Biology ETH Zurich HPT C75 Wolfgang-Pauli-Str. 16 8093 Zurich Switzerland http://www.imsb.ethz.ch/researchgroup/malars/people/abdullah_kahraman abdul...@imsb.biol.ethz.ch work: +41-(0)44-633 39 45 mobile: +41-(0)76-317 0305 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ 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
[PyMOL] spectrum
Hi All Is there a way to set a user defined string palette. I'd like to generate a grey to red(or any other color of my choice) and a full grey10 to grey90 spectrum. I have used the color_b script but the min/max setting of the spectrum command are easier for adjusting the scaling. Thanks Mark -- 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
[PyMOL] spectrum by atomic properties
Dear all, i would like to color a molecule according to its partial charge. i used spectrum partial_charge, rainbow, selection=test without any success, although spectrum b, rainbow, selection=test works just fine. are the properties that can be selected limited to b-factor (b) and occupancy (q)? if so, where does the built-in mol2 parser expect the entry for the occupancy? cheers, peter
[PyMOL] spectrum
Hi all, I have a question regarding the spectrum command and b-factors. How are the color-ranges calculated by spectrum? I.e. i would like to know the values for the different shades like in the color_b.py-script, which gives you not only a total range, but also the bins. I would like to put a color-gradient-bar below a picture which shows numbers as well, and for that I need to know the ranges of blue, green, yellow, etc. Or is it possible to do this from within Pymol automatically (like for iso-surfaces)? Thanks in advance. -- Bye, Marc Saric
[PyMOL] spectrum, util.rainbow
Hi folks: Why is spectrum and the internal gui (which I assume invokes spectrum) so much faster than util.rainbow ? I like the util.rainbow default color scheme a bit better, but it takes forever for large complexes. Is there a simple way to get spectrum to mimic the rainbow color scheme? Thanks. Bill