## jmol-users

 [Jmol-users] color temperature on an absolute scale From: Miguel - 2004-08-12 15:07:30 ```Yossi and Rich said that it would be nice to have an option to 'color temperature' based upon an absolute scale rather than a relative scale. Yossi said: > The range usually runs from 0.00 to 100 (only positive values). Good. Yossi also said: > However, the temperature field is often used to color different > properties than thermal disorder. Hmmm ... not so good ... but I suppose I can deal with it. -- a short while later -- What about this ... The command is called 'temperatureRange' The default range is 0 - 100 If you want to change the range you can say: set temperatureRange -50 50 To apply the command we say: color atoms temperatureRange In every case, we will map the temperatureRange to the 33 colors of the red -> white -> blue scale. If values fall outside the current temperatureRange limits we can either: 1. map them to the extreme values of the range (easy) 2. map them to some other color outside the range (not quite as easy). Let me know what you think. Miguel ```
 [Jmol-users] Re: temperature scale From: Miguel - 2004-08-14 16:19:15 ```Yossi wrote: > Okay...I think I can adjust my values to fall between 0-100 > and retain their relativity. Also, can you please let me know > how the colors are implemented, e.g. division into 10 bins, > or else (, and what is the options for the color scale (e.g. rgb,rwb). Values should be in the range 0.00 - 100.00 min & max values are found to determine the range for the particular molecule. Values are linearly mapped into one of 33 bins. 16 blue bins + 1 white bin + 16 red bins RGB values are: 0x0000FF # blue 0x1010FF 0x2020FF ... 0xF0F0FF 0xFFFFFF #white 0xFFF0F0 ... 0xFF1010 0xFF0000 # red There is no control over the color ... for temp it goes from blue to red. Miguel ```
 [Jmol-users] Re: temperature scale From: Miguel - 2004-09-01 15:01:51 ```> I have a question regarding the values and the color bins. > I understood (perhaps wrongly) that the coloring scheme is fixed, > thus, a value of 50.00 should be colored white. No. The 'color temperature' scale is relative, not fixed. This is for RasMol compatibility. (although RasMol goes red->green->blue & Jmol goes red->white->blue) I apologize if I was not clear about this. In my message to the mailing list on 12 Aug 2004 I said: > The range is linearly scaled and mapped to > the temperature values in the file. I now see that this statement was not very clear. also: > ----- Original Message ----- > From: "Miguel" > To: "Yossi Shaul" > Cc: ; Sent: Saturday, August 14, 2004 7:18 PM > Subject: Re: temperature scale [snip] >> min & max values are found to determine the range for the particular molecule. Now for the good news ... I am now in a position to add the 'fixed temperature scale' functionality. We need to come up with a name. Suggestions are: color atoms byTempFactorValue color atoms absoluteTemperature color atoms fixedTemperature color atoms temperatureFixed color atoms temperatureAbsolute Please let me know which one you like, or make another suggestion. Miguel ```
 [Jmol-users] Re: temperature scale From: Yossi Shaul - 2004-09-01 15:46:04 ```Rasmol is actually implemented as fixed, at least with version 2.6. In any case, can we have an option for fixed bins? yossi ----- Original Message ----- From: "Miguel" To: "Yossi Shaul" Cc: ; Sent: Wednesday, September 01, 2004 6:00 PM Subject: Re: temperature scale > > I have a question regarding the values and the color bins. > > I understood (perhaps wrongly) that the coloring scheme is fixed, > > thus, a value of 50.00 should be colored white. > > No. The 'color temperature' scale is relative, not fixed. This is for > RasMol compatibility. (although RasMol goes red->green->blue & Jmol goes > red->white->blue) > > I apologize if I was not clear about this. In my message to the mailing > list on 12 Aug 2004 I said: > > > The range is linearly scaled and mapped to > > the temperature values in the file. > > I now see that this statement was not very clear. > > also: > > > ----- Original Message ----- > > From: "Miguel" > > To: "Yossi Shaul" > > Cc: ; > Sent: Saturday, August 14, 2004 7:18 PM > > Subject: Re: temperature scale > > [snip] > > >> min & max values are found to determine the range for the particular > molecule. > > > Now for the good news ... I am now in a position to add the 'fixed > temperature scale' functionality. > > We need to come up with a name. Suggestions are: > > color atoms byTempFactorValue > color atoms absoluteTemperature > color atoms fixedTemperature > color atoms temperatureFixed > color atoms temperatureAbsolute > > Please let me know which one you like, or make another suggestion. > > > Miguel > > > ```
 Re: [Jmol-users] Re: temperature scale From: Miguel - 2004-09-01 16:54:15 ```> Rasmol is actually implemented as fixed, at least with version 2.6. If you check again you will find that the 'color temperature' scale in RasMol is relative. The following sample file demonstrates this: ATOM 1 N HIS A 26 1.916 9.763 68.811 1.00 70.0 N ATOM 2 CA HIS A 26 1.359 8.377 68.773 1.00 80.0 C ATOM 3 C HIS A 26 2.372 7.383 68.181 1.00 90.0 C The temp values are 70, 80, and 90, but when you say 'color atoms temperature' in rasmol26b2 you get one red atom, one green atom, and one blue atom. > In any case, can we have an option for fixed bins? Yes, we just need to come up with a name. color atoms ? Miguel ```
 Re: [Jmol-users] color temperature on an absolute scale From: Jaime Prilusky - 2004-08-13 03:12:35 ```Miguel, Thank you for implementing the temperature coloring. Looking forward to the next Jmol release. According to Miguel: > In every case, we will map the temperatureRange to the 33 colors of the > red -> white -> blue scale. Will it be possible to request colors for these 3 points? Something like temperatureColor [green,white,blue] > If values fall outside the current temperatureRange limits we can either: > 1. map them to the extreme values of the range (easy) > 2. map them to some other color outside the range (not quite as easy). There's a third option: just ignore coloring the out-of-scale point. By requesting a non standard temperatureRange we can filter the display based on temperature values. Jaim -- Dr Jaime Prilusky | Jaime.Prilusky@... R&D Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ ```
 Re: [Jmol-users] color temperature on an absolute scale From: Miguel - 2004-08-13 06:49:42 ```Jaim wrote: >> In every case, we will map the temperatureRange to the 33 colors of the >> red -> white -> blue scale. > > Will it be possible to request colors for these 3 points? > Something like temperatureColor [green,white,blue] My first reaction was "No". Then I gave it a little more thought and decided that the answer is "Maybe". Q: If I do it, will you really *use* it? Q: Other people: will anybody else use it? Q: If I do it for 'temperature', are we going to want it for other things too (like charge) ? >> If values fall outside the current temperatureRange limits we can >> either: >> 1. map them to the extreme values of the range (easy) >> 2. map them to some other color outside the range (not quite as easy). > > There's a third option: just ignore coloring the out-of-scale point. This is not an option. At the point at which we are applying the color it is too late. > By requesting a non standard temperatureRange we can filter > the display based on temperature values. The proper way to handle this is by using atom expressions to restrict your set. You can do this by saying: select temperature > 50; color temperature -- 2 minutes later -- I just checked this and there is a bug. Internally I scale all bfactors by 100. So, in order for this to work you have to say 'select temperature > 5000'. It is a trivial fix and will be in the next release. Miguel ```
 Re: [Jmol-users] color temperature on an absolute scale From: Jan Reichert - 2004-08-13 07:25:45 ```Miguel wrote: >Jaim wrote: > > >>>In every case, we will map the temperatureRange to the 33 colors of the >>>red -> white -> blue scale. >>> >>> >>Will it be possible to request colors for these 3 points? >>Something like temperatureColor [green,white,blue] >> >> > >My first reaction was "No". > >Then I gave it a little more thought and decided that the answer is "Maybe". > >Q: If I do it, will you really *use* it? > >Q: Other people: will anybody else use it? > >Q: If I do it for 'temperature', are we going to want it for other things >too (like charge) ? > > > I want it for all. I want carbon green I want helix red and sheet blue and I don't want to say it every time, I want to manipulate the color schemes, *too*. Regards, Jan > > >>>If values fall outside the current temperatureRange limits we can >>>either: >>>1. map them to the extreme values of the range (easy) >>>2. map them to some other color outside the range (not quite as easy). >>> >>> >>There's a third option: just ignore coloring the out-of-scale point. >> >> > >This is not an option. At the point at which we are applying the color it >is too late. > > > >>By requesting a non standard temperatureRange we can filter >>the display based on temperature values. >> >> > >The proper way to handle this is by using atom expressions to restrict >your set. You can do this by saying: > > select temperature > 50; color temperature > >-- 2 minutes later -- > >I just checked this and there is a bug. Internally I scale all bfactors by >100. So, in order for this to work you have to say 'select temperature > >5000'. It is a trivial fix and will be in the next release. > > >Miguel > > > > >------------------------------------------------------- >SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media >100pk Sonic DVD-R 4x for only \$29 -100pk Sonic DVD+R for only \$33 >Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. >http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ```
 Re: [Jmol-users] color temperature on an absolute scale From: E.L. Willighagen - 2004-08-13 07:35:03 ```=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Friday 13 August 2004 09:25, Jan Reichert wrote: > >Then I gave it a little more thought and decided that the answer is > > "Maybe". > > > >Q: If I do it, will you really *use* it? > > > >Q: Other people: will anybody else use it? > > > >Q: If I do it for 'temperature', are we going to want it for other things > >too (like charge) ? > > I want it for all. > I want carbon green > I want helix red and sheet blue > and I don't want to say it every time, I want to manipulate the color > schemes, *too*. The downside of a responsive community: they're demanding too :) Egon =2D --=20 e.willighagen@... PhD on Molecular Representation in Chemometrics Radboud University, Nijmegen http://www.cac.sci.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 "Again a chemist did something useful with a computer" =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBHG8dd9R8I9Yza6YRAg+2AJ4iXKD9ck3Yyw4bOECm9M6W/Wm35wCgniUb VzOM9vnjFa9whPxW6Gr4k8s=3D =3Deq14 =2D----END PGP SIGNATURE----- ```
 [Jmol-users] More color flexibility From: Miguel - 2004-08-13 08:00:03 ```Jan wrote: >>Q: If I do it for 'temperature', are we going to want it for other things >>too (like charge) ? >> > I want it for all. Of course you want it for all ... everybody wants it all :-) > I want carbon green select carbon; color atoms green > I want helix red and sheet blue select helix; color atoms red; select sheet; color atoms blue > and I don't want to say it every time, I want to manipulate the color > schemes, *too*. That represents quite a bit of tedious work for me and I am not going to get much personal satisfaction out of it. And since I do not receive any financial compensation for this work, the 'personal satisfaction quotient' is quite important :-) Plus, it just isn't clear to me that changing colors is a good thing. As someone from outside the chemistry community, it seems to me that the publishers and standards boards have been somewhat delinquent in this area. I think that there should be a standard set of recommended colors for published manuscripts and for software packages. Since I want Jmol used on public web sites, where students and casual users can come and go from time to time, I generally think that the colors should be consistent. Right now I am struggling to wrap this thing up and ship the official v10 release. I am supposed to be in 'bug-fix mode'. The only reason I implemented the 'temperature' colors is because it was a very isolated change and the command exists in RasMol/Chime. Look, at some point I will probably open up the color palettes and give you the coloring options that you want. But it probably is not going to happen until 2005. Miguel ```
 Re: [Jmol-users] More color flexibility From: William Reusch - 2004-08-13 12:56:09 Attachments: Message as HTML ```Miguel, I agree with your evaluation and support your decision. Bill Miguel wrote: >Jan wrote: > > > >>>Q: If I do it for 'temperature', are we going to want it for other things >>>too (like charge) ? >>> >>> >>> >>I want it for all. >> >> > >Of course you want it for all ... everybody wants it all :-) > > > >>I want carbon green >> >> > >select carbon; color atoms green > > > >>I want helix red and sheet blue >> >> > >select helix; color atoms red; select sheet; color atoms blue > > > >>and I don't want to say it every time, I want to manipulate the color >>schemes, *too*. >> >> > >That represents quite a bit of tedious work for me and I am not going to >get much personal satisfaction out of it. And since I do not receive any >financial compensation for this work, the 'personal satisfaction quotient' >is quite important :-) > >Plus, it just isn't clear to me that changing colors is a good thing. As >someone from outside the chemistry community, it seems to me that the >publishers and standards boards have been somewhat delinquent in this >area. I think that there should be a standard set of recommended colors >for published manuscripts and for software packages. > >Since I want Jmol used on public web sites, where students and casual >users can come and go from time to time, I generally think that the colors >should be consistent. > >Right now I am struggling to wrap this thing up and ship the official v10 >release. I am supposed to be in 'bug-fix mode'. The only reason I >implemented the 'temperature' colors is because it was a very isolated >change and the command exists in RasMol/Chime. > >Look, at some point I will probably open up the color palettes and give >you the coloring options that you want. But it probably is not going to >happen until 2005. > > >Miguel > > > >------------------------------------------------------- >SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media >100pk Sonic DVD-R 4x for only \$29 -100pk Sonic DVD+R for only \$33 >Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. >http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ```
 Re: [Jmol-users] More color flexibility From: Jan Reichert - 2004-08-13 09:06:27 ```Miguel wrote: >Jan wrote: > > > >>>Q: If I do it for 'temperature', are we going to want it for other things >>>too (like charge) ? >>> >>> >>> >>I want it for all. >> >> > >Of course you want it for all ... everybody wants it all :-) > > > >>I want carbon green >> >> > >select carbon; color atoms green > > > >>I want helix red and sheet blue >> >> > >select helix; color atoms red; select sheet; color atoms blue > > > >>and I don't want to say it every time, I want to manipulate the color >>schemes, *too*. >> >> > >That represents quite a bit of tedious work for me and I am not going to >get much personal satisfaction out of it. And since I do not receive any >financial compensation for this work, the 'personal satisfaction quotient' >is quite important :-) > >Plus, it just isn't clear to me that changing colors is a good thing. As >someone from outside the chemistry community, it seems to me that the >publishers and standards boards have been somewhat delinquent in this >area. I think that there should be a standard set of recommended colors >for published manuscripts and for software packages. > > who mad that standard? e.g. I like MolMol (sheet blue, helix red (outside) yellow (inside)) or in WebMol (coloring carbon green, sheet blue) or AstexViewer (carbon green) >Since I want Jmol used on public web sites, where students and casual >users can come and go from time to time, I generally think that the colors >should be consistent. > >Right now I am struggling to wrap this thing up and ship the official v10 >release. I am supposed to be in 'bug-fix mode'. The only reason I >implemented the 'temperature' colors is because it was a very isolated >change and the command exists in RasMol/Chime. > > I only repeated my demand on simple color scheme manipulation now, because I thought it was the opportunity for a general implementation of scheme manipulations set temperatureColor [-1=>red,0=>white,1=>blue,else=>yellow] set structureColor [helix=>red,sheet=>blue,turn=>yellow,else=>gray] set cpkColor [H=>white,C=>green,O=>red] Regards, Jan >Look, at some point I will probably open up the color palettes and give >you the coloring options that you want. But it probably is not going to >happen until 2005. > > >Miguel > > > >------------------------------------------------------- >SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media >100pk Sonic DVD-R 4x for only \$29 -100pk Sonic DVD+R for only \$33 >Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. >http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > ```
 Re: [Jmol-users] More color flexibility From: Miguel - 2004-08-13 09:33:50 ```> I only repeated my demand on simple color scheme manipulation now, > because I thought it was the opportunity for a general implementation of > scheme manipulations > set temperatureColor [-1=>red,0=>white,1=>blue,else=>yellow] > set structureColor [helix=>red,sheet=>blue,turn=>yellow,else=>gray] > set cpkColor [H=>white,C=>green,O=>red] > Regards, Jan OK Miguel ```