From: R. K. W. <we...@cs...> - 2010-03-18 16:20:40
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I'm trying to use the "connect" command to connect various atoms that are not chemically bonded (to show distance restraints). My question is, how do I add a color option to the connect command? I've looked at the documentation, and tried everything I could think of, but I haven't gotten it to work -- one example would be *extremely* helpful. If I do connect (atomno=442) (atomno=410); it works, but the color is not what I want. I've tried stuff like this: connect (atomno=442) (atomno=410) (color="white"); and all kinds of varations with and without parenthesis, quotes, <>, etc., and nothing has worked... Kent -- R. Kent Wenger (we...@cs..., 608-262-6627, http://www.cs.wisc.edu/~wenger/) Computer Sciences Department University of Wisconsin-Madison |
From: Jonathan G. <gu...@uw...> - 2010-03-18 17:30:50
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Kent, Since you've selected your bonds in the connect command just follow that line with color bond blue You can insert your favorite color:) Are you doing this in relation to the Condor project or something else? What are you using Jmol to look at. Jonathan On Mar 18, 2010, at 11:05 AM, R. Kent Wenger wrote: > I'm trying to use the "connect" command to connect various atoms > that are > not chemically bonded (to show distance restraints). My question > is, how > do I add a color option to the connect command? I've looked at the > documentation, and tried everything I could think of, but I haven't > gotten > it to work -- one example would be *extremely* helpful. > > If I do > > connect (atomno=442) (atomno=410); > > it works, but the color is not what I want. > > I've tried stuff like this: > > connect (atomno=442) (atomno=410) (color="white"); > > and all kinds of varations with and without parenthesis, quotes, <>, > etc., > and nothing has worked... > > Kent > -- > R. Kent Wenger (we...@cs..., 608-262-6627, > http://www.cs.wisc.edu/~wenger/) > Computer Sciences Department > University of Wisconsin-Madison > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers Dr. Jonathan H. Gutow Chemistry Department gu...@uw... UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow |
From: R. K. W. <we...@cs...> - 2010-03-18 17:35:35
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On Thu, 18 Mar 2010, Jonathan Gutow wrote: > Since you've selected your bonds in the connect command just follow > that line with > > color bond blue > > You can insert your favorite color:) So you're saying that the color part is an entirely separate command? > Are you doing this in relation to the Condor project or something else? > > What are you using Jmol to look at. This is not connected to Condor. It's for the BioMagResBank (http://www.bmrb.wisc.edu/). We're already using Jmol, but I'm working right now on adding visualizations of distance restraints (in proteins, etc.). Kent |
From: Jonathan G. <gu...@uw...> - 2010-03-18 17:52:48
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On Mar 18, 2010, at 12:35 PM, R. Kent Wenger wrote: > On Thu, 18 Mar 2010, Jonathan Gutow wrote: > >> Since you've selected your bonds in the connect command just follow >> that line with >> >> color bond blue >> >> You can insert your favorite color:) > > So you're saying that the color part is an entirely separate command? Yep. Probably best for you to spend a little time looking at the scripting documentation: http://chemapps.stolaf.edu/jmol/docs/ > >> Are you doing this in relation to the Condor project or something >> else? >> >> What are you using Jmol to look at. > > This is not connected to Condor. It's for the BioMagResBank > (http://www.bmrb.wisc.edu/). We're already using Jmol, but I'm > working > right now on adding visualizations of distance restraints (in > proteins, > etc.). > > Kent That makes more sense. I was trying to figure out how it might be related to the project you were listed as working on. Dr. Jonathan H. Gutow Chemistry Department gu...@uw... UW-Oshkosh Office:920-424-1326 800 Algoma Boulevard FAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow |
From: R. K. W. <we...@cs...> - 2010-03-18 18:02:52
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On Thu, 18 Mar 2010, Jonathan Gutow wrote: > > On Mar 18, 2010, at 12:35 PM, R. Kent Wenger wrote: > >> On Thu, 18 Mar 2010, Jonathan Gutow wrote: >> >>> Since you've selected your bonds in the connect command just follow >>> that line with >>> >>> color bond blue >>> >>> You can insert your favorite color:) >> >> So you're saying that the color part is an entirely separate command? > Yep. Probably best for you to spend a little time looking at the > scripting documentation: > http://chemapps.stolaf.edu/jmol/docs/ Hmm. If I do this: connect (atomno=442) (atomno=410); connect (atomno=586) (atomno=266); color bond green; I end up with all of the bonds colored green, not just the ones I added. If I make the whole thing one command, I get an error. The documentation makes it look to me like you should be able to have a color option as part of the connect command, but I haven't been able to come up with any syntax that makes that work. I've looked at the documentation, but I'm still having a hard time understanding some of it. More examples would help, at least for me... Kent -- R. Kent Wenger (we...@cs..., 608-262-6627, http://www.cs.wisc.edu/~wenger/) Computer Sciences Department University of Wisconsin-Madison |
From: Angel H. <ang...@ua...> - 2010-03-18 18:13:51
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R. Kent Wenger wrote: > connect (atomno=442) (atomno=410); connect (atomno=586) (atomno=266); > color bond green; > > I end up with all of the bonds colored green, not just the ones I added. > If I make the whole thing one command, I get an error. That's right. You need a select command to apply colors, connect won't do that. connect (atomno=442) (atomno=410); connect (atomno=586) (atomno=266); select atomno=442, atomno=410, atomno=586, atomno=266; color bond green; # or: select atomno=442, atomno=410; connect (selected); color bond green; select atomno=586, atomno=266; connect (selected); color bond green; > The documentation makes it look to me like you should be able to have a > color option as part of the connect command, but I haven't been able to > come up with any syntax that makes that work. No, I don't think there's such a choice. Connect bonds are normal bonds, once defined, and they take the connected atoms' colors. Only the bond type is an option. I still recommend that you use the draw method. · Dr. Angel Herraez Dep. Bioquimica y Biologia Molecular, Universidad de Alcala E-28871 Alcala de Henares (Madrid), Spain |
From: Robert H. <ha...@st...> - 2010-03-18 19:43:15
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Just don't put parentheses around your color option: connect (atomno=442) (atomno=410) color green connect (atomno=586) (atomno=266) color green On Thu, Mar 18, 2010 at 1:02 PM, R. Kent Wenger <we...@cs...> wrote: > On Thu, 18 Mar 2010, Jonathan Gutow wrote: > > > > > On Mar 18, 2010, at 12:35 PM, R. Kent Wenger wrote: > > > >> On Thu, 18 Mar 2010, Jonathan Gutow wrote: > >> > >>> Since you've selected your bonds in the connect command just follow > >>> that line with > >>> > >>> color bond blue > >>> > >>> You can insert your favorite color:) > >> > >> So you're saying that the color part is an entirely separate command? > > Yep. Probably best for you to spend a little time looking at the > > scripting documentation: > > http://chemapps.stolaf.edu/jmol/docs/ > > Hmm. If I do this: > > connect (atomno=442) (atomno=410); connect (atomno=586) (atomno=266); > color bond green; > > I end up with all of the bonds colored green, not just the ones I added. > If I make the whole thing one command, I get an error. > > The documentation makes it look to me like you should be able to have a > color option as part of the connect command, but I haven't been able to > come up with any syntax that makes that work. > > I've looked at the documentation, but I'm still having a hard time > understanding some of it. More examples would help, at least for me... > > Kent > -- > R. Kent Wenger (we...@cs..., 608-262-6627, > http://www.cs.wisc.edu/~wenger/ <http://www.cs.wisc.edu/%7Ewenger/>) > Computer Sciences Department > University of Wisconsin-Madison > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Angel H. <ang...@ua...> - 2010-03-18 18:07:43
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Hi Kent > So you're saying that the color part is an entirely separate command? Certainly. Once you define bonds, they are treated as such, and that's the command. However, I would advise you not to use bonds for this. You can draw objects (lines, cylinders), and they will be treated separately by Jmol. For example, if you use connect, your connections will be altered by any user that opens the popup menu and changes the style. If you use draw, you retain control over them (and the chemical meaning is preserved). The command is "draw". I think you'd be OK with just lines. And you can color them as you draw them (hopefully) or later. Example: draw diameter 0.2 {atomno=442} {atomno=410} color cyan; |
From: R. K. W. <we...@cs...> - 2010-03-18 18:14:16
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On Thu, 18 Mar 2010, Angel Herráez wrote: >> So you're saying that the color part is an entirely separate command? > > Certainly. Once you define bonds, they are treated as such, and > that's the command. > > However, I would advise you not to use bonds for this. You can draw > objects (lines, cylinders), and they will be treated separately by > Jmol. > For example, if you use connect, your connections will be altered by > any user that opens the popup menu and changes the style. If you use > draw, you retain control over them (and the chemical meaning is > preserved). > > The command is "draw". I think you'd be OK with just lines. And you > can color them as you draw them (hopefully) or later. > Example: > > draw diameter 0.2 {atomno=442} {atomno=410} color cyan; Ah -- this sounds better! Since I want to draw things that are not actually bonds, I guess they shouldn't be bonds in the Jmol world. I just tried that worked for me -- I think that is the answer. Thanks much! Kent |
From: Angel H. <ang...@ua...> - 2010-03-18 19:43:55
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> Thanks much! Good! I forgot this: if you want to control later the connection visibility, color, etc., it's better to give it a name when created: draw myConnectionA diameter 0.2 {atomno=442} {atomno=410} color cyan; then draw myConnectionA off; draw myConnectionA on; color $myConnectionA green; etc. Also, draw list displays a list of all drawn objects with their names/IDs and properties |
From: Robert H. <ha...@st...> - 2010-03-18 19:56:34
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ah -- I see that's in Jmol 11.9.... In Jmol 11.8 it is a bit different. Use OPAQUE or TRANSLUCENT instead of COLOR and the deal is that if you just say: connect {atomno=442} {atomno=129} opaque cyan then that bond already has to be there. (MODIFY assumed) but if you are making a new bond, you need: connect {atomno=442} {atomno=129} opaque cyan CREATE and probably then will also want to set the radius as well: connect {atomno=442} {atomno=129} opaque cyan radius 0.15 CREATE Bob 2010/3/18 Angel Herráez <ang...@ua...> > > Thanks much! > > Good! > > I forgot this: if you want to control later the connection visibility, > color, etc., it's better to give it > a name when created: > > draw myConnectionA diameter 0.2 {atomno=442} {atomno=410} color cyan; > > then > > draw myConnectionA off; > draw myConnectionA on; > color $myConnectionA green; > etc. > Also, > draw list > displays a list of all drawn objects with their names/IDs and properties > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: R. K. W. <we...@cs...> - 2010-03-22 22:23:59
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A couple more (hopefully final) questions about this. I'm doing a command like this: draw diameter 0.2 {atomno=586} {atomno=266} color cyan; as was suggested before. A couple of issues: I seem to always get an error message like this: ERROR: Jmol error evaluating script <draw diameter 0.2 {atomno=586} {atomno=266} color cyan;>: pending Also, if I give two consecutive "draw" commands, only the second one seems to take effect. (I'm guessing that these two errors are related.) I'm passing in the commands via the JmolViewer.script() or JmolViewer.evalString() methods -- they both seem to produce the same errors. *All* of the commands seem to produce the error messages, whether they work or not. I'm obviously doing something wrong here, but I'm not sure what... Kent -- R. Kent Wenger (we...@cs..., 608-262-6627, http://www.cs.wisc.edu/~wenger/) Computer Sciences Department University of Wisconsin-Madison |
From: Robert H. <ha...@st...> - 2010-03-23 02:48:29
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Hmm, I don't know. I don't see "Jmol error evaluating script" anywhere in my code. Is that your code saying that? "pending" is the correct standard return from JmolViewer.script() or JmolViewer.evalString(), so I think you are OK. Maybe you were thinking that should come back null? loadInLine() returns an error or null, but those two just say "pending" because the scripts are just queued at that point. Bob On Mon, Mar 22, 2010 at 5:23 PM, R. Kent Wenger <we...@cs...> wrote: > A couple more (hopefully final) questions about this. I'm doing a command > like this: > > draw diameter 0.2 {atomno=586} {atomno=266} color cyan; > > as was suggested before. > > A couple of issues: > > I seem to always get an error message like this: > > ERROR: Jmol error evaluating script <draw diameter 0.2 {atomno=586} > {atomno=266} color cyan;>: pending > > Also, if I give two consecutive "draw" commands, only the second one seems > to take effect. (I'm guessing that these two errors are related.) > > I'm passing in the commands via the JmolViewer.script() or > JmolViewer.evalString() methods -- they both seem to produce the same > errors. *All* of the commands seem to produce the error messages, whether > they work or not. I'm obviously doing something wrong here, but I'm not > sure what... > > Kent > -- > R. Kent Wenger (we...@cs..., 608-262-6627, > http://www.cs.wisc.edu/~wenger/ <http://www.cs.wisc.edu/%7Ewenger/>) > Computer Sciences Department > University of Wisconsin-Madison > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Angel H. <ang...@ua...> - 2010-03-23 00:31:54
|
Hi Kent > Also, if I give two consecutive "draw" commands, only the second one seems > to take effect. Try to assign a name/ID to each draw object: draw ob1 diameter 0.2 {atomno=586} {atomno=266} color cyan; draw ob2 diameter 0.2 {atomno=596} {atomno=276} color cyan; (the ob1 and ob2 may be any names as long as they are not commands) > (I'm guessing that these two errors are related.) Don't think so. > I'm passing in the commands via the JmolViewer.script() or > JmolViewer.evalString() methods -- they both seem to produce the same > errors. I cannot help with that. Have you tried the script console? Must be somethink specific to those methods. > *All* of the commands seem to produce the error messages, whether > they work or not. So there you are. It's something in that method. |
From: R. K. W. <we...@cs...> - 2010-03-23 00:49:12
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On Tue, 23 Mar 2010, Angel Herráez wrote: > Try to assign a name/ID to each draw object: > > draw ob1 diameter 0.2 {atomno=586} {atomno=266} color cyan; > draw ob2 diameter 0.2 {atomno=596} {atomno=276} color cyan; > > (the ob1 and ob2 may be any names as long as they are not commands) Okay! That did the trick! >> I'm passing in the commands via the JmolViewer.script() or >> JmolViewer.evalString() methods -- they both seem to produce the same >> errors. > > I cannot help with that. Have you tried the script console? > Must be somethink specific to those methods. Hmm, I just tried that, and when I run the same command with the script console, I don't get the errors. I guess I'll check what the script console code is doing. Thanks for the help! Kent |