Re: [Jmol-developers] JSmol as network viewer
On 10/07/2014 06:12 PM, Robert Hanson wrote: Q: Does JSmol allow that an atom is part of more than one residue or would this interfere with something? Certainly an atom can only be in one residue. Each atom has a group property that points to its residue. Sorry, I should have posed the question differently: Would it be possible without too much trouble and work to extend the current group property by a grouplist property that would enable to put an atom into multiple groupsand integrating this seamlessly into the current group concept? Since the basic 'Jena3D Viewer' system was designed in 2005/2006 Jmol math wasn't available yet. And I must admit that I havn't looked in detail how self-defined atom set containing variables might be more helpful in this context. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
Rolf, Would it be possible without too much trouble and work to extend the current group property by a grouplist property that would enable to put an atom into multiple groupsand integrating this seamlessly into the current group concept? To me, that sounds exactly like setting a new, user-defined, atom property. That's what I was suggesting previously. however, you said that would work very slowly for subsequent action/selection. I am not sure about this, but I do not see a reason why a group property would be faster than a user property. -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
On 10/08/2014 11:54 AM, Herráez Sánchez Ángel wrote: Rolf, Would it be possible without too much trouble and work to extend the current group property by a grouplist property that would enable to put an atom into multiple groupsand integrating this seamlessly into the current group concept? To me, that sounds exactly like setting a new, user-defined, atom property. That's what I was suggesting previously. however, you said that would work very slowly for subsequent action/selection. I am not sure about this, but I do not see a reason why a group property would be faster than a user property. Sorry, I misunderstood you there. I thought you were refering to custom atom sets not custom atom properties. I don't know how this would influence performance. But performance is just one aspect. Even more important would be that observations could be handled in the same way like residues are now. This means you would be able to use the same syntax and use them in all places were residues can be used. There would be less need for self-build functions and future enhancements would automatically be available for observations too. Since I am just at the beginning I can't name here any detailed benefits. Besides I could imagine that this kind extension to the group concept might also be helpful in the original JSmol cotext of structural chemistry/biology. Maybe even more because many people will are already familiar with the standard syntax. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
On 10/08/2014 02:11 PM, Robert Hanson wrote: Groups are at the core of Jmol for PDB files, which are among the largest (slowest to process). They are key to all processing, including rendering. The idea of going from a one-group simple pointer method to a multi-group look-up table for something that is not a core molecular property is not really an option. There must be another way. I suspected this. But I didn't want to miss an opportunity for the optimal solution prior to actually designing the system and asked. Certainly there are other ways to handle this. Thank you for the bitset variable example. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
On 10/06/2014 08:38 PM, Robert Hanson wrote: Probably not. I didn't realize we were talking about quite so many nodes. Still, the UFF field is interesting because it might work with any geometry -- leaving angles out all together. We might have to add something to get it to ignore certain energy components. Angles and dihedrals, for instance. The more I think about it the more I doubt it really makes sense for me to dig deep into UFF and spend a lot of time just to find out that it doesn't really fit to the task. I took a quick look at a paper on UFF from Rappe et al (J. Am. Chem. Soc. 114:10024-10035, 1992) and can't really imagine how I would be able to fit this into my task. Bob, maybe if I would describe some possibly suitable (initial) layout strategies that came into my mind you could give me a hint if it would really be worth the effort to try to make UFF work for networks. For a specific ageing factor there will be for example two types of networks: 1) All observations in which the ageing factor participates and all other ageing factors that are also involved in these observations. This means there will be one central ageing factor node connected to all observations. And each observation will be connected to currently up to six other ageing factors. 2) An iterative combination of type 1 networks for each ageing factor from type 1 into a huge combined network. This will be much more complex with a lot of smaller and larger centers, connected by one or more observations. Finding a suitable layout for type 1 might not be too complicated. I thought about two strategies: 1a) The observation nodes are evenly distributed within a sphere around the central ageing factor node. The other ageing factor nodes are then again distributed evenly within a sphere around their observation node. Nodes with more connections are preferably positioned in the outer parts. 1b) The other ageing factor nodes are evenly distributed within a sphere around the central ageing factor node. The observation nodes are then evenly distributed in the non-overlapping part of a second larger sphere around the central ageing factor. This will be more complicated to achieve than 1a but it has the advantage that it will be possible to group the ageing factors and separately also the observations by user-defined criteria. For example on one side of the sphere could be placed all observations that decrease the lifespan. On the other side could be the observations that increase the lifespan. And in the middle could be the neutral ones. Building type 2 will presumably be more complicated. Only strategy 1a would fit in here I would guess. I don't think that strategy 1b is compatible with type 2, at least not without containing nodes redundantly. (But maybe without a real center...?) My final goal would be to develop a general purpose JSmol-based network viewer (not just AgeFactDB-related). I guess it will be somehow similar to the Jena3D viewer for PDB structures but ideally without a server backend (except maybe as additional information source). Finally I have a related question: Q: Does JSmol allow that an atom is part of more than one residue or would this interfere with something? I ask this because it would enable to use residue-based functions for handling observations. (A residue would consist of the observation node and all connected ageing factor nodes. Ageing factor nodes might then be part of a larger number of residues.) I really hope that this is possible because it would speed up things a lot and also spare me a lot of development time. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
Hi Rolf This is interesting but not what I can really discuss about, but I'd contribute one or two hints: One really nice thing (I've seen it in other tree viewers) would be the ability for the user to pull a node and have the whole thing rearrange dynamically. That's a force field and Jmol already does this with dragMinimze. However, probably not easy to achieve seeing the complexity of your trees (i.e. many bonds tied to an atom). Q: Does JSmol allow that an atom is part of more than one residue or would this interfere with something? Quick answer: no atom can belong to 2 residues. But I would forget about residues. I'd just define Jmol variables as atom sets and assign each node to as many of them as you wish (using a script). It is as easy to select by user variables / atomsets as by residue. Another possibility is to assign custom atom properties, instead of atom sets. -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
On 10/07/2014 04:50 PM, Angel Herráez wrote: Hi Rolf This is interesting but not what I can really discuss about, but I'd contribute one or two hints: One really nice thing (I've seen it in other tree viewers) would be the ability for the user to pull a node and have the whole thing rearrange dynamically. That's a force field and Jmol already does this with dragMinimze. However, probably not easy to achieve seeing the complexity of your trees (i.e. many bonds tied to an atom). Yes, Angel. It would be one of the next steps to make the layout directly editable by the user. It could be completely manually or manually-directed like you describe it. But for this you need a reasonable initial layout. I will keep this in mind if I ever get past the first step. Q: Does JSmol allow that an atom is part of more than one residue or would this interfere with something? Quick answer: no atom can belong to 2 residues. But I would forget about residues. I'd just define Jmol variables as atom sets and assign each node to as many of them as you wish (using a script). It is as easy to select by user variables / atomsets as by residue. Another possibility is to assign custom atom properties, instead of atom sets. That is what I do within the 'Jena3D Viewer' for the different mappings (SAPs/SNPs, PROSITE motifs etc.). And from there I know that commands can be very slowly this way. Handling for example several hundred SNPs by using sets already takes quite some time (see for example http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1A00APPLET=HTML5). And in the network viewer the number of sets would potentially be much higher. It will also require to rebuild a lot of built-in functions to get similar (slower) functionalities. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] JSmol as network viewer
Hi developers, I am in the brainstorming phase for a possible use of JSmol as an interactive 3D network viewer. In April 2008 there was a thread on the 'jmol-users' list (Hub and Non-Hub) where this kind of application was described to some extent by Joe Ivanic. Although it is not a focus of JSmol I would agree with Joe that JSmol would be very flexibel and powerful as a Javascript (and Java) tool to visualize and manipulate complex networks. Now even much more than in 2008. There are a few other tools available but none I could find was nearly as powerful as JSmol. And besides I am already quite familiar with the JSmo scripting language. The major problem, as Joe also pointed out, will be to define the coordinates for the nodes within the network. Here is an example to illustrate one kind of network I am interested in: Our group has developed 'AgefactDB' (http://agefactdb.jenage.de), an ageing factor database. An ageing factor can be for example a gene like 'daf-16' in Caenorhabditis elegans that influences the lifespan of the organism. Our database contains currently 398 individual experimental observations where the effect on lifespan in combination with other genes, chemical compounds or other factors like caloric restriction was determined (http://agefactdb.jenage.de/cgi-bin/jaDB.cgi?RKEY=r001SEARCH=AF_005812TYPE=d_faVIEW=detail#section_observation_d_fa). In 291 observations the lifespan was decreased, in 56 it was increased and in 51 there was no effect. This results in a network involving about 200 different ageing factors. I think it could be very helpful to visualize this interactively with JSmol. The idea would be to have two different types of nodes (atoms): observations and ageing factors. And the edges (bonds) would be the connections between observations and ageing factors. The result would be network (molecule) where all nodes are connected with at least one other node of the network. Another level would be to combine several of these networks into a single view, e.g. all ageing factors from a single species or all homologous genes from several different species. This would lead to several not connected networks (molecules) which would most probably require a different kind of positioning algorithm. Q: I was wondering if it might be possible to achieve this by tuning the 'minimize' command with some extra parameters or maybe by enabling to define a custom 'minimize' function? Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi developers, Q: I was wondering if it might be possible to achieve this by tuning the 'minimize' command with some extra parameters or maybe by enabling to define a custom 'minimize' function? I think if you did UFF minimization you could adapt j2s/J/minimize/forcefield/data/UFF.txt to just about anything you wanted to. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
On 10/06/2014 02:22 PM, Robert Hanson wrote: On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi developers, Q: I was wondering if it might be possible to achieve this by tuning the 'minimize' command with some extra parameters or maybe by enabling to define a custom 'minimize' function? I think if you did UFF minimization you could adapt j2s/J/minimize/forcefield/data/UFF.txt to just about anything you wanted to. Bob, do you really think that it will be possible to adapt the parameters in the UFF file to cope with atoms that can have several hundred or even thousands of bonds and get a reasonable network layout? At a first glance it doesn't look very likely for me. But I must admit that I have never dealt with UFF or something similar before. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] JSmol as network viewer
Probably not. I didn't realize we were talking about quite so many nodes. Still, the UFF field is interesting because it might work with any geometry -- leaving angles out all together. We might have to add something to get it to ignore certain energy components. Angles and dihedrals, for instance. On Mon, Oct 6, 2014 at 9:55 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 10/06/2014 02:22 PM, Robert Hanson wrote: On Mon, Oct 6, 2014 at 6:32 AM, Rolf Huehne rhue...@fli-leibniz.de wrote: Hi developers, Q: I was wondering if it might be possible to achieve this by tuning the 'minimize' command with some extra parameters or maybe by enabling to define a custom 'minimize' function? I think if you did UFF minimization you could adapt j2s/J/minimize/forcefield/data/UFF.txt to just about anything you wanted to. Bob, do you really think that it will be possible to adapt the parameters in the UFF file to cope with atoms that can have several hundred or even thousands of bonds and get a reasonable network layout? At a first glance it doesn't look very likely for me. But I must admit that I have never dealt with UFF or something similar before. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- Slashdot TV. Videos for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471iu=/4140/ostg.clktrk___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
