Bugs item #2860299, was opened at 2009-09-16 16:35 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2860299&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Resolution: Fixed Priority: 5 Private: Yes Submitted By: Ann Stock (astock) Assigned to: Nobody/Anonymous (nobody) Summary: missing alpha carbon in residues displayed on backbone/trace Initial Comment: In all versions of Jmol 11.0 and beyond (coincident with the change in the menu from "render" to "style"), when residues (in stick or ball-and-stick style) are displayed on a backbone or trace, the alpha carbon of the residue is missing from the display (along with bonds to the beta carbon of the side chain and to adjacent alpha carbons). Please see the attached file for images and text that illustrate the problem. This is a terribly annoying bug that limits the usefulness of Jmol for many applications such as displaying the side chains of an active site. For this reason we use only Jmol v. 10.2, but would love to upgrade to a current version to take advantage of many of the new features. Thanks for your help with this. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-09-23 23:12 Message: Please try again. You probably got a piece of it while it was uploading - or I messed up on the upload. I've uploaded http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip again just tonight. ---------------------------------------------------------------------- Comment By: Ann Stock (astock) Date: 2009-09-21 12:57 Message: Bob, It is wonderful to hear that this problem is fixed going forward. I wanted to check it out, but I can't unzip the Jmol-11.zip file at the link you sent. It appears to be a rather small file compared to the other files in the same directory. When you have a chance, can you confirm that the file is OK. Thanks, Ann ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-09-19 19:33 Message: This bug is fixed in Jmol 11.9.5 and 11.8.6. Should be no need for special menus. see http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-09-19 14:54 Message: Ann, The basic custom menu idea is documented in two sample files. http://chemapps.stolaf.edu/docs/misc/Jmol.mnu http://chemapps.stolaf.edu/docs/misc/test.mnu The exact menu may change with Jmol versions. For the full list of menu commands for your application version, use write MENU "somefilename.txt" from the Jmol application and see what is there, and then adapt that. But this still might be a subtle Jmol bug. The current menu item reads: renderSticks = restrict not selected;select not selected;wireframe 0.3;color cpk Way, way back (seriously, 7232 revisions ago) that read: renderSticks = backbone off;spacefill off;wireframe 0.3 That's why that was working the way it was. The difference is the "restrict". In the default mode of "set bondmode AND" the command "backbone off" does nothing when only one residue is selected. But the "restrict not selected" command doesn't respect that and turns off the backbones to that residue. That's what you are seeing. maybe it's a bug. I have to think about that.... In any case, if you just create a file "myfix.mnu" that contains this: renderSticks = backbone off;spacefill off;wireframe 0.3 And then load that as the menu using jmolSetCallback("menuFile", "myfix.mnu") just after jmolInitialize, then you should have the behavior you are after. Bob ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2009-09-17 11:20 Message: Hi Ann. Custom menus are documented in the Wiki: http://wiki.jmol.org/index.php?title=Custom_Menus The mixture of backbone + sticks is called "vines" by Eric Martz in Protein Explroer. Bob, despite your mentioning "trace only"; what I see in the source is using "restrict". I think that is quite old and should have been substituted with display and hide, don't you think so? ---------------------------------------------------------------------- Comment By: Ann Stock (astock) Date: 2009-09-17 09:54 Message: Thank you for this solution. Where can I find help/instructions for customizing the menu? In answer to your question of mixing modes, it is very common to display a small selected set of side chains on a protein backbone/trace to illustrate a group of active site residues or a structural feature such as a hydrogen bond network that might not be contiguous in primary sequence. If all sidechains are displayed the image becomes too cluttered. Examples of this abound in figures in published structural articles. There is rarely a structural paper that does not include such an image. Thanks ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-09-16 21:30 Message: The change is that the menu operations now implement an "only" operation -- "rockets only" "trace only" etc. The feeling was that this is the reasonable expectation of the menu items -- which are meant for general users who want to see a particular style -- not a mixture of styles. In your examples you are doing something much more sophisticated, mixing menu commands with script commands. I think you might be better off not using the popup menu items in this case. Just do it all with scripts. Can you explain the importance of mixing these two modes? The backbone + wireframe sidechain display (what is that called?) is really very nice. I would implement it this way: select *;backbone only;backbone 0.1;color backbone lightblue; select sidechain or *.CA;wireframe 0.1 Also, you know, you can set those menu items to anything you want --- you aren't restricted to what we have defined in Jmol. Why not just design your own custom menu? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2860299&group_id=23629 ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. 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