[Jmol-developers] adding hydrogens
I'm working on adding hydrogens. That's been in there for simple models, what I did today was set that up for amino acid and nucleic acid polymers. Seems to be working OK, but just a warning for heads up -- there were some problems with selecting groups after adding hydrogens. I think I've got that fixed, but maybe not. Be on the lookout for strange select problems. Bob -- 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 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Question about coordinates in Jmol
well, the molecular coordinates are just the molecular coordinates. This slicing is by them, right? Not the screen coordinates? There are three coordinate systems: -- molecular coordinates -- relation of those by rotation to the original view (the orientation quaternion/matrix) -- translation of that into screen coordinates (the transformation matrix) I'd sure like to hear more about what the specs are going to be on this slice command. Before you go too far, Jonathan, can you remind us of what exactly it is going to do? Q: Are we slicing in molecular coordinates (like isosurface slab plane... and slab plane...) or screen coordinates (like slab/depth and isosurface slab nnn)? Q: Does the slab change when you rotate the model, or is it fixed? (Basically the same as the previous question.) Q: What functionality does this add that does not already exist in the other commands? There is no point in adding a new command unless it makes *scripting* far easier. This sounds a lot more like a GUI thing -- which would use the already-existent commands, possibly with a few modifications to suit. It seems to me a popup window is a nice idea -- at least for the application. Not convinced with respect to the applet -- we don't do that, so far, except with the signed applet for file read/write. A good dialog can take lots and lots of code to produce and work with. If possible, with the applet, we should do that in JavaScript, not Java. (My opinion.) By the way, you asked about the possibility of duplicating an isosurface so there was a translucent shadow. Since rendering is a two-pass system, a better way On Wed, Jun 29, 2011 at 3:39 PM, Jonathan Gutow gu...@uwosh.edu wrote: As I am working on figuring out what I have to track for a GUI to control slabbing/slicing, I have encountered the issue that the coordinate system for the molecule and the viewing space are not always the same. Do I have to worry about relative rotations of these axes or just the offset of the center? All the examples I've found so far have the origins translated versus each other, but no relative rotations. I'm also trolling the code, but if somebody knows the answer that will save me time. Thanks, Jonathan Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net 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 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Question about coordinates in Jmol
By the way, you asked about the possibility of duplicating an isosurface so there was a translucent shadow. Since rendering is a two-pass system, a better way... ... to do that might be to set a flag to render the translucent pass without slab and the opaque one with. Something on that order would be way preferable to creating a whole new object just for that. Bob -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] update of CARBOHYDRATE atom set definition
I have NOT removed the obsolete IDs. They are still there for backwards compatibility. I just moved them all to the last line so they are easily identified as such. After all, we are supporting old atom and residue names like A T G C in DNA, both 3' and 3* etc. Unless the same IDs are now used for non-carbohydrate groups (see below). That would lead to strange groups being taken as carbohydrate, which I think should not happen. ASF is N-GLYCOSYL CHAIN When was that? ASF, when I check in the PDB, says a totally different group. That's why I removed it. http://ligand-expo.rcsb.org/ld-search.html ASF = 3-(butylsulfonyl)propanoic acid NAM = NAPTHYLAMINOALANINE I haven't changed 12.0 yet, probably will do tonight. I wonder how hard it would be to get the whole list of carbohydrates from PDB. I guess that could be a long list Yes, it may well be. At least we should have the most common. Please check out the wiki page I put up yesterday for this. Particularly the cathegorized section, that's more helpful. The reason to include them is that carbohydrates is used in its more inclusive term, not just for Cx(H2O)y. Right? No, I wasn´t that picky. For me, anything that goes in an oligosaccharide in a glycoprotein should be included (as it is part of the macromolecule). More those than ligands like lactose or cellotriose, which are fine. Anyone knows of other group IDs that should be added? Please email or use the Talk page for http://wiki.jmol.org/index.php/AtomSets/Carbohydrate -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] update of CARBOHYDRATE atom set definition
Don't get me wrong -- I'm totally supportive of this effort. I just got mixed up because I didn't realize that PDB had a different name for NAM than what biochemists all know as NAM (AMU). So that was missing. Here's an example (probably of no more than 8 examples total) of where NAM is NAM: !-- Jaime Prilusky Jul 1996 -- BODYHTMLTITLEPDB Full entry for 9LYZ/TITLE ... PREHEADERHYDROLASE (O-GLYCOSYL) 06-DEC-79 9LYZ 9LYZ 3 COMPNDLYSOZYME (NAM-NAG-NAM SUBSTRATE ONLY) A HREF= http://expasy.hcuge.ch/cgi-bin/get-enzyme-entry?3.2.1.17;(E.C.3.2.1.17)/A 9LYZ 4 ... REMARK 5 CORRECTION. INSERT REVDAT RECORDS. 30-SEP-83. 9LYZA 4 SEQRES 1 S3 NAM NAG NAM 9LYZ 27 a href=/cgi-bin/send-het?NAMHETNAM/a S 1 19 2-ACETAMIDO-2-DEOXY-D-MURAMIC ACID9LYZ 28 a href=/cgi-bin/send-het?NAGHETNAG/a S 2 14 2-ACETAMIDO-2-DEOXY-D-GLUCOSE 9LYZ 29 a href=/cgi-bin/send-het?NAMHETNAM/a S 3 20 2-ACETAMIDO-2-DEOXY-D-MURAMIC ACID9LYZ 30 FORMUL 1 NAM2(C11 H19 N1 O8) 9LYZ 31 FORMUL 2 NAGC8 H11 N1 O6 9LYZ 32 But the new name for that is AMU, and I'm totally for only using that, and I added it, along with the epimer of NAG, NDG. Do we still then need NAM? -- 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 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Question about coordinates in Jmol
Last comment first. On Jun 30, 2011, at 1:10 AM, Robert Hanson wrote: By the way, you asked about the possibility of duplicating an isosurface so there was a translucent shadow. Since rendering is a two-pass system, a better way... ... to do that might be to set a flag to render the translucent pass without slab and the opaque one with. Something on that order would be way preferable to creating a whole new object just for that. That might be good. It certainly would help with memory. The only issue I see with this option is need for another separate control of the ghost rendering (mostly I think mesh versus fill and level of transparency). What people have been doing is rendering two surfaces one opaque and slabbed and then a ghost unslabbed. In playing around with orbitals and cavities where you may want to see the inside surfaces of the slice through the ghost, I've found that the ghost settings that seems to work best are a transparecy of ~200 and mesh nofill. However, most of the SageMath people have been using filled. The math people also have a tendency to use a different color for the ghost. I'm partial to the same surface color rendering/mapping as the slabbed region. Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Question about coordinates in Jmol
I try to answer your questions below. In summary, now that you've changed the isosurface slab command so that it can be done after the surface is defined I am mostly concerned with building a GUI that is intuitive enough that people don't have to understand the details of the isosurface and slab commands to look at a section through the displayed object. My first goal is to get this working well for isosurfaces, but I don't think it will be hard to extend it to do everything. On Jun 30, 2011, at 1:07 AM, Robert Hanson wrote: well, the molecular coordinates are just the molecular coordinates. This slicing is by them, right? Not the screen coordinates? There are three coordinate systems: -- molecular coordinates -- relation of those by rotation to the original view (the orientation quaternion/matrix) -- translation of that into screen coordinates (the transformation matrix) I'd sure like to hear more about what the specs are going to be on this slice command. Before you go too far, Jonathan, can you remind us of what exactly it is going to do? Q: Are we slicing in molecular coordinates (like isosurface slab plane... and slab plane...) or screen coordinates (like slab/depth and isosurface slab nnn)? The first draft will be slicing in molecular coordinates, although I think some people might also like a GUI for slab/depth like behavior. Q: Does the slab change when you rotate the model, or is it fixed? (Basically the same as the previous question.) People wanted to be able to look at the slice from different angles so that's why molecular coordinates. Q: What functionality does this add that does not already exist in the other commands? Other than a ghost feature, which presently requires building a duplicate surface, I cannot think of anything. Anyway, the issue is that people want the ability to specify the slice in a way that is logical relative to the view. Tentatively, I am going to make the controls relative to the origin of the boundingbox. If they are relative to the view orientation, things change on rotation and translation. I think that would be confusing. I think there should also be an option to do everything relative to the absolute coordinates (molecular). I'll just set a switch. So I am still at my original question, which is will the boundbox coordinates always be parallel to the molecular coordinates? There is no point in adding a new command unless it makes *scripting* far easier. This sounds a lot more like a GUI thing -- which would use the already-existent commands, possibly with a few modifications to suit. I agree. Initially as I began looking at what Jmol could do, I thought it would help. Now I'm not sure. It seems to me a popup window is a nice idea -- at least for the application. Not convinced with respect to the applet -- we don't do that, so far, except with the signed applet for file read/write. A good dialog can take lots and lots of code to produce and work with. If possible, with the applet, we should do that in JavaScript, not Java. (My opinion.) I agree for another usability reason as well. When you have more than one applet on a page it is difficult to tell which one the pop-ups go with. A javascript tool that is anchored on the page in the vicinity of the applet is much easier to understand. That is one of the reasons, I thought about a special command. The idea being that the smaller the scripts that have to be passed the better the potential for speed. By the way, you asked about the possibility of duplicating an isosurface so there was a translucent shadow. Since rendering is a two-pass system, a better way I like your idea and have sent a comment in a separate message. Jonathan Dr. Jonathan H. Gutow Chemistry Departmentgu...@uwosh.edu UW-Oshkosh Office: 920-424-1326 800 Algoma BoulevardFAX:920-424-2042 Oshkosh, WI 54901 http://www.uwosh.edu/facstaff/gutow -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] update of CARBOHYDRATE atom set definition
Bob Hanson wrote: Don't get me wrong I didn't. No worries. PREHEADER HYDROLASE (O-GLYCOSYL) 06-DEC-79 I think that date is the key here. PDB has been doing a lot of change. But on the other hand we all keep old files around in our disks and webpages, so the conservative attitude is fine. Do we still then need NAM? Since it points now to a different compund in PDB official doc, I think better not to include it. The deprecated names that are stated as such and have no new meaning can be left. -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of 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-d2d-c2 ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
