From: David L. <d.l...@bi...> - 2007-05-15 15:21:27
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I asked about representing mainchain-sidechain H-bonds for short three-dimensional hydrogen bonded motifs. Bob replied: >If the motifs are well-described in the PDB file, this would be no >problem. If they are to be generated from scratch, that's more of a problem. No. The way the thing works is that the H-bonds are generated from the PDB files using HBPlus, which is then parsed by a Perl script to generate a table of H-bonds for the SQL database. The motif definitions are cast as SQL queries to populate the database with them. (They could be done on the fly, but it would be too slow.) When a user makes a query for a particular motif in a particular, the residues are retrieved (as residue numbers), and this info is used to generate a pop-up page with the appropriate PDB file displayed in Jmol and the buttons scripted to to highlight or restrict the display to the motif. Jmol calculates mainchain-mainchain H-bonds on the fly, so if the display is restricted to the motif residues, they show fine, so if Jmol could also calculate the other H-bonds that would be ideal. One alternative would be to query the db for the HBonds associated with the motif and retrieve these, but this would add complexity and might slow things down. The other might appear to be to compute the sidechain-mainchain H-bond for a particular definition. This might be Ok for eg the Asx Turn in which an Asx O at residue 1 is H-bonded to a mainchain NH at residue 3, but for other motifs the mainchain residue can be one of two positions. However Angel suggested: >say, >connect 3.0 (AS?.N??) (SER.O??) hbond >to create Hbonds between nitrogen atoms in Asx and oxygen atoms in >serine if they are less than 3 angstroms apart Which might be more promising, but would require generate pages with different jmol scripts depending on the motif. Sigh. There's probably a good reason why none of the protein graphics programs calculate the mainchain-sidechain H-bonds. David -- _______________________________________________________________ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader _______________________________________________________________ |
From: David L. <d.l...@bi...> - 2007-05-16 08:37:28
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Thanks, Bob, for specific suggestions for using the H-bond data in our database to display sidechain mainchain H-bonds in motifs. I'll have to consider the best way to proceed within the constraints of our setup. As a general comment, however, I would say that I appreciate that Jmol is in a different phase at the moment from what it was when Miguel was doing most of the work. At that time the emphasis was to reproduce the RasMol/Chime capabilities, which were especially directed towards representing proteins. Miguel did an incredible job, to the extent that Chime can now be considered to have been replaced completely by Jmol. However, given that one of the features of Rasmol introduced in Jmol is the automatic calculation of mainchain-mainchain H-bonds, which is obviously of interest to some protein chemist, if it had been possible to introduce mainchain-sidechain calculations this would have been of similar benefit. It may be worth bearing in mind, should the wheel ever turn again and the protein features are ever subject to reexamination. Clearly, at the moment the emphasis - and interest of the people that are doing the work - is in other areas which will extend the usefulness of Jmol to a larger section of the scientific community. I appreciate that and am grateful for it. David -- _______________________________________________________________ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader _______________________________________________________________ |
From: Bob H. <ha...@st...> - 2007-05-16 11:37:01
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Thank you, David. Yes, I agree completely. An interesting aspect of Jmol is that it is a mix of implementing what others have successfully done elsewhere and innovating totally new ways of doing things that either haven't ever been done or haven't ever been done effectively. In every case what we try to do is find out (a) whether a problem has already been satisfactorily solved, (b) if so, if that algorithm is freely available and useable within the GNU Lesser Public License, and (c) if it is reasonable to implement within Jmol. If any one of these answers is "no" as, for example, was the case with translucency (not c) or JVXL format (not a) then the real fun begins. But if (a-c) are yes, then we can still get to work. Code size is not necessarily an issue anymore. The really nice thing about Jmol 11 is that it doesn't so much matter any more if something takes space -- we'll just isolate it in a JAR file that only gets downloaded if the capability is needed. This new feature of Jmol will be particularly useful for just such situations. So, regarding the mainchain-sidechain hydrogen bond, you can help by finding out about (a) and (b). What is HBPLUS? Is the algorithm published? Is the code available for checking? Is it reasonably efficient? Please enter this as a feature request with as much background information as you can find -- URLs, personal experience, suggestions -- so that we can continue a thread specifically in relation to it. It's possible, for example, that we would expand upon it and produce a Jmol that can calculate reasonable hydrogen bonds for ANY situation, not just PDB files. Bob David Leader wrote: >Thanks, Bob, for specific suggestions for using the H-bond data in >our database to display sidechain mainchain H-bonds in motifs. I'll >have to consider the best way to proceed within the constraints of >our setup. > >As a general comment, however, I would say that I appreciate that >Jmol is in a different phase at the moment from what it was when >Miguel was doing most of the work. At that time the emphasis was to >reproduce the RasMol/Chime capabilities, which were especially >directed towards representing proteins. Miguel did an incredible job, >to the extent that Chime can now be considered to have been replaced >completely by Jmol. However, given that one of the features of Rasmol >introduced in Jmol is the automatic calculation of >mainchain-mainchain H-bonds, which is obviously of interest to some >protein chemist, if it had been possible to introduce >mainchain-sidechain calculations this would have been of similar >benefit. It may be worth bearing in mind, should the wheel ever turn >again and the protein features are ever subject to reexamination. >Clearly, at the moment the emphasis - and interest of the people that >are doing the work - is in other areas which will extend the >usefulness of Jmol to a larger section of the scientific community. I >appreciate that and am grateful for it. > >David > > |
From: Bob H. <ha...@st...> - 2007-05-15 15:33:56
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David Leader wrote: >I asked about representing mainchain-sidechain H-bonds for short >three-dimensional hydrogen bonded motifs. Bob replied: > > > >>If the motifs are well-described in the PDB file, this would be no >>problem. If they are to be generated from scratch, that's more of a problem. >> >> > >No. The way the thing works is that the H-bonds are generated from >the PDB files using HBPlus, which is then parsed by a Perl script to >generate a table of H-bonds for the SQL database. > So a particular pdb file generates a particular set of H-bonds in a table that is stored in the database? Then why not just send the table to the web page along with the rest of the information you send? It shouldn't be hard for you to do a little server-side or client-side manipulating of that to create the Jmol script necessary to do the connections. It would look like: connect (atomno=3430) (atomno=2234) hbond; connect (atomno=3431) (atomno=2567) hbond; connect (atomno=3432) (atomno=2345) hbond; connect (atomno=3433) (atomno=2134) hbond; connect (atomno=3434) (atomno=2245) hbond; Or, for that matter, you could append the hydrogen bonding information to the PDB file in the proper PDB format for hydrogen bond CONECT records, and then I think Jmol would (or should) just handle that directly. Should be quite feasible. In fact, if you wanted to, you could just have Jmol not do the hbonding and take all the hbonds from the table sent from the server, if it were important to display the HBPlus determinations precisely. Bob > The motif >definitions are cast as SQL queries to populate the database with >them. (They could be done on the fly, but it would be too slow.) When >a user makes a query for a particular motif in a particular, the >residues are retrieved (as residue numbers), and this info is used to >generate a pop-up page with the appropriate PDB file displayed in >Jmol and the buttons scripted to to highlight or restrict the display >to the motif. > >Jmol calculates mainchain-mainchain H-bonds on the fly, so if the >display is restricted to the motif residues, they show fine, so if >Jmol could also calculate the other H-bonds that would be ideal. One >alternative would be to query the db for the HBonds associated with >the motif and retrieve these, but this would add complexity and might >slow things down. The other might appear to be to compute the >sidechain-mainchain H-bond for a particular definition. This might be >Ok for eg the Asx Turn in which an Asx O at residue 1 is H-bonded to >a mainchain NH at residue 3, but for other motifs the mainchain >residue can be one of two positions. > >However Angel suggested: > > > >>say, >>connect 3.0 (AS?.N??) (SER.O??) hbond >>to hbond creates between nitrogen atoms in Asx and oxygen atoms in >>serine if they are less than 3 angstroms apart >> >> > >Which might be more promising, but would require generate pages with >different jmol scripts depending on the motif. > >Sigh. There's probably a good reason why none of the protein graphics >programs calculate the mainchain-sidechain H-bonds. > >David > > > > |
From: Angel H. <ang...@ua...> - 2007-05-15 17:08:00
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> >Sigh. There's probably a good reason why none of the protein graphics > >programs calculate the mainchain-sidechain H-bonds. Probably, that it is not a trvial and generalizable task. David, if you already have a program that computes the Hbonds, I think you should use that data, rather than asking Jmol to compute them again. I agree with Bob that you could possibly pass that info to a Jmol script --doesn=B4t mean generating different pages-- > >When > >a user makes a query for a particular motif in a particular, the > >residues are retrieved (as residue numbers), and this info is used to > >generate a pop-up page with the appropriate PDB file displayed in > >Jmol and the buttons scripted to to highlight or restrict the display > >to the motif. (...and the Hbonds info is also retrived and used while generating the page or the buttons) |