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] 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
[Jmol-developers] update of CARBOHYDRATE atom set definition
Dear developers, I have committed code that updates the definition of the 'carbohydrate' atom set. This is based on a list of residue IDs (provided by Eric some time ago). While working with some glycans in glycoproteins, I have found out a few common residues (N-acetyl-galactosamine and sialic acid) that were not included in the set, so I have added them in the list. While doing that, I reviewed the whole list against the PDB Ligand Expo site, http://ligand- expo.rcsb.org/ld-search.html and found out - that some listed residue IDs are now deprecated from the PDB. I have still left them in the list but have separated them and included a comment (in case we want to remove them in future) - that two listed residue IDs were not carbohydrates (maybe a typo), so I have removed them The list will now be documented at http://wiki.jmol.org/index.php/AtomSets Now my question: I'd like to introduce this change too in the 12.0.x series. Do you think it qualifies as a bug fix and so it can go there, or is it a change in behaviour and it should only go in the 12.1.x? Thanks for your views Angel -- 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 vote for bug-fix and inclusion in 12.0 Jonathan On Jun 29, 2011, at 1:35 PM, Angel Herráez wrote: Dear developers, I have committed code that updates the definition of the 'carbohydrate' atom set. This is based on a list of residue IDs (provided by Eric some time ago). While working with some glycans in glycoproteins, I have found out a few common residues (N-acetyl-galactosamine and sialic acid) that were not included in the set, so I have added them in the list. While doing that, I reviewed the whole list against the PDB Ligand Expo site, http://ligand- expo.rcsb.org/ld-search.html and found out - that some listed residue IDs are now deprecated from the PDB. I have still left them in the list but have separated them and included a comment (in case we want to remove them in future) - that two listed residue IDs were not carbohydrates (maybe a typo), so I have removed them The list will now be documented at http://wiki.jmol.org/index.php/AtomSets Now my question: I'd like to introduce this change too in the 12.0.x series. Do you think it qualifies as a bug fix and so it can go there, or is it a change in behaviour and it should only go in the 12.1.x? Thanks for your views Angel -- 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 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
You can do that, but we are very close to not doing any more bug fixes in 12.0. I'd like to release 12.0 in mid to late July. On Wed, Jun 29, 2011 at 1:42 PM, Jonathan Gutow gu...@uwosh.edu wrote: I vote for bug-fix and inclusion in 12.0 Jonathan On Jun 29, 2011, at 1:35 PM, Angel Herráez wrote: Dear developers, I have committed code that updates the definition of the 'carbohydrate' atom set. This is based on a list of residue IDs (provided by Eric some time ago). While working with some glycans in glycoproteins, I have found out a few common residues (N-acetyl-galactosamine and sialic acid) that were not included in the set, so I have added them in the list. While doing that, I reviewed the whole list against the PDB Ligand Expo site, http://ligand- expo.rcsb.org/ld-search.html and found out - that some listed residue IDs are now deprecated from the PDB. I have still left them in the list but have separated them and included a comment (in case we want to remove them in future) - that two listed residue IDs were not carbohydrates (maybe a typo), so I have removed them The list will now be documented at http://wiki.jmol.org/index.php/AtomSets Now my question: I'd like to introduce this change too in the 12.0.x series. Do you think it qualifies as a bug fix and so it can go there, or is it a change in behaviour and it should only go in the 12.1.x? Thanks for your views Angel -- 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 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] update of CARBOHYDRATE atom set definition
I mean 12.2 On Wed, Jun 29, 2011 at 4:15 PM, Robert Hanson hans...@stolaf.edu wrote: You can do that, but we are very close to not doing any more bug fixes in 12.0. I'd like to release 12.0 in mid to late July. On Wed, Jun 29, 2011 at 1:42 PM, Jonathan Gutow gu...@uwosh.edu wrote: I vote for bug-fix and inclusion in 12.0 Jonathan On Jun 29, 2011, at 1:35 PM, Angel Herráez wrote: Dear developers, I have committed code that updates the definition of the 'carbohydrate' atom set. This is based on a list of residue IDs (provided by Eric some time ago). While working with some glycans in glycoproteins, I have found out a few common residues (N-acetyl-galactosamine and sialic acid) that were not included in the set, so I have added them in the list. While doing that, I reviewed the whole list against the PDB Ligand Expo site, http://ligand- expo.rcsb.org/ld-search.html and found out - that some listed residue IDs are now deprecated from the PDB. I have still left them in the list but have separated them and included a comment (in case we want to remove them in future) - that two listed residue IDs were not carbohydrates (maybe a typo), so I have removed them The list will now be documented at http://wiki.jmol.org/index.php/AtomSets Now my question: I'd like to introduce this change too in the 12.0.x series. Do you think it qualifies as a bug fix and so it can go there, or is it a change in behaviour and it should only go in the 12.1.x? Thanks for your views Angel -- 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 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 -- 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] update of CARBOHYDRATE atom set definition
I returned NAM and ASF for 12.1 -- I suggest they be returned for 12.0 as well. NAM is *N*-acetylmuramic acidhttp://en.wikipedia.org/wiki/N-Acetylmuramic_acid ASF is N-GLYCOSYL CHAIN Was there some reason you were considering these not to be carbohydrates, Angel? The reason to include them is that carbohydrates is used in its more inclusive term, not just for Cx(H2O)y. Right? Bob 2011/6/29 Angel Herráez angel.herr...@uah.es Dear developers, I have committed code that updates the definition of the 'carbohydrate' atom set. This is based on a list of residue IDs (provided by Eric some time ago). While working with some glycans in glycoproteins, I have found out a few common residues (N-acetyl-galactosamine and sialic acid) that were not included in the set, so I have added them in the list. While doing that, I reviewed the whole list against the PDB Ligand Expo site, http://ligand- expo.rcsb.org/ld-search.html and found out - that some listed residue IDs are now deprecated from the PDB. I have still left them in the list but have separated them and included a comment (in case we want to remove them in future) - that two listed residue IDs were not carbohydrates (maybe a typo), so I have removed them The list will now be documented at http://wiki.jmol.org/index.php/AtomSets Now my question: I'd like to introduce this change too in the 12.0.x series. Do you think it qualifies as a bug fix and so it can go there, or is it a change in behaviour and it should only go in the 12.1.x? Thanks for your views Angel -- 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
