Re: [Jmol-users] Advice on display of cyclic DNA: more ...
>Henry, I've devised a (very) dirty solution: >duplicate residue 1 as nr. 9 > >The trace or cartoon is very sharp at the connection, agreed > so things get >better if we shift the residue numbering, such as making >1 -> 6 >2 -> 7 >3 -> 8 >4 -> 1 >5 -> 2 >6 -> 3 >7 -> 4 >8 -> 5 >9 is a copy of the new residue 1 (former 6); this is in the >straightest part of the chain, so the conection looks better. > Not easy to code in a general sense! Perhaps that is why no-one has tried to! Thanks again. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf (FOAF) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
Henry, I've devised a (very) dirty solution: duplicate residue 1 as nr. 9 The trace or cartoon is very sharp at the connection, so things get better if we shift the residue numbering, such as making 1 -> 6 2 -> 7 3 -> 8 4 -> 1 5 -> 2 6 -> 3 7 -> 4 8 -> 5 9 is a copy of the new residue 1 (former 6); this is in the straightest part of the chain, so the conection looks better. You must reorder the data so that the residues are in order 1..9 in the file. If you still don't like the bent joining, duplicate another residue (new 10 = new 2); you will then see two close stretches of trace: hide the added 9,10 residues using "hide" so that duplicate atoms, bonds and trace are not seen, but the trace trajectory will still be smooth. Dirty, as I said, but good-looking enough ;-) And the hidden state of added residues is something not easy to be changed by users. I will attach a sample in a separate message off-list -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
>Hi Henry >Nice molecule! It (sort of ) has D2 symmetry, and is therefore dissymetric in its own right > I had only known cyclic DNA molecules as in >"circular" DNA, e.g. procariotic DNA and plasmids. Chemicaly there is >not much difference. >Just for info, RasMol and Accelrys DS Visualizer don't link the ends >either. Yes, the connection, as others have now noted, is a covalent bond between P C A 1 O3* T A 8 but for some reason, no-one appears to have incorporated this into the cartoons. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf (FOAF) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
Well, it is not based on residue numbering. A possible way to deal with this ould be to parse the pdb information in LINK records. Henry's file (2HK4.pdb) has them: LINK P C A 1 O3* T A 8 LINK P C B 1 O3* T B 8 They are meant to supplement info in CONECT records, and to be used for: 1. Bonds between HET groups or between a HET group and standard residue, 2. Inter-residue linkages not implied by the primary structure 3. etc. Point 2 looks to me like the current case. Point 1 would also be interesting (not sure now whether Jmol currently links hetgroups and residues in cartoons, will check) This is the PDB spec: ·· The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. [snip] Record Format COLUMNS DATA TYPE FIELD DEFINITION - 1 - 6 Record name"LINK " 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1Residue name. 22 Character chainID1Chain identifier. 23 - 26 IntegerresSeq1 Residue sequence number. 27 AChar iCode1 Insertion code. 43 - 46 Atom name2 Atom name. 47 Character altLoc2 Alternate location indicator. 48 - 50 Residue name resName2Residue name. 52 Character chainID2Chain identifier. 53 - 56 IntegerresSeq2 Residue sequence number. 57 AChar iCode2 Insertion code. 60 - 65 SymOP sym1Symmetry operator atom 1. 67 - 72 SymOP sym2Symmetry operator atom 2. 74 - 78 Real(5.2) Length Link distance ·· -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
the bonds are there; it's just the cartoons that are not. On Wed, Jan 28, 2009 at 5:16 AM, Rzepa, Henry wrote: > Quick follow up to http://www.ch.ic.ac.uk/local/organic/pericyclic/2HK4.html > > Kinemage (which is more veritable than Jmol), also fails to close the cycle > on cyclic DNA, so I presume that Jmol is merely following the convention > in this regard in how it also does this. > > I guess this is a bit of disconnect between molecular biologists, who care > less about "covalent bonds", and chemists, who do care! Or have they all > simply missed a trick with this one? > -- > > Henry Rzepa. > +44 (020) 7594 5774 (Voice); http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf (FOAF) > http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 > 2AZ, UK. > > (Voracious anti-spam filter in operation for received email. > If expected reply not received, please phone/fax). > > -- > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Advice on display of cyclic DNA: more ...
Hi Henry Nice molecule! I had only known cyclic DNA molecules as in "circular" DNA, e.g. procariotic DNA and plasmids. Chemicaly there is not much difference. I don't know the exact code being used fior calculating and rendering cartoons et al., but I guess it is based on phosphorus IDs and residue numbering. Since in your example the missing link is between residues 1 and 8, Jmol is not guessing that (what criterion should it use, distance? probably that will give trouble in more than one molecule because of proximity). This needs some thinking. Just for info, RasMol and Accelrys DS Visualizer don't link the ends either. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
