Re: [Jmol-users] Bug? in select by atom number?
On 06/11/2012 06:21 PM, Gutow, Jonathan H wrote:
> I am trying to explain how the select statement in 12.2.28, works to one of
> my students and am confused by the following example.
>
> load =1lcd
> select ({553:559})
>
> This selects the carbons in a phenyl ring plus the C it is attached to.
> Here's what has me confused. The atoms selected are:
>
> #556, #557,#558,#559, #560, #561, #562
>
> These are clearly not within the selection range indicated. My first
> interpretation is that it maybe this is based on connectivity, because it
> selects atoms connected to #553 following bonds to #559. But that's not what
> it is doing either. If you try:
>
> select ({557:559})
>
> You get three atoms selected #560, 561 and 562. It certainly is three atoms,
> but why these three and not #558, 560 and 561, which are nearest neighbors in
> the ring to #557 rather than 559?
>
> How is Jmol interpreting these select statements? I'd like to be able to
> explain this too him.
>
The syntax you used "select ({553:559})" uses the unique atom index
numbers assigned by Jmol to each atom. These are different from the atom
numbers provided in a PDB file.
You would need a command like "select atomno>=553 and atomno<=559" to
use the "official" atom numbers.
You can see the difference by labelling the atoms with both numbers:
label "%a ind=%D atomno=%i"
Regards,
Rolf
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[Jmol-users] Bug? in select by atom number?
I am trying to explain how the select statement in 12.2.28, works to one of my
students and am confused by the following example.
load =1lcd
select ({553:559})
This selects the carbons in a phenyl ring plus the C it is attached to.
Here's what has me confused. The atoms selected are:
#556, #557,#558,#559, #560, #561, #562
These are clearly not within the selection range indicated. My first
interpretation is that it maybe this is based on connectivity, because it
selects atoms connected to #553 following bonds to #559. But that's not what
it is doing either. If you try:
select ({557:559})
You get three atoms selected #560, 561 and 562. It certainly is three atoms,
but why these three and not #558, 560 and 561, which are nearest neighbors in
the ring to #557 rather than 559?
How is Jmol interpreting these select statements? I'd like to be able to
explain this too him.
Thanks,
Jonathan
Dr. Jonathan H. Gutow
Chemistry Department gu...@uwosh.edu
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow/
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: [Jmol-users] bug in "select"
this is corrected for 11.4.7 Sérgio Ceroni da Silva wrote: > Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA > bases are selected as backbone. > Did it resurface or the fix was applied only to 11.5.x ? > >-- >Dr. Sérgio Ceroni da Silva >Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul >Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 >Porto Alegre, RS - Brasil - 91501-970 >== >Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 >http://www6.ufrgs.br/bioquimica > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >___ >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 Northfield, MN http://www.stolaf.edu/people/hansonr 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 the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
Sérgio Ceroni da Silva wrote: > Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA > bases are selected as backbone. > Did it resurface or the fix was applied only to 11.5.x ? I think the fix was only applied to 11.5.x. We need to move to 11.6 soon and abandon 11.4. Bob > >-- >Dr. Sérgio Ceroni da Silva >Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul >Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 >Porto Alegre, RS - Brasil - 91501-970 >== >Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 >http://www6.ufrgs.br/bioquimica > > > > >- >This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >Build the coolest Linux based applications with Moblin SDK & win great prizes >Grand prize is a trip for two to an Open Source event anywhere in the world >http://moblin-contest.org/redirect.php?banner_id=100&url=/ > > > >___ >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 Northfield, MN http://www.stolaf.edu/people/hansonr 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 the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
Just noticed that 11.4.6 has the old bug where H1, H2 and H3 from DNA bases are selected as backbone. Did it resurface or the fix was applied only to 11.5.x ? -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 == Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 http://www6.ufrgs.br/bioquimica - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
Sérgio Ceroni da Silva wrote: >version=11.5.40 ># bug fix: H1 and H3 in DNA are NOT backbone > >H1 from bases in 1JVE and H2 in 1Z04 still showing up. 1CGP now is fine. >Doubt: is it the bug or a problem with the PDBs? > > > H2 should be fixed for 11.5.41 -- The only problem I'm seeing with 1JVE is the H2 problem. -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
version=11.5.40 # bug fix: H1 and H3 in DNA are NOT backbone H1 from bases in 1JVE and H2 in 1Z04 still showing up. 1CGP now is fine. Doubt: is it the bug or a problem with the PDBs? -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 == Tel.: +55 (51) 3316-6091 | Fax: +55 (51) 3316-7309 http://www6.ufrgs.br/bioquimica - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
many attached hydrogens are included in backbone. From the code Where should the nucleic acid backbone atoms stop? Bob // everything from here on is backbone // protein backbone // "OXT", // 64 - second carbonyl oxygen, C-terminus only // protein backbone hydrogens // "H", // 65 - amino hydrogen // these appear on the N-terminus end of 1ALE & 1LCD "1H", // 66 - N-terminus hydrogen "2H", // 67 - second N-terminus Hydrogen "3H", // 68 - third N-terminus Hydrogen "HA", // 69 - H on alpha carbon "1HA", // 70 - H on alpha carbon in Gly only "2HA", // 71 - 1ALE calls the two GLY hdrogens 1HA & 2HA // Terminal nuclic acid "H5T", // 72 - 5' terminus hydrogen which replaces P + O1P + O2P "O5T", // 73 - 5' terminus oxygen which replaces P + O1P + O2P "O1P", // 74 - first equivalent oxygen on phosphorus of phosphate "OP1", // 75 - first equivalent oxygen on phosphorus of phosphate -- new designation "O2P", // 76 - second equivalent oxygen on phosphorus of phosphate "OP2", // 77 - second equivalent oxygen on phosphorus of phosphate -- new designation "O4'", // 78 - sugar ring 4' oxygen ... not present in +T ... maybe others "O2'", // 79 - sugar 2' oxygen, unique to RNA // nucleic acid backbone hydrogens // "1H5'", // 80 - first equivalent H on sugar 5' carbon "2H5'", // 81 - second equivalent H on sugar 5' carbon "H4'", // 82 - H on sugar ring 4' carbon "H3'", // 83 - H on sugar ring 3' carbon "1H2'", // 84 - first equivalent H on sugar ring 2' carbon "2H2'", // 85 - second equivalent H on sugar ring 2' carbon "2HO'", // 86 - H on sugar 2' oxygen, unique to RNA "H1'", // 87 - H on sugar ring 1' carbon "H3T", // 88 - 3' terminus hydrogen // add as many as necessary "HO3'", // 89 - 3' terminus hydrogen (new) "HO5'", // 90 - 5' terminus hydrogen (new) "HA2", "HA3", "HA2", "H1", "H2", "H3", "H5'", "H5''", "H2'", "H2''", "HO2'", Frieda Reichsman wrote: >On Jun 12, 2008, at 9:38 AM, Sérgio Ceroni da Silva wrote: > > > >>I think there is a bug in 11.5.38 and 11.5.39 (not sure when it >>started, >>but old versions didn't have it): >>using "select dna and backbone" selects also some H from the DNA >>bases. >>Tested on 1CGP, 1JVE, 1Z04. >> >> >> > >I have seen some similar, strange behavior with hydrogens and DNA >bases vs. backbone, making it very difficult to work with the >structure. I assumed that the PDB files I was using were not correctly >naming the hydrogen atoms, but I'm not sure. Bob, I can send files if >that would be helpful. > >Frieda > > >// > >Frieda Reichsman, PhD >Molecules in Motion >Interactive Molecular Structures >http://www.moleculesinmotion.com >413-253-2405 > >// > > >- >Check out the new SourceForge.net Marketplace. >It's the best place to buy or sell services for >just about anything Open Source. >http://sourceforge.net/services/buy/index.php >___ >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 Northfield, MN http://www.stolaf.edu/people/hansonr 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 - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
This is an old problem. Maybe it was fixed and has come back, maybe it's the PDB internal naming of atoms (old vs. remediated) - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bug in "select"
On Jun 12, 2008, at 9:38 AM, Sérgio Ceroni da Silva wrote: > I think there is a bug in 11.5.38 and 11.5.39 (not sure when it > started, > but old versions didn't have it): > using "select dna and backbone" selects also some H from the DNA > bases. > Tested on 1CGP, 1JVE, 1Z04. > I have seen some similar, strange behavior with hydrogens and DNA bases vs. backbone, making it very difficult to work with the structure. I assumed that the PDB files I was using were not correctly naming the hydrogen atoms, but I'm not sure. Bob, I can send files if that would be helpful. Frieda // Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com 413-253-2405 // - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] bug in "select"
I think there is a bug in 11.5.38 and 11.5.39 (not sure when it started, but old versions didn't have it): using "select dna and backbone" selects also some H from the DNA bases. Tested on 1CGP, 1JVE, 1Z04. -- Dr. Sérgio Ceroni da Silva Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul Av. Bento Gonçalves, 9500 - Prédio 43421 - Campus do Vale - Caixa Postal 15005 Porto Alegre, RS - Brasil - 91501-970 == Tel.: +55 (51) 3308-6091 | Fax: +55 (51) 3308-7309 http://www6.ufrgs.br/bioquimica - Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
