Re: [Jmol-users] Where's my ATP?
Jaim, I think ths may be what you need, picking up the older definition of
ligand:
http://wiki.jmol.org/index.php/AtomSets
ligand:
The new definition (Jmol 12.2) includes atoms that do not belong to
protein, nucleic or solvent. That includes water, other solvent, ions and
carbohydrate, but excludes nonstandard amino acid or nucleotide residues.
Clasically defined as hetero and not solvent (and so not always what
you would expect from the word ligand).
e.g.
load =1A5U;
select atp; // 186 atoms selected
select atp and hetero; // 186 atoms selected
select atp and ligand; // 0 atoms selected
select atp and nucleic; // 186 atoms
// that's the problem, atp is seen as nucleic and hence not ligand
select ligand; // 70 atoms
select hetero; // 2066 atoms
select hetero and not solvent; // 256 atoms
select hetero and not solvent and not ligand; // 186 atoms
select hetero and not solvent and not ligand and atp; // 186 atoms
So maybe
getProperty atomInfo {hetero and not solvent and not ligand }
?? quite a complex output though
I think the best way may be to define based on hetero and not connected to
other groups, but that needs some ellaboration. And in the end the only exit
seems to be getProperty atomInfo which is very complex and so needs
careful parsing, certainly not so straightforward as ligandInfo
Another idea:
Do you need just the list of names? Maybe parsing the file header for
HETNAM
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Re: [Jmol-users] Where's my ATP?
select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
definitely: boolean isHetero = line.startsWith(HETATM); On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson hans...@stolaf.edu wrote: select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
I'm looking for the equivalent to getProperty ligandInfo that will return the complete list of names in HET or HETAM definitely: boolean isHetero = line.startsWith(HETATM); On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson 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 -- Robert M. Hanson Larson-Anderson 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Where's my ATP?
getProperty ligandInfo returns a nice list of elements in the HET record of the PDB file, with some exceptions, like ATP and ADP. Those are not included in the ligandInfo report. Tested on Jmol 14.0.7 (both Java and HTML5) on several structures, including 1s22 and 1php Is there other getProperty I can use to retrieve all the HET elements? Where’s my ATP? Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
