From: <ha...@st...> - 2006-10-22 18:01:16
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Just want to point out something I noticed when writing the scientific notation compiler modification: Generally you don't need [] around residue names -- select ALA select LEU but if that residue starts with a number: 5EE 2E1 then brackets have been (and continue to be) required. Am I right that with Jmol you could not (ever?) say select 5EE but you could certainly say select [5EE] With scientific notation introduced, I looked through the ENTIRE heterogen dictionary for complications and only find one: 2E1. This is compiled as "100.0" and at first I thought that would be a problem. But then I realized that "5EE" doesn't work by itself either, because it is taken as the integer 5 followed by "EE". I believe the advantage to being able to use integers and scientific notation outweighs the inconvenience of needing to use brackets, and I'm interested in others' opinions on this. If you have a site that allows for selecting ANY HETATM residue, I recommend ensuring that your code uses those brackets. I just changed the pop up menu so that it does, as without it 2cct throws an error when the user tries to select the 2E1 residue using the menu. Please read what I have added to http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.0#atomexpressions and comment. Bob |
From: Angel H. <ang...@ua...> - 2006-10-24 20:00:55
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On 22 Oct 2006 at 13:00, ha...@st... wrote: > Generally you don't need [] around residue names -- > > select ALA > select LEU > > but if that residue starts with a number: > > 5EE > 2E1 > > then brackets have been (and continue to be) required. As far as I remember, this is so also in Rasmol: use brackets if the residue name contains numbers. So, I see no problem in enforcing it. |
From: Rolf H. <rh...@fl...> - 2006-10-24 13:27:04
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ha...@st... wrote: >Just want to point out something I noticed when writing the scientific >notation compiler modification: > >Generally you don't need [] around residue names -- > >select ALA >select LEU > >but if that residue starts with a number: > >5EE >2E1 > >then brackets have been (and continue to be) required. > >Am I right that with Jmol you could not (ever?) say > >select 5EE > >but you could certainly say > >select [5EE] > >With scientific notation introduced, I looked through the ENTIRE heterogen >dictionary for complications and only find one: 2E1. This is compiled as >"100.0" and at first I thought that would be a problem. But then I >realized that "5EE" doesn't work by itself either, because it is taken as >the integer 5 followed by "EE". > >I believe the advantage to being able to use integers and scientific >notation outweighs the inconvenience of needing to use brackets, and I'm >interested in others' opinions on this. > >If you have a site that allows for selecting ANY HETATM residue, I >recommend ensuring that your code uses those brackets. I just changed the >pop up menu so that it does, as without it 2cct throws an error when the >user tries to select the 2E1 residue using the menu. > > But this doesn't prevent all problems. Even within brackets hetero component names that are token names (e.g. [AND] in PDB entries 1coy,1e3r,1j99,1q22 and 3dhe) will produce an error. My current workaround for this problem is to use the residue number + insertion code + chain to select any hetero component. Regards, Rolf |
From: <ha...@st...> - 2006-10-24 13:31:52
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That's a bug. I can fix that. Nothing in brackets will be a token. > But this doesn't prevent all problems. Even within brackets hetero > component names that are token names (e.g. [AND] in PDB entries > 1coy,1e3r,1j99,1q22 and 3dhe) will produce an error. My current > workaround for this problem is to use the residue number + insertion > code + chain to select any hetero component. > > Regards, > Rolf > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > |
From: Rolf H. <rh...@fl...> - 2006-10-24 13:38:55
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ha...@st... wrote: >That's a bug. I can fix that. Nothing in brackets will be a token. > > >>But this doesn't prevent all problems. Even within brackets hetero >>component names that are token names (e.g. [AND] in PDB entries >>1coy,1e3r,1j99,1q22 and 3dhe) will produce an error. My current >>workaround for this problem is to use the residue number + insertion >>code + chain to select any hetero component. >> >>Regards, >>Rolf >> Miguels comment on this problem was that it would require a major rewrite of the parser to solve this problem. Regards, Rolf |
From: <ha...@st...> - 2006-10-25 00:14:34
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nah! Just three lines of code. :) Rolf Huehne wrote: ha...@st... wrote: That's a bug. I can fix that. Nothing in brackets will be a token. But this doesn't prevent all problems. Even within brackets hetero component names that are token names (e.g. [AND] in PDB entries 1coy,1e3r,1j99,1q22 and 3dhe) will produce an error. My current workaround for this problem is to use the residue number + insertion code + chain to select any hetero component. Regards, Rolf Miguels comment on this problem was that it would require a major rewrite of the parser to solve this problem. Regards, Rolf ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-developers |