Re: [Jmol-users] Tinker xyz files as Jmol input
Hi George, The problem in loading pdb file may be due to column positions. The PDB spec assigns columns to the fields but I have seen other software producing misaligned columns. Your example may have lost the spacing while you pasted it, or instead it has single spaces and so no correct columns. I do not think that the SOURCE tag would create any problems --but I don't know the details of Jmol import parser. PDB spec does have a SOURCE line, and indeed is said mandatory, http://www.wwpdb.org/documentation/format32/sect1.html#Order For column positions: http://www.wwpdb.org/documentation/format32/sect9.html#ATOM http://www.wwpdb.org/documentation/format32/sect9.html#HETATM (All those links may not point to the latest version of the PDB spec, but it should be the same for our purposes here) -- 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] Jmol 14.0.6 released
The SMILES/SMARTS comparison in Jmol is great! As Bob says, you don't have to worry about the origin of the SMILES strings (as long as they are valid, of course), Jmol will get the comparison right every time. One useful additional feature that is not mentioned in the interactive scripting documentation page, is that Jmol can ignore stereochemical information present in the strings using the /nostereo/ option, e.g. var result = Jmol.evaluate(myJSmol, '' + studentSMILES + '.find(SMILES,/nostereo/' + correctSMILES + ')'); where 'studentSMILES' and 'correctSMILES' are variables containing SMILES strings. The /nostereo/ option must be documented in one of Bob's other demonstration pages, I can't remember which one. It can be very useful because users sometimes use dashed/wedged bonds where they are not needed. Mike From: Robert Hanson [mailto:hans...@stolaf.edu] Sent: 22 January 2014 03:10 To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Jmol 14.0.6 released The nice thing about Jmol's SMILES comparisons is that it is totally independent of what program was used to make the SMILES string in the first place. There is no need for a canonical string for our purposes (as there might be for database look-ups). Thus, it matches any matching structure, regardless of method of construction. And it can detect isomerism. So it's really a very convenient solution to this problem of checking answers. -- 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] type docu list access inconsistency
Hi,
- the hash type is missing in the description of the type method under the
heading general .xxx functions
I do not know if this is intentional. Range selecting from lists returns a list
when there is more then one item in the list but only the item for single item
lists (and not a single item list)
var l = [0]; l=l[1][50]; show l;
= l = 0
var l = [0,1]; l=l[1][50]; show l;
= l = [0,1]
I had some code where I expected a list after range selecting from a list. Took
me a while to find out what was the cause. For now I wrap it in a listify
function (see below) but one gets into trouble with lists of lists.
Best
Alexander
function listify( x ){
if( x.type==array ){
return x;
}else{
return [ x ];
}
}
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Re: [Jmol-users] New Java security requirements for RIAs in 7u51 (January 2014)
Thanks! For my needs it's working beautifully!) Yan -Original Message- From: Angel Herráez [mailto:angel.herr...@uah.es] Sent: Monday, January 20, 2014 3:34 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] New Java security requirements for RIAs in 7u51 (January 2014) Hello Yana Yes, Jmol 14 is designed to overcome that. You must deploy it using the Jmol-JSO method (JSmol) in order for the applet to be properly defined with the security information. http://wiki.jmol.org/index.php/Jmol_JavaScript_Object -- 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
[Jmol-users] Bug in break command in the Jmol application 14.0.4?
Is break n broken in Jmol 14.0.4?
function xxx {
for (i=0;i4;i++) {
for (j=0;j4;j++) {
print i
break 0
}
}
}
xxx
0 \
1 \ ok
2 /
3 /
function xxx {
for (var i=0;i4;i++) {
for (var j=0;j4;j++) {
print i
break 1
}
}
}
xxx
0 \ not ok, function called twice?
0 /
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[Jmol-users] Some commands inside user function fail only when the function is called for its return value
Is calling a user function for a return value broken in Jmol application
14.0.4?
Delay, rotateSelected etc. seem to fail in the function only when called
for the return value
function xyz {
print now(xxx)
delay 1
print now(xxx)
return true
}
function test {
xxx=now()
xyz
z=xyz
}
test
0\ ~1 sec = ok
1047 /
1047 \ ~0 sec = not ok
1112 /
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[Jmol-users] ModelKit add atom kills side-chain atomNames in polypeptides?
The atomName of all polypeptide side-chain atoms is reduced to just the element name when an atom is added anywhere with the model kit in Jmol 14.0.4. *example:*CB=C -- 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] Audio?
Could a play audio.file command similar to the Java play function be added to scripting? This would allow clicks and beeps or even entire narrations to be added to Jmol animations. Hopefully it would run in a separate thread. -- 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
