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

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

[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

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)

[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

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.

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

[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

[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

[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

[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.