Re: [Jmol-users] Potential bug in reading xyz files

No changes ever. On Mon, Sep 26, 2016 at 9:08 AM, Angel Herráez wrote: > > OK, I will ammend the wiki to clarify the issue. > > But, important: Peter, has this behaviour changed across Jmol versions? > It is one thing that Jmol identifies or not the format, as Bob has >

Re: [Jmol-users] Potential bug in reading xyz files

Hi Bob (and the others), thanks for your answer - this helps enormously. I have a bunch of legacy files created by a legacy utility - I modified the code to no longer put stuff after the integer. As a side note: the xyz::broken.xyz trick also works on the command line (which is how I start

Re: [Jmol-users] JSMOL load inline function

Glad you solved it As far as I remember, the pipe character serves the same as your \n Inline loading is always tricky! On 26 Sep 2016 at 12:49, Matthew Kennedy wrote: Thank you Angel, in the end, it appears the issue was that it needs to print out the literal \n's in the script line. So

Re: [Jmol-users] JSMOL load inline function

Thank you Angel, in the end, it appears the issue was that it needs to print out the literal \n's in the script line. So the following worked for me: script: 'load inline "25\n 0QURM735R7BTNZJNL\n C 1.417382 -0.002747 -0.016830 \n C -0.728040 1.261000 0.12 \n C -0.728040 -1.261000 0.12

[Jmol-users] JSMOL load inline function

Dear all, I have the following code inside a jsmol applet embedded in an html page with some php at the top. script: 'load inline ;' This code correctly prints out the expected geometry but when it is loaded into the jsmol applet on the page, it is completely incorrect compared to if I load

Re: [Jmol-users] JSMOL load inline function

Hi Angel, The script line is as follows: script: 'load inline "25 0QURM735R7BTNZJNL C 1.417382 -0.002747 -0.016830 C -0.728040 1.261000 0.12 C -0.728040 -1.261000 0.12 C -0.000200 -0.001120 -2.476610 C 0.681964 -1.257343 -2.046422 C 0.689513 -1.259021 -0.497124 C 0.686920

Re: [Jmol-users] JSMOL load inline function

Mathew, that lacks newline characters apparently. Jmol needs either those or vertical lines (the 'pipe' character, | ) Try inserting a pipe before each new line· Dr. Angel Herráez Biochemistry and Molecular Biology, Dept. of Systems Biology, University of Alcalá E-28871 Alcalá de Henares

Re: [Jmol-users] JSMOL load inline function

Hi Mathew Possible sources of trouble (just a guess) - quotes (particularly when they get nested) - line breaks all that related to Javascript handling of your text string If you could provide a sample as plain text of what the php variable outputs., it would help diagnosis. Another idea:

[Jmol-users] Protein sequence alignment display/analysis: MSAReveal.Org

Apologies for this off-topic message which involves Jmol only tangentially, but will hopefully be of interest to some Jmol users. Recently I wanted to view some FASTA format protein sequence alignments and was not able to find free software that made me happy. So I made MSAReveal.Org (free,

Re: [Jmol-users] JSMOL load inline function

You may also need a space between the pipe and the element symbol, so it seems > that lacks newline characters apparently. Jmol needs either those or > vertical > lines (the 'pipe' character, | ) Try inserting a pipe before each new line·

Re: [Jmol-users] Potential bug in reading xyz files

Peter, On my editor, your “broken” file has an additional text (the letter “a’) on the first line. Could that be the problem? Matt Kubasik On Sep 26, 2016, at 6:46 AM, Peter Brommer > wrote: Hi, This concerns Jmol Version:

Re: [Jmol-users] Potential bug in reading xyz files

The *xyz reader *ignores everything else on the first line after the integer. The *reader format resolver *is what requires just an integer (the number of atoms) and white space on the first line in order to send the data to the xyz reader, because there are several other formats that start with

[Jmol-users] Potential bug in reading xyz files

Hi, This concerns Jmol Version: 14.6.1_2016.08.11 2016-08-11 22:11. There is an issue with reading/recognising xyz files. On the wiki page http://wiki.jmol.org/index.php/File_formats/Formats/XYZ those are described as having two header lines per step in a multi-step format, the first of which

Re: [Jmol-users] Potential bug in reading xyz files

OK, I will ammend the wiki to clarify the issue. But, important: Peter, has this behaviour changed across Jmol versions? It is one thing that Jmol identifies or not the format, as Bob has explained; it is another if there has been a change in behaviour. Thanks

Re: [Jmol-users] Protein sequence alignment display/analysis: MSAReveal.Org

Wow, Eric. You are a busy guy! Very cool. ​ -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users