JSON from Mol 2.0 desktop version

[nkoylas1@…]

Hi Elaine,

The desktop version provides an XML file. I converted this to a JSON using the XML to JSON Converter (codeshack.io)

I attached the XML and the respective JSON file to the email.
The specific bug is " molepore-7sqf.json does not look like Mole Online json file, does not contain Channels."
Thank you for you help
Respectfully,
Nicholas

Nicholas Koylass
Ph.D. Candidate, Department of Physiology, Qiu Lab
XDBio Graduate Program
Johns Hopkins School of Medicine
nkoylas1@…
From: Elaine Meng <meng@…>
Sent: Wednesday, August 21, 2024 11:05 AM
To: Nicholas Koylass <nkoylas1@…>
Cc: chimerax-users@… <chimerax-users@…>
Subject: Re: [chimerax-users] Mol 2.0 desktop version

External Email - Use Caution

Hi Nicholas,
Not all JSON is the same, and it is also unclear how you converted from XML to JSON. The ability to read JSON specifically from the MOLE Online server and to interpret it as channel data was added to ChimeraX, but if you have some other JSON it may not be simple to convert it to what the MOLE Online JSON reader expects. (We have also added readers for other specific kinds of JSON files such as PAE information from AlphaFold 3.) It is a very broad file specification.

Does the desktop MOLE version give you a json file, or does it only give you an XML file? If so, how did you convert it to JSON? You could use menu: Help... Report a Bug and describe the issue (including the answers to these questions) and most importantly, attach an example JSON file, but it's not really a bug. We could open a ticket and take a look, but I can't promise that you will be able to use that file in the future. We might also ask for the XML if that's what the program actually gives you.

I hope this helps,
Elaine

---

Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 20, 2024, at 10:31 PM, Nicholas Koylass via ChimeraX-users <chimerax-users@…> wrote:

Good day,

I am trying to interface ChimeraX with a XML file that was converted to json to perform MOLE Channel Coloring by Property.

However, I did not use the mole server. I used the desktop version since the server was unavailable. Thus, I received this error : molepore-7sqf.json does not look like Mole Online json file, does not contain Channels.
Can anyone assist me with this?
Thanks,
Respectfully,
Nicholas

[Tom Goddard]

Your converted MOLE XML file to JSON does not match the format produced by the moleonline server. I'll attach an example JSON file from the server so you can look at its contents and understand that better. Also the conversion of your attached XML to JSON lost almost all of the data from the XML file. For instance here are lines from your attached XML file

<Tunnels>
  <Tunnel Id="3" Cavity="1" Auto="0">
    <Properties Charge="0" Ionizable="8" NumPositives="4" NumNegatives="4" Hydrophobicity="0.08" Hydropathy="0.07" LogP="0.69" LogD="0.09" LogS="0.12" Polarity="14.48" Mutability="93" />
    <Profile>
      <Node Radius="2.261" FreeRadius="2.421" BRadius="4.330" T="0.00000" Distance="0.000" X="146.894" Y="156.269" Z="154.424" />
      <Node Radius="2.342" FreeRadius="2.489" BRadius="4.411" T="0.00365" Distance="0.132" X="146.930" Y="156.147" Z="154.390" />
      <Node Radius="2.423" FreeRadius="2.559" BRadius="4.493" T="0.00730" Distance="0.263" X="146.967" Y="156.025" Z="154.356" />
...

while lines from your converted JSON file contain only

{
	"Tunnels": {
		"Tunnel": [
			{
				"Properties": "",
				"Profile": {
					"Node": [
						"",
						"",
						"",
						"",
...

[Tom Goddard]

Your problems are all with getting proper JSON output from MOLE, not with ChimeraX. I can't help you with that as I don't know anything about the MOLE software except for the JSON produces by the online server.

[Tom Goddard]

Example of a correctly formatted JSON file from the MOLE online server for PDB 1tqn.