Mol 2.0 desktop version
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 Nicholas Koylass Ph.D. Candidate, Department of Physiology, Qiu Lab XDBio Graduate Program Johns Hopkins School of Medicine nkoylas1@jh.edu
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@cgl.ucsf.edu> 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
Hi Elaine, The desktop version provides an XML file. I converted this to a JSON using the XML to JSON Converter (codeshack.io)<https://codeshack.io/xml-to-json-converter/> 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@jh.edu ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, August 21, 2024 11:05 AM To: Nicholas Koylass <nkoylas1@jhu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> 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@cgl.ucsf.edu> 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
Hi Nicholas, It would have been better if you had followed my suggestion of using ChimeraX menu: Help... Report a Bug, because that would automatically make a ticket for us. However, we will try to make a ticket out of your email manually instead. Elaine
On Aug 21, 2024, at 11:03 PM, Nicholas Koylass via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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@jh.eduFrom: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, August 21, 2024 11:05 AM To: Nicholas Koylass <nkoylas1@jhu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> 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@cgl.ucsf.edu> 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
<molepore-7sqf.json><His98.xml>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Elaine Meng -
Nicholas Koylass