Re: [Jmol-developers] Reloading current structure fails
Thanks Bob, this approach does seem to work, so I shall change my code accordingly. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohomanageengine ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Reloading current structure fails
Hi Angel, Thank you for the examples. First I tried running your code in the console == load data "model example"|@MOLECULE|Molecule Name|5 4|SMALL|NO_CHARGES|||@ATOM|1 C1-0. 0. -0.6300 C 1 fluromethane 0.123871|2 H2 0. 1.0330-0.9980 H 1 fluromethane 0.035745|3 H3-0.8946-0.5165-0.9980 H 1 fluromethane 0.035745|4 H4 0.8946-0.5165-0.9980 H 1 fluromethane 0.035745|5 F5-0.-0. 0.7527 F 1 fluromethane -0.231384|@BOND|1 1 2 1|2 1 3 1|3 1 4 1|4 1 5 1|end "model example"; == ... but got the usual error message: == File Error:No atoms found for file null type Mol2 script ERROR: No atoms found for file null type Mol2 == Then I tried it with replacing the vertical bars with newline chars and the structure was loaded successfully. Why is loading the data with vertical bars not working for me? When I ran the reload command (load "";), however, I got this error: == File Error:unrecognized file format for file string model example script ERROR: unrecognized file format for file string model example load "" == The same happens with this simple data taken from the documentation: == load data "model example" 2 testing C 1 1 1 O 2 2 2 end "model example"; == Loading is fine but reloading fails with the "unrecognized file format" message. I get the same behaviour for all of the above whether I run the scripts in JSmol in a browser or in Jmol directly. All of the above works absolutely fine in version 14.2.7. Any idea what might cause this? Regards, Abel LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmas...@ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] Reloading current structure fails
Hi Angel,
The exact version is 14.6.0_2016.05.24.
It seems to be happening to any structure I have.
Have only tried it with mol2 files.
As the simple load command (load "") triggers the same error, I don't think
it's related to the use of the spacegroup filter.
This is how the structures are loaded:
set antialiasDisplay; save orientation; load DATA "mol2 data"
... structure data comes here ...
end "mol2 data"
And then running any of these commands:
load ""
load "" {1 1 1}
load "" {1 1 1} SPACEGROUP "x,y,z;-x,y,1/2-z;-x,-y,-z;x,-y,1/2+z"
gives the error (as seen in the console history):
File Error:No atoms found
for file null
type Mol2
script ERROR: No atoms found
for file null
type Mol2
Thanks
Abel
LEGAL NOTICE
Unless expressly stated otherwise, information contained in this
message is confidential. If this message is not intended for you,
please inform postmas...@ccdc.cam.ac.uk and delete the message.
The Cambridge Crystallographic Data Centre is a company Limited
by Guarantee and a Registered Charity.
Registered in England No. 2155347 Registered Charity No. 800579
Registered office 12 Union Road, Cambridge CB2 1EZ.
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] Reloading current structure fails
Hello,
I've been using version 14.2.7 for quite a long time and want to upgrade to the
latest version.
However, I've found an issue with 14.6.0.
When I try to reload a mol2 structure with unit cell information like so
load "" {1 1 1} SPACEGROUP "x,y,z;-x,y,1/2-z;-x,-y,-z;x,-y,1/2+z";
I get the error message "No atoms found for file null".
Even simply reloading the current structure (load "") yields this error.
I get the same behaviour when using the "File > Load > Reload" command in the
menu.
According to the 14.6 documentation
(http://chemapps.stolaf.edu/jmol/docs/?ver=14.6#load), the load command by
itself reloads the current file, so this hasn't changed. In theory.
This is working fine in version 14.2.7.
Regards,
AL
LEGAL NOTICE
Unless expressly stated otherwise, information contained in this
message is confidential. If this message is not intended for you,
please inform postmas...@ccdc.cam.ac.uk and delete the message.
The Cambridge Crystallographic Data Centre is a company Limited
by Guarantee and a Registered Charity.
Registered in England No. 2155347 Registered Charity No. 800579
Registered office 12 Union Road, Cambridge CB2 1EZ.
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers
