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
Does seem odd. Here is a way to do it, though:
data "example"
2
testing
C 1 1 1
O 2 2 2
end "example";
load inline @{data("example")} {1 1 1} spacegroup 22 unitcell [3 4 5 90 90
90]
then you can use
load ""
or
load inline @{data("example")}
any time. Or you could define
x = data("example")
then use
load inline @x
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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
The documentation under "data" says
http://chemapps.stolaf.edu/jmol/docs/#data
Using load data instead of just data you can load model data with all of the
loading options of the standard LOAD command.
Also, it says that you should probably use model as part of your data label;
this may be the problem:
If the data type is "model" as in the following example, then the data is
interpreted as an in-line model (and loaded using the default lattice, if
crystallographic).
So maybe you could combine both your load commands into one, i.e.
load DATA "model Abel"|... structure data comes here ...|end "model Abel" {1 1
1} SPACEGROUP "x,y,z;-x,y,1/2-z;-x,-y,-z;x,-y,1/2+z"
I tried with a simple mol2 data and load "" is working fine (see below)
The problem may be either with the symmetry options or with your "mol2
data" label.
zap;
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"; // this works
load ""; // this works too
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" {1 1 1} ; // no error, model loads
load "" {1 1 1}; // no error, model loads
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Re: [Jmol-developers] Reloading current structure fails
Ok, Abel So you are not loading a mol2 file, you are loading data. Reloading of data might not be possible, or may need a different syntax. More investigation is needed on this, I cannoy say right now. What happens if you copy that data into a text file and load it into Jmol? Bob will know, but from his silence I guess he may be traveling... I will try to find out a way if I can -- 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
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Unless expressly stated otherwise, information contained in this
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please inform postmas...@ccdc.cam.ac.uk and delete the message.
The Cambridge Crystallographic Data Centre is a company Limited
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Re: [Jmol-developers] Reloading current structure fails
Hello Abel We need to narrow the problem I've just tested with Jmol 14.6.0_2016.05.24, with a pdb file, a mol file and a mol2 file, and "load" works fine. e.g. load =1crn; load ""; load $caffeine; load ""; load "https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/mol2/csc l.mol2?format=raw"; load ; load ""; So, please, What is the exact version you are using? Is this happening just with a certain file or file type or command? Is it somehow related to the use of the spacegroup filter (I have no experience on this) -- 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
