[Jmol-developers] myJmol as variable in Jmol.script

[Klaus Schaper]

Thanks to Robert,

 

that did the trick

 

„show orientation

 

you will see a parameter "rotation radius"

 

You can set that to a new number, then disable zoom. It sets the
magnification for "100%".“

 

 

However, is there an easy way to get the rotationRadius only? I want to read
it out from the applet and using “show orientation” will result in a complex
string. I have to split the string and cut out the rotationRadius in order
to do math on it. It would be nice do directly get the rotationRadius as
number.

 

Thanks to all of you,

 

Klaus

 

 




 

PD Dr. Klaus Schaper

 

http://www.photochemie.hhu.de/ oder http://www.klaus-schaper.de
 

 

e-mail: scha...@klaus-schaper.de

 

Arbeitsgruppe für Organische Photochemie

Institut für Organische Chemie und Makromolekulare Chemie I

Raum 26.43.00.27

 

Heinrich-Heine-Universität Düsseldorf

Universitätsstr. 1

D-40225 Düsseldorf

Deutschland

 

Telefon: +49 211 81 12571

FAX: +49 211 81 14324

 




 

 

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Re: [Jmol-developers] Reloading current structure fails

[Angel Herráez]

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



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Re: [Jmol-developers] myJmol as variable in Jmol.script

[Angel Herráez]

Hi Klaus

Go to http://chemapps.stolaf.edu/jmol/docs/ and search for "rotationRadius"
You will see there is "set rotationRadius"
therefore you can try

show rotationRadius

and it works!

Examples of use:

show rotationRadius  // rotationRadius = 20.94923
rr = rotationRadius; print rr;  // 20.94923



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Re: [Jmol-developers] Reloading current structure fails

[Angel Herráez]

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

[Abel Lovas]

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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[Jmol-developers] Reloading current structure fails

[Abel Lovas]

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


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Re: [Jmol-developers] Reloading current structure fails

[Angel Herráez]

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)




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