[Jmol-developers] [ jmol-Bugs-988592 ] cif issues

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Bugs item #988592, was opened at 2004-07-10 20:58
Message generated for change (Comment added) made by migueljmol
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=988592&group_id=23629

Category: Applet
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: cif issues

Initial Comment:
There is one more important CIF format that Jmol needs 
to be able to read. This comes from the Inorganic 
Crystal Structure Database, 

http://www.fiz-informationsdienste.de/en/DB/icsd/

For an example, see 

http://www.stolaf.edu/people/hansonr/jmol/cif/viewdir.ht
m

and select "ic1166.cif"

To download the file, check for it at 

http://www.stolaf.edu/people/hansonr/jmol/cif

Basically, this is a slight variant of the Cambridge Crystal 
Structure Database. Mostly the format of the atom 
information is different. I note that in this file there can 
be atoms designated with no coordinates! So we have 
here:

Re1 Re3+ 4 e 0.0736(1) -.00119(7) 0.07901(8) 0. 1.
Re2 Re3+ 4 e 0.4356(1) 0.06192(7) 0.45604(8) 0. 1.
Cs1 Cs1+ 4 e 0.3809(2) 0.3961(2) 0.3240(2) 0. 1.
Cs2 Cs1+ 4 e 0.1175(2) -.3131(1) -.0456(1) 0. 1.
Cl1 Cl1- 4 e 0.2775(7) -.0799(4) 0.0192(5) 0. 1.
Cl2 Cl1- 4 e -.0577(8) 0.0757(5) 0.2110(5) 0. 1.
Cl3 Cl1- 4 e -.2203(7) 0.0564(4) 0.5429(5) 0. 1.
Cl4 Cl1- 4 e 0.3159(7) -.0246(4) 0.3056(5) 0. 1.
Cl5 Cl1- 4 e 0.4982(7) 0.2012(4) 0.5660(5) 0. 1.
Cl6 Cl1- 4 e 0.1978(7) 0.1484(4) 0.0706(5) 0. 1.
Cl7 Cl1- 4 e 0.0166(7) -.1522(4) 0.1619(5) 0. 1.
Cl8 Cl1- 4 e 0.5887(7) 0.1235(5) 0.3295(5) 0. 1.
O1 O2- 4 e 0.272(4) 0.194(2) 0.338(3) 9.6 1.
H1 H1+ 4 e    0. 2.

Note the H1 H1+ line has no coordinate. A single space 
is being used, not just generic white space, to separate 
fields.

The error given is:

Java(TM) Plug-in: Version 1.4.0_01
Using JRE version 1.4.0_01 Java HotSpot(TM) Client VM
User home directory = C:\Documents and 
Settings\hansonr

Proxy Configuration: Browser Proxy Configuration

FileManager.openFile(icsd_1166.cif)

SmarterModelAdapter:The model resolver thinks:Cif

java.lang.NullPointerException

	at 
org.jmol.adapter.smarter.ModelReader.parseFloat
(ModelReader.java:45)

	at 
org.jmol.adapter.smarter.CifReader.processAtomSiteLoopB
lock(CifReader.java:288)

	at 
org.jmol.adapter.smarter.CifReader.processLoopBlock
(CifReader.java:144)

	at org.jmol.adapter.smarter.CifReader.readModel
(CifReader.java:65)

	at 
org.jmol.adapter.smarter.ModelResolver.resolveModel
(ModelResolver.java:57)

	at 
org.jmol.adapter.smarter.SmarterModelAdapter.openBuffe
redReader(SmarterModelAdapter.java:55)

	at 
org.openscience.jmol.viewer.managers.FileManager$FileO
penThread.openReader(FileManager.java:409)

	at 
org.openscience.jmol.viewer.managers.FileManager$FileO
penThread.openInputStream(FileManager.java:402)

	at 
org.openscience.jmol.viewer.managers.FileManager$FileO
penThread.run(FileManager.java:379)

	at 
org.openscience.jmol.viewer.managers.FileManager.openF
ile(FileManager.java:100)

	at 
org.openscience.jmol.viewer.JmolViewer.openFile
(JmolViewer.java:897)

	at org.openscience.jmol.viewer.script.Eval.load
(Eval.java:1566)

	at 
org.openscience.jmol.viewer.script.Eval.instructionDispatc
hLoop(Eval.java:337)

	at org.openscience.jmol.viewer.script.Eval.run
(Eval.java:281)

	at java.lang.Thread.run(Unknown Source)

error opening file:/D:/js/struc/data/csd/icsd_1166.cif
java.lang.NullPointerException

openFile(icsd_1166.cif) 210 ms

InterruptedException!

But there are more problems. The following block seems 
to be causing great difficulty:

loop_
_atom_site_aniso_label
_atom_site_aniso_type_symbol
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_12
_atom_site_aniso_U_13
_atom_site_aniso_U_23
Re1 Re3+ 0.0046(1) 0.00294(4) 0.00353(6) -.0008(1) 
0.0005(1) -.0002(1)
Re2 Re3+ 0.0049(1) 0.00264(4) 0.00456(6) 0.0005(1) 
0.0019(1) 0.0005(1)
Cs1 Cs1+ 0.0097(2) 0.00993(14) 0.0068(1) 0.0024(3) 
0.0049(3) 0.0037(2)
Cs2 Cs1+ 0.0082(2) 0.00459(9) 0.0080(1) 0.0015(3) 
0.0001(3) -.0029(2)
Cl1 Cl1- 0.0059(8) 0.0050(4) 0.0068(5) 0.0028(9) 0.001
(1) -.0014(7)
Cl2 Cl1- 0.0104(9) 0.0054(4) 0.0049(5) 0.0007(11) 0.004
(1) -.0019(7)
Cl3 Cl1- 0.0062(7) 0.0041(3) 0.0074(5) 0.0015(9) 0.004
(1) -.0006(7)
Cl4 Cl1- 0.0088(8) 0.0050(4) 0.0047(4) -.0021(10) -.001
(1) 0.0011(6)
Cl5 Cl1- 0.0083(8) 0.0033(3) 0.0070(5) 0.0007(9) 0.000
(1) -.0004(7)
Cl6 Cl1- 0.0075(8) 0.0035(3) 0.0062(5) -.0038(9) 0.000
(1) -.0002(7)
Cl7 Cl1- 0.0101(9) 0.0033(3) 0.0052(5) -.0028(9) 0.000
(1) 0.0020(6)
Cl8 Cl1- 0.0100(9) 0.0053(4) 0.0056(5) -.0039(10) 0.005
(1) 0.0029(7)

and charges on the type symbol is causing the atom 
symbol to be misinterpreted.

see 
http://www.stolaf.edu/people/hansonr/jmol/cif/ic1166b.ci
f
for what this should (probably) look like. (It's not a great 
data set.)

similarly:

http://www.stolaf.edu/people/hansonr/jmol/cif/ic30516.ci
f

and

http://www.stolaf.edu/people/hansonr/jmol/cif/ic30516b.
cif

Bob Hanson

----------------------------------------------------------------------

>Comment By: Miguel (migueljmol)
Date: 2004-07-12 12:01

Message:
Logged In: YES 
user_id=1050060

I am glad that PeterMR saw this ... I was going to send it
to him and ask him if it was valid. 

I do not believe that there is any way that we can reliably
read this file in the context of a CIF reader. I believe
that there is nothing special about newline characters
within the context of a data loop. That is, some files have
newline characters to separate the data values associated
with a single atom. Therefore, the reader cannot reliably
'guess' when to move to a new atom. 

I understand that you are going to ask ICSD about this file
... let's see what their stance is ...

Miguel

----------------------------------------------------------------------

Comment By: Nobody/Anonymous (nobody)
Date: 2004-07-12 05:38

Message:
Logged In: NO 

I will contact ICSD and enquire, but it is quite possible
that they are doing exactly this. IMHO, their software reads
the file. So should Jmol. Standards aside...
Bob Hanson

----------------------------------------------------------------------

Comment By: Nobody/Anonymous (nobody)
Date: 2004-07-11 19:00

Message:
Logged In: NO 

This is an invalid CIF. CIFs have two data structures, loops 
and items. In a loop like this all rows must have the same 
number of (whitespace-separated) fields. Note that the 
number of fields in each row and their semantics is given by 
the list of names in the loop whose length must equal each 
row.

For more information on CIF syntax, from which no 
deviations are allowed, see http://www.iucr.org

PeterMR

NB I doubt that the ICSD is emitting invalid CIFs on a 
systematic basis. 

----------------------------------------------------------------------

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[Jmol-developers] [ jmol-Bugs-988592 ] cif issues

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[Jmol-developers] [ jmol-Bugs-988592 ] cif issues