>> Q: Jan, can you find me an entry with FORMUL records that include a
>> continuation onto a second line? If it is not easy to do then do not do
>
> I found 5039 different ligands/hetgroups in the latest release of PDB
> and none seems to have a two lines FORMUL record.
Very good.
The file forma
> and the brand new cvs up -dP didn't compile
>
> [javac] Jmol/src/org/openscience/jmol/viewer/JmolConstants.java:34:
> unclosed string literal
> [javac] public final static String version = "10pre10l;
How embarrassing ... now checked in.
Miguel
--
According to Miguel:
> Q: Jan, can you find me an entry with FORMUL records that include a
> continuation onto a second line? If it is not easy to do then do not do
I found 5039 different ligands/hetgroups in the latest release of PDB
and none seems to have a two lines FORMUL record.
The longests
and the brand new cvs up -dP didn't compile
[javac] Jmol/src/org/openscience/jmol/viewer/JmolConstants.java:34: unclosed
string literal
[javac] public final static String version = "10pre10l;
regards, Jan
---
This SF.Net email is
Hello,
Jmol Version 10pre10k 2004/06/07 22:48 freezes on
select nucleic
cartoon on
java.lang.NullPointerException
at org.openscience.jmol.viewer.datamodel.Polymer.getInitiatorPoint(Polymer.java:200)
at
org.openscience.jmol.viewer.datamodel.Polymer.calcLeadMidpointsAndWingVectors(Polymer.java
We are now using Gaussion file format in the loadInLine format to create
vibrating models of actual experimentally-determined structures (in the
database in the form of internal coordinates). I was struck by the fact
that the parser is extremely tight. Any paticular reason coordinate
values hav
Q: What does "set debugscript on" do?
Suggestion: It would be helpful if menu items put out information to the
console or the message callback to monitor the effect of these
menu-driven changes.
Bob
Miguel wrote:
please check
http://www.stolaf.edu/people/hansonr/jmol/docs/testdoc.htm?search=colo
I really like
show pdbheader
because it allows JavaScript access to the header. This would be
valuable for all file types, as there is often a comment line in there
that could provide more context.
Q: How hard would it be to add "show file"?
(Which would dump the input data to the message callba
Miguel wrote:
please check
http://www.stolaf.edu/people/hansonr/jmol/docs/testdoc.htm?search=color
Looks OK.
1. remove references to the 'prueba' shape
Too bad. I finally took a look at it. A neat idea.
2. I think the following should be written as
formalCharge
partialCharge
done
3. F
Per Jan's suggestion, the PdbReader in Jmol now uses FORMUL records to
decide which atom types are present in the group.
When FORMUL records are present, only element names that are present in
the FORMUL record will be used for
Q: Jan, can you find me an entry with FORMUL records that include a
c
> please check
>
> http://www.stolaf.edu/people/hansonr/jmol/docs/testdoc.htm?search=color
Looks OK.
1. remove references to the 'prueba' shape
2. I think the following should be written as
formalCharge
partialCharge
3. From a documentation perspective, I don't think that 'background'
shoul
> Done. (Took less that 30 seconds because of the spreadsheet! :)
>
> see
>
> http://www.stolaf.edu/people/hansonr/jmol/docs/testdoc.htm?search=anim
>
Very good.
> (note--I also implemented the column for descriptions of "subcommands")
>
> Bob
>
> ps--I've really learned a lot reading this "toke
Peter,
>>But the *updated* specification is dated October 25, 1996. I would think
>>that > 7.5 years would be long enough for them to act on it.
>
> Without knowing I suspect this was part of the backlog before the
> addition. Part of what I was involved in was seeing whether
> the conversion coul
please check
http://www.stolaf.edu/people/hansonr/jmol/docs/testdoc.htm?search=color
thanks,
Bob
Miguel wrote:
OK, so after an hour here I'm pretty well convinced the color business
is ultra tricky to describe.
Agreed.
Here is what I see:
color [RGB-color]
color [color-scheme]
color [col
Done. (Took less that 30 seconds because of the spreadsheet! :)
see
http://www.stolaf.edu/people/hansonr/jmol/docs/testdoc.htm?search=anim
(note--I also implemented the column for descriptions of "subcommands")
Bob
ps--I've really learned a lot reading this "token" business. The nice
thing is that
Miguel wrote:
Do you have any recommendations as to how we can address this problem?
this mostly addresses nucleotidic HET groups (large HET)
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html
' - In large het groups it sometimes is not possible to follow the
convention ...'
so if
Miguel wrote:
Jan wrote:
by the way, why does hetero not select all HETERO groups, this must be a
Jmol bug
select hetero
should select every atom that is identified in a HETATM record,
independent of anything else.
Do you have an example where this is failing?
Hi Miguel,
I'm sorry, I can
>>It will pause 1 second on the first frame, play, and pause .5 seconds on
>>the last frame ... repeatedly.
>>
> Three numeric parameters are required. We have:
>
> void animationMode() throws ScriptException {
> if (statementLength != 3 && statementLength != 6)
> badArgumentCount();
>
Jan wrote:
> by the way, why does hetero not select all HETERO groups, this must be a
> Jmol bug
select hetero
should select every atom that is identified in a HETATM record,
independent of anything else.
Do you have an example where this is failing?
Miguel
-
>>Do you have any recommendations as to how we can address this problem?
>>
>>
> this mostly addresses nucleotidic HET groups (large HET)
> http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html
> ' - In large het groups it sometimes is not possible to follow the
> convention ...'
> so if th
At 13:20 08/06/2004 +0200, Miguel wrote:
>> > Jmol would have recognized the element type if the PDB had bothered to
>> > follow their own file format specification of 1996 and had filled in
>> > columns 77-78 with the element symbol.
>
> This was a later addition - not in the original format.
But
Miguel wrote:
Bob wrote:
particularly on load, but not just then. Something like:
...script completed: 0
...script completed: 1
What I meant was, this would be what the message callback would look
like. See below
Does Chime offer something similar?
Yes. But it looks like errors just
animation and echo:
Miguel wrote:
Let's just assume that there are two, not three.
And they will apply to loop as well.
They represent delays on the first frame and the last frame.
So if you say:
animation mode loop 1 1
It will pause 1 second on the first frame, play, and pause .5 seconds on
the
Miguel wrote:
Jmol seems to have a problem with defining bonds, eg
Contacts of the ligand COA1350C in PDB entry 1EBL
Yes, unfortunatly Jmol (in differance with Chime plug-in) does not
recognises atoms marked in pdb as AC, BC, as carbon; AN, BN, as
nitrogen; and AO, BO as oxygen. Because of
Bob wrote:
> Miguel,
>
> I could really use a message callback when a script is completed,
I think that is easily accomplished.
> particularly on load, but not just then. Something like:
>
> ...script completed: 0
> ...script completed: 1
Does Chime offer something similar?
> one of these would
>> > Jmol would have recognized the element type if the PDB had bothered to
>> > follow their own file format specification of 1996 and had filled in
>> > columns 77-78 with the element symbol.
>
> This was a later addition - not in the original format.
But the *updated* specification is dated Oc
Miguel,
I could really use a message callback when a script is completed,
particularly on load, but not just then. Something like:
...script completed: 0
...script completed: 1
one of these would indicate an error condition
Bob
Miguel wrote:
Jmol seems to have a problem with defining bonds, eg
Co
At 11:40 08/06/2004 +0200, E.L. Willighagen wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Tuesday 08 June 2004 11:31, Miguel wrote:
> [complain]
>
> Jmol would have recognized the element type if the PDB had bothered to
> follow their own file format specification of 1996 and had filled i
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Tuesday 08 June 2004 11:31, Miguel wrote:
> [complain]
>
> Jmol would have recognized the element type if the PDB had bothered to
> follow their own file format specification of 1996 and had filled in
> columns 77-78 with the element symbol.
>
> [/c
>> Jmol seems to have a problem with defining bonds, eg
>> Contacts of the ligand COA1350C in PDB entry 1EBL
>
> Yes, unfortunatly Jmol (in differance with Chime plug-in) does not
> recognises atoms marked in pdb as AC, BC, as carbon; AN, BN, as
> nitrogen; and AO, BO as oxygen. Because of this, J
> OK, so after an hour here I'm pretty well convinced the color business
> is ultra tricky to describe.
Agreed.
> Here is what I see:
>
> color [RGB-color]
> color [color-scheme]
> color [colorable-object] [color-or-none]
> color [shape-token] [color-scheme]
> color [shape-token] none
>
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