Yves,
The .xyz formats that are accepted are:
<elementSymbol> <x> <y> <z>
<elementSymbol> <x> <y> <z> <formalCharge>
<elementSymbol> <x> <y> <z> <x-vector> <y-vector> <z-vector>
<elementSymbol> <x> <y> <z> <formalCharge> <x-vector> <y-vector> <z-vecto=
r>
In a previous message
(http://sourceforge.net/mailarchive/message.php?msg_id=3D10608399),
I have found that the charge must be in column 4 or 7 (with or without
vibs).
I made a mistake in this message.
The formalCharge (if present) must come immediately after the atom
coordinates.
NOTE: If it is the case that this conflicts with the behavior of other
packages then please let me know and we can correct it.
Is the atom Symbol column 0? or is it in fact column 5 or 8?
Element symbol is always column 0
Should all the atoms have a charge column? (I tried both)
No.
Each atom line is considered independently.
If an atom does not have a formal charge then it will be considered
uncharged (charge of 0)
Note that Jmol maintains a table of which formal charges are acceptable
for which elements. Atoms that have 'invalid' charges will be given a
charge of 0.
Is there a way to unconnect atoms? For example in the same way as
polyhedra
(something like =22select silicon; nobond magnesium=22 or =22select oxy=
gen;
nobond (2.1)=22 or =22select atmono=3D46; nobond atomno=3D23;=22)
One can disable all 'autobond' behavior by saying
set autobond off
prior to loading a data file.
By default Jmol will run 'autobonding' if there is no bond information in=
the underlying file format. Pdb and mmcif files have special rules becaus=
e
the file format calls for specification of only 'unusual' bonds.
There is currently no way to add or remove specific bonds.
One can, however, turn off the display of specific bonds.
set bondmode and;
select atomno=3D46 OR atomno=3D23;
wireframe off;
Miguel
--__--__--
Message: 4
Date: Fri, 07 Oct 2005 18:23:47 +0200
From: Nicolas Vervelle <[EMAIL PROTECTED]>
To: Jmol Users <[email protected]>
Subject: Re: [Jmol-users] anim command with multiple files
Reply-To: [email protected]
Well, it took me a long time to find some time to look at this new file
format.
It's really more difficult than what I first expected.
I was thinking that the big work would be to merge several
AtomSetCollection,
but the big problem is that with the current Reader architecture,
a Reader is missing a lot of informations to do this.
I will think again on this, but don't expect results soon.
Miguel, do you know if I can get the main missing informations from the
Reader in the readAtomSetCollection() method :
- which file is currently being read (especially to have its path)
- FileManager (to convert a file name to a Stream)
- Adapter
Nicolas
Brandon Hespenheide wrote:
Nicolas,
Thank-you for the quick reply. What you outlined below would be
very useful for me. As I mentioned, I generally have 10-30 protein
structures that I would like to string together into a movie or
animation. I understand your concern with the I/O (I do a lot of
programming myself...), but I wonder how your proposed method of reading
a list of files would compare the loading of a single large,
concatenated file.
I would be happy to test any modifications you make.
Thanks,
Brandon
-----Original Message-----
From: Nicolas Vervelle [mailto:[EMAIL PROTECTED]
Sent: Wednesday, August 10, 2005 10:48 AM
To: [email protected]
Cc: Brandon Hespenheide
Subject: Re: [Jmol-users] anim command with multiple files
Hello,
Brandon Hespenheide wrote:
Hi,
I've been looking through the archive for a way around concatenating
files (PDB format) in order to utilize the animation command in a jmol
script. We have software that can explore conformational motion in
proteins. Generally, 10-100 unique conformations can be produced, it
depends on the user input. These files are then made available for
download and further analysis by the user. I would like to display a
movie of the conformational motion, but I do not want to have to
create an additional PDB file that is simply a cat'ed version of all
the other output files, as this will essentially double the amount of
space each run requires.
Does anyone know if it is possible with scripting to load each of my
conformers sequentially, and then display them as an animation? A
results similar to the anim command would be desirable. Otherwise, I
think we'll need to hack something with php and rpc in order to
dynamically create and destroy a concatenated file for viewing.
At the time being, it's not possible to load several files in Jmol (no
script, no menu, ...).
The best option available is loading a concatenated file.
I am thinking of a new feature that would probably help you : adding a
new file format to Jmol that would only contains a list of other files
to load.
If you open a file like that with Jmol, it would be as if you have
loaded all the files listed.
Would this feature work for you ?
Would anybody else would be interested ?
A potential drawback could be performance : instead of opening one URL,
Jmol will have to open several URLs to load the files.
It may put more load on the web server and slow load time.
I will have a look at implementing this feature in Jmol.
I am not completely sure that it is easily feasible, so I make no
guarantee as whether or not I will manage to do it.
If it happens to be really easy, I may be able to finish before going on
holidays saturday.
Nicolas
--__--__--
Message: 5
Date: Fri, 7 Oct 2005 12:27:16 -0400 (EDT)
Subject: Re: [Jmol-users] Tripos format
From: "Miguel" <[EMAIL PROTECTED]>
To: [email protected]
Reply-To: [email protected]
Quoting Miguel <miguel=40jmol.org>:
Jmol already supports both formal charges and partial charges.
Some file formats support one ... other file formats support the other=
.
CML, for example, supports both.
So it should be quite simple to write a perl script
to convert =22.mol2 files=22 into =22CML files=22
Yes.
The task would be simple for some developers, but not simple for others :=
-)
to be able to display _partial_ charge values
as Labels in Jmol (as Atom Name Labels are displayed).
select <set-of-atoms>;
label =22%P=22; =23 show partial charge as the label
and it would be great to display these charges in Jmol
as the three other labels...
I do not know what you mean by 'three other labels'
You load a PDB or MDL file in Jmol, you click right,
in the 'Labels' pulldown,
you can display _only_ three Labels: Element Symbol,
Atom Name or Atom Number.
No partial charge 'type' label is available...
You have complete control over the formatting of atom labels.
Only a few simple/common examples are shown in the menu system.
For example, one can say:
select all;
label =22element %e at %x,%y,%z partial charge %C formal charge %E=22
For a full list of label formatting characters see the Jmol interactive
scripting documentation at:
http://www.stolaf.edu/people/hansonr/jmol/docs/=23label
Miguel
--__--__--
Message: 6
Date: Fri, 07 Oct 2005 19:51:10 +0200
From: FyD <[EMAIL PROTECTED]>
To: [email protected]
Cc: [EMAIL PROTECTED]
Subject: Re: [Jmol-users] Tripos format
Reply-To: [email protected]
Quoting Miguel <[EMAIL PROTECTED]>:
So it should be quite simple to write a perl script
to convert ".mol2 files" into "CML files"
Yes.
The task would be simple for some developers, but not simple for others=
:-)
OK, we will work on this...
to be able to display _partial_ charge values
as Labels in Jmol (as Atom Name Labels are displayed).
select <set-of-atoms>;
label "%P"; # show partial charge as the label
and it would be great to display these charges in Jmol
as the three other labels...
I do not know what you mean by 'three other labels'
You load a PDB or MDL file in Jmol, you click right,
in the 'Labels' pulldown,
you can display _only_ three Labels: Element Symbol,
Atom Name or Atom Number.
No partial charge 'type' label is available...
You have complete control over the formatting of atom labels.
Only a few simple/common examples are shown in the menu system.
For example, one can say:
select all;
label "element %e at %x,%y,%z partial charge %C formal charge %E"
For a full list of label formatting characters see the Jmol interactive
scripting documentation at:
http://www.stolaf.edu/people/hansonr/jmol/docs/#label
ouf... looks pretty impressive...
Thanks Miguel, it is exactly what we need...
Regards, Francois
--__--__--
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