Further discussion below:
On Feb 28, 2007, at 2:22 PM, Bob Hanson wrote:
Frieda Reichsman wrote:
Hi,
I am loading multiple pdb files into the applet, for example,
load "fileset" "file1.pdb" "file2.pdb" "file3.pdb"
I am having trouble understanding the correct uses use of the
commands file and display. The documentation has not cleared it up
completely for me.
So, for example, with this script:
restrict none
select file=2 or file=3
trace 0.2
select [fe] and file=2
spacefill
display file=2 or file=3
the traces appear, but the spacefilled [fe] does not appear. Why
does the rest of the structure in file2.pdb appear (in trace), and
not the iron atom (in spacefill) ?
Be sure you issue first
model 0
OK, good- this almost works - however in some instances with this set-
up, I want to NOT show the first file first, and instead only the
second two. When I say
file 0
restrict none
prior to displaying files 2 and 3, the representation of file 1
appears briefly in the applet, then disappears, then the desired 2nd
and 3rd appear. If I use
restrict none
file 0
the file 1 structure is mostly NOT displayed- except for an existing
monitor line, which appears briefly. If a monitor does this then I
assume a halo will do it, etc., that is, objects not covered by
'restrict'.
So, if I use
restrict none
file 0
select *
script all_off.spt # this turns of monitors, halos, echos, etc.
before displaying files 2 and 3, now I get a pretty clean switch
between views, with nobody appearing and disappearing.
Is there a simpler way to do this?
<snip>
What I think you are missing is that we might have three files and
multiple models:
-------File1---------|-----File2----------|----File3------------
--model--|---model---|------model---------|---model--|--model---
1.1 1.2 2.1 3.1 3.2
This is useful to know - but I do not have multiple models...
When Jmol starts, the default is only to show the first model,
numbered 1.1.
The default is:
select *
model 1.1
display *
Now, that select refers to ALL atoms in ALL models in ALL files, but
only the first model is "displayable" and only its atoms are
displayed.
So whenever you need to display more than one model at the same
time, you
issue:
model 0 # make all models displayable
display 1.2 or 2.1
or
display file=1 or file=2
or
display file < 3
etc.
What you are missing is the "model 0", or the equivalent in a
context of animations, "frame 0". Those two commands are 100%
synonymous.
By the way, the reason [Fe] works here is that "Fe" is the PDB
group. That's not a general method of showing iron, and if there
were "Fe1" instead, it would not show it. I recommend instead:
select _Fe
I have noticed the underscore before an element name is some previous
posts but not really known how to use it. Would _c be carbon, and
_ca, calcium? Is this documented (yet)?
Finally, I have made no progress in being able to load jvxl data and
have it appear - see previous post - help is needed... I used to be
able to do this, cannot find my error. Using
isosurface mysurface "abcd.jvxl"
or
isosurface "abcd.jvxl"
or
isosurface file "abcd.jvxl"
... no surface appears... can anyone confirm?
Frieda
///////////////////////////////////////////
Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
///////////////////////////////////////////
-------------------------------------------------------------------------
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
