Rolf Huehne wrote:
Dear all,
I just tried out Jmol 10.00.13 and noticed a vast difference in
cartoon rendering to version 10.00. In the new version the cartoons
look now just as poorly as in rasmol.
When I searched for an answer for that I found the following message
in the jmol-users ar
Miguel wrote:
Jan wrote:
I would prefer to define a wild card for exact one alpha or number, this
offers more flexibility in other selection context, too.
I think that allowing single char wild card for this field could be
valuable, but I do not think that it solves the problem.
Miguel wrote:
Q: What is the syntax that one would use to select the atoms in the
'space' alternate location? That is, the base atoms that are invariant.
select [ARG]21 and not (*;A or *;B)
not good.
I think that we need something else.
I think that we should allow the underscor
Miguel wrote:
I am continuing to work on support for alternate conformations ... and I
am having difficulties getting my head around some aspects of the problem.
Q: In practice, will there be files that have both alternate conformations
and multiple models?
it isn't disallowed.
Q: What is
Miguel wrote:
...
So, down in the Jmol implementation I think that they need to be separate
models.
I agree
It would be helpful if we could think about the scripting commands (other
than selection) that we would want to use to control the display of
alternate conformations.
because al
Miguel wrote:
I have several other issues to bring up regarding alternate conformations ...
Q: What is the syntax for selecting the 'space' conformation? That is, how
do I select atoms that are not part of an alternate conformation?
?
When a molecule is loaded, currently only the ' ' conf
Miguel wrote:
I need the pdb ID of a small file (or the smallest file) that has
alternate conformations.
currently in the Jmol/samples/PDB/3OVO.pdb
in RasMol e.g.
select [ARG]21.NH1;A
select [ARG]21.NH1;B
Regards, Jan
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timothy driscoll wrote:
On 2005-06-03 (17:48) Old Address wrote:
timothy driscoll wrote:
...
% would brake Chime scripts as well and the use as RasMolScript,
too.
hi Jan,
I think it is reasonable to assume that most people have Chime scripts that
they want to run in Jmol
...
If we did make it a setting then I would personally like to see the
default value for case sensitivity be 'on'.
... but if, ... , I agree with a default 'on'.
Regards, Jan
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timothy driscoll wrote:
...
select *;A
Because ; denotes the end of statement.
I believe it was a mistake for the open rasmol folks to use ; and I
do not want to propogate that error.
This was no mistake, because RasMol uses "\n" for command end syntax
and a ";" like in the JmolScri
Miguel wrote:
...
OK, so I understand that you believe it would be good to make chain
specifications case-sensitive.
yes.
(At this point I'll mention again that it would be a good, too, to
recognize the alternate conformation identifier as RasMol does, e.g.
select "*;A"
)
I also t
Miguel wrote:
The PDB specification allows upper and lower case chars for the chain
identifier ... I think it says any non-space char.
...
Q: If Jmol stopped automatically converting chain specifiers to UPPER
CASE, would this break a large number of existing scripts?
No, there had been only
Miguel wrote:
...
The range selection operator works as follows:
select -
If both seqcodeA and seqcodeB are present in the chain, then all atoms in
all groups in the range [seqcodeA, seqcodeB] inclusive, based upon the
ordering in the underlying file, will be selected.
Miguel
very good.
Miguel wrote:
Jmol prerelease 10.00.12 is now available for download.
This is a prerelease version that is being made available for those who
wish to test new features.
Major features introduced in this release includes:
- Daniel and Nico have reworked the internationalization infrastructure
Bob Hanson wrote:
As Miguel suggests and my demo shows, the thing you need to do is to
separate
the different models using
MODEL
ENDMDL
as shown, for example, at
http://rcsb-deposit.rutgers.edu/adit/docs/pdb_atom_format.html
from the PDB Format Description Version 2.2
http://www.rcsb.org/pdb/docs
Joost Van Durme wrote:
Hello!
I'm investigating rotamer distributions of residues and I write a new PDB file including the found rotamers for one position. These are written at the end of the PDB file.
The result is that multiple rotamers of one residue are displayed in the molecule.
This is a
Miguel wrote:
Tim wrote:
would solid hbonds be difficult to accomplish from a programming
standpoint?
Nope.
We need a command to turn on the setting.
set hbonds solid
I would prefer this
set hbonds solid
and in addition to
set hbonds backbone
set hbonds sidechain
I have been asked, if it
surements window serves to
store/delete them.
Jan, in case you haven't noticed, your messages are signed "Old Address" with no name.
I'm sad, but now I'm only guest at this address and searching for a new
opportunity,
Chris Pudney wrote:
G'day,
By the way, I tried some of the double-click method, but I did not
fins how to remove the measurements from the viewer window;
unchecking the "show measurements" option in the pop-up menu did not
work.
How can it be done?
You've preempted my next question.
measurement
Miguel wrote:
Burk wrote:
I am loving this render-er, and am directing my undergrads to it. But
there is one serious inconvenience- the lack of a convenient way to
select individual chains. Selecting chains is a major way of
highlighting items of interest, and is easy on rasmol
I am not fam
Miguel wrote:
G'day,
> I'm a Jmol newbie. Could someone please explain this to me?
Apologies for not making it clearer - I was asking for an additional way
of
performing measurements to be added to both the Jmol applet and
application.
Brian's comments echo my users' experience; it was primarily ne
Bob Hanson wrote:
Miguel wrote:
Q: Is it acceptable to say that an 'animation' is one where every frame
has the same number of atoms in the same order?
This sounds good to me.
This is restrictive, I don't think it is necessary.
Q: In this case, should measurements be automatically transferred fr
Miguel wrote:
G'day,
as a user, I would say no, because this would be less flexible and not
consistent with the behavior of all the other property changing
commands.
Regards, Jan
> Would it be possible to have the "set measurements ..." command
update
> the units on *all* distance labels?
Chris Pudney wrote:
G'day,
Currently, "set measurements ..." sets the units used for all
subsequent measurements. Any existing measurement labels remain
unchanged. This seems a little odd (at least from our users
point-of-view) as you end up with a mixture of units on your
measurement labels.
Philip Bays wrote:
In an act of incompetence, stupidity, or good luck, I accidently
deleted the directory containing all of my browsers. I took the
opportunity to delete anything related to Firefox. Upon reinstalling
them all, I find that Firefox works fine -- no overlay of the
"contextual menu
Eric Martz wrote:
Thanks very very much, Miguel, for making the choices so well
organized and clear.
I vote for 3C (or 3B OK as second choice).
I vote for 1B, which would be the most flexible.
1 because you may easily use select commands before using color group to
mimic the other effects 0, 2,
Miguel wrote:
Jan,
Hi Miguel,
yes I did
ant clean main
and tied again with 10pre17 and the problem persists:
$ ./jmol --script ../tst
/usr/bin/egrep: 1: Syntax error: redirection unexpected
Q: What is this call to egrep?
this is not important (it is in the jmol sh script included in the
Hi Miguel,
yes I did
ant clean main
and tied again with 10pre17 and the problem persists:
$ ./jmol --script ../tst
/usr/bin/egrep: 1: Syntax error: redirection unexpected
splash_image=jar:file:/D:/Jmol/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg
using Smarter Model Adapter
(C) 2004 The Jm
Miguel wrote:
I developed a small solution for displaying PDB Entries in a comfort
way with the applet that is great (With Ball and Stick what you
recommended me and a very useful cartoon visualisation). I must say
that the v10 beta works really great...
I am glad that it was useful.
Apart
Miguel wrote:
For those of you who are using the new moveTo command in the v10
prerelease ...
Be advised that the order of parameters is going to change.
Currently, the last parameter is the number of seconds over which the move
will be animated. This is going to change to become the first paramete
Miguel wrote:
Jan,
Thanks for the great hint. I am able to figure out some ways using the
example you gave.
Could u help me in making Jmol Applet read a file on the client and
display it. Or should i write my own code to read a file on the
client and send it to JMol Applet. I wanted to wether ther
Siv Chand Koripella wrote:
Jan,
Thanks for the great hint. I am able to figure out some ways using the
example you gave.
Could u help me in making Jmol Applet read a file on the client and
display it. Or should i write my own code to read a file on the
client and send it to JMol Applet. I wanted t
Egon Willighagen wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On Wednesday 29 September 2004 08:26, Siv Chand Koripella wrote:
How can I read a pdb or cml file and give it to jmol applet instead of
giving a file name it the param of applet tag?
Hi Siv, could you elaborate on the env
Siv Chand Koripella wrote:
How can I read a pdb or cml file and give it to jmol applet instead of
giving a file name it the param of applet tag?
it has to come from the same source protocol://server:port/ as the
applet, than you may load it with
zap;load ./relativePath/file.name;
e.g.
http://ww
Miguel wrote:
Jan wrote:
I didn't intend to vote for an alteration of show center, my intention
was that
show rotation should be a synonym for show axisangle because it was the
same (if no bond was selected) but the output
show rotation
rotate x 30
rotate y 10
rotate z 20
I didn't vote for conse
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