OK, Miguel and I agree:
connect hbonds auto (*) (*)
is the preferred exact replacement for
hbonds on
Upon review of a variety of systems, we find:
Rasmol 2.6 and Chime 2.6:
- hydrogen bonds present in PDB file CONECT are never displayed.
- "hbonds ON" only displays calculated hydrogen
Jmol prerelease 10.00.58 is now available for download from:
http://www.jmol.org/files
This release includes:
* fixed i18n bug for 'stereographic' in menus
* hbond calc popup menu entry
* null pointer bug for %r when file was not PDB
* allow commas in polyhedra command
* bug fix so that 'delet
Miguel wrote:
>> connect hbonds auto (nitrogen) (all)
>>
>> are precise replacements for "hbonds on" in this context.
>
> Be advised that there *is* another twist to this to this story. I tried to
> point it out in my email notification, but it may not be clear to all.
>
> In RasMol/Chime/Jmol 10.0
Can the Jmol application be used inside a PowerPoint presentation? I know
that the applet can be used with LiveWeb, but only on a PC. For Mac users,
is this possible. Apparently RasMol can be run from a PPT presentation by
running a script; is it possible for Jmol?
Patrick J. Carroll, Ph.D.
D
> Thank you, Miguel. Right, there are many ways to do this. This note is
> intended specifically for those users who already have "hbonds on"
> built into their pages that involve links or buttons. The key point is
> to make sure you do not use just
>
> connect hbonds auto;
>
> in your scripts as
Thank you, Miguel. Right, there are many ways to do this. This note is
intended specifically for those users who already have "hbonds on"
built into their pages that involve links or buttons. The key point is
to make sure you do not use just
connect hbonds auto;
in your scripts as a replaceme
On Apr 5, 2006, at 8:33 AM, Bob Hanson wrote:hbonds onwill appear "broken" if you just replace 10.00 jar files with the proposed 10.1 jar files.Instead, you will need to use:connect hbonds auto (oxygen) (nitrogen)The quick question is: *How much of a problem will this be for you?*Breaking the old c
>> connect hbonds auto (oxygen) (nitrogen)
>
> For DNA, it is also needed:
>connect hbonds auto (nitrogen) (nitrogen)
Saying
select *; connect hbonds auto;
OR
connect hbonds auto (*) (*);
Will run exactly the same hbond calculation code as before.
Below is an excerpt from the 10.00.53 pre
AH, good point. So the recommendation should be
connect hbonds auto (nitrogen) (all)
try it out at
http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
Angel Herraez wrote:
Bob Hanson wrote:
hbonds on
will appear "broken" if you just replace 10.00 jar files with the
proposed 10.1
The XYZ file with added vibrational vectors is a fine way to go. Here
is a very simple example, an animation showing two frames with two
different frequencies. It's a flexible format in terms of white space.
3
freq=test freq 1
S -1.5 0 0 0 0 .10 0
C0 0 0 0 0 -.10 0
S 1.5 0 0
Bob Hanson wrote:
> hbonds on
>
> will appear "broken" if you just replace 10.00 jar files with the
> proposed 10.1 jar files.
>
> Instead, you will need to use:
>
> connect hbonds auto (oxygen) (nitrogen)
For DNA, it is also needed:
connect hbonds auto (nitrogen) (nitrogen)
---
Dear all,
Thanks in advance for any help that you may be able to give.
I would like to know the format for vibrational files in Jmol v10 so
that I can adapt a local vibrational structure code to output files
in this format, thereby allowing me to display mormal mode vibrations
with the Jm
Important note to all users: Implications of proposed Version 10.1
change re hydrogen bonds.
The current prerelease of 10.1 includes a major improvement in the way
bonds can be created, modified, and deleted. It is the "connect"
command. Miguel has created an amazingly powerful command here an
another documentation need
Jan wrote:
should I see an effect of ?
color cpk translucent
I can't see behind or into cpk
color atoms translucent
sorry, this is at least the second time I make this mistake.
Regards, Jan
---
This
OK, so that suggests a clear documentation note.
Interesting that in general, if you delete a bond, you can very easily
replace it, because
that "void" will be all that will be targeted by the next connect
command similar to
connect 2.0 (*) (*)
(for example). This is because in general, that
Miguel meant
select connectED()
see that demo page
http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
[EMAIL PROTECTED] wrote:
Miguel wrote:
Jmol prerelease 10.00.57 is now available for download from:
http://www.jmol.org/files
This release:
* reintroduces the connect() e
>Miguel wrote:
>> Jmol prerelease 10.00.57 is now available for download from:
>>
>> http://www.jmol.org/files
>>
>> This release:
>>
>> * reintroduces the connect() expression (see below)
>>
>select connect(2)
>invalid expression token:connect : select connect(2)
>as all other connect(min,ma
Bob,These work as expected and make the new features very clear.My only comment is that I did not expect that connect DELETE AROMATIC would leave nothing between those atoms. Co3porph shows this clearly.Of course it makes sense but Organic chemists expect to see bonds of some sort! All the bestNic
Miguel wrote:
Jmol prerelease 10.00.57 is now available for download from:
http://www.jmol.org/files
This release:
* reintroduces the connect() expression (see below)
select connect(2)
invalid expression token:connect : select connect(2)
as all other connect(min,max,selection) forms in 1
should I see an effect of ?
color cpk translucent
I can't see behind or into cpk
color atoms translucent
sorry, this is at least the second time I make this mistake.
Regards, Jan
---
This SF.Net email is sponsored by xPML, a groun
Miguel wrote:
not for the upcoming release but I want to mention it:
coloring of aromatic broken bonds differ from hbonds
hbond: N blue blue'n'red red O
aromatic: N blue'n'gray blue'n'gray blue'n'gray C
Interesting :-) Which is preferred?
I prefer the hbond version
Regards, Jan
---
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