Yes, it is not the need for other than the ATOM line. I did a quick test (in an
old Jmol version)
and it reads as pdb but does not display anything, for whatever reason
Add e.g.
spacefill 23%
and you see the atom
> I also tried that, but I'm not sure how to do it with Visual Basic.
> Essenti
On 12/09/2014 17:30, Angel Herráez wrote:
> Yes, it's possibly that. You can check trying yo put that text in a
> file and load it in Jmol application. If it does not load there,then
> you need some key word so Jmol knows, maybe HEADER or REMARK For load
> command the format may be indicate
Hi Michael
> No atoms are shown. If I click on "show" / "file contents", the
> information is there. So it would seem to be a problem of interpretation.
> Do I need to explicitly say it is a pdb file ?
Yes, it's possibly that.
You can check trying yo put that text in a file and load it in Jmol
(following "File Paths .." of Aug 14)
Reminder, I am using Visual Basic to construct a string variable
JmolStr1, which is then sent to a WebBrowser running Jmol:
WebBrowser3.Document.parentWindow.execScript "jmolScript(' " + JmolStr1
+ " ')"
This works well for loading and “decorating” proteins.
On 09/12/2014 02:57 PM, Rolf Huehne wrote:
> On 09/12/2014 12:29 PM, Anders Østergaard Madsen wrote:
>> Dear Rolf,
>> Thanks, I am now trying the connect command.
>> That will perhaps make my script shorter, but
>> does it solve my problem of
>> selecting the same set of atoms in different frames?
On 09/12/2014 12:29 PM, Anders Østergaard Madsen wrote:
> Dear Rolf,
> Thanks, I am now trying the connect command.
> That will perhaps make my script shorter, but
> does it solve my problem of
> selecting the same set of atoms in different frames?
>
No.
If the atom numbers are the only reliable i
On Fri, Sep 12, 2014 at 2:55 AM, Anders Østergaard Madsen wrote:
> Dear Robert,
>
> The atoms do not appear to have unique labels, only
> the numbers, i.e. #76 : clicking on the same atom in two
> different frames gives:
>
> C/1 #76 (and then the atomic coordinates in cartesian frame)
> C/2 #76
see http://chemapps.stolaf.edu/jmol/docs/examples-11/density/slide.htm
Haven't tried that in JSmol. Maybe you can do that
On Fri, Sep 12, 2014 at 6:04 AM, wrote:
> Thanks for all the explanation – it’s very useful. I’d realised that
> anything using client-side code wouldn’t be as fast as
Hello Anders
If I may come into the question, here are some ideas that may or not suit your
situation.
1. I know that your file has no connectivity info. Have you tried having Jmol
to determine
bonding? Looking at your script, it seems that you define bonded based on vdw
distance. SO
I guess J
Thanks for all the explanation – it’s very useful. I’d realised that anything
using client-side code wouldn’t be as fast as compiled code, but I thought it
might be interesting to see if it worked, even for small maps.
Chris
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 11 September 20
Dear Rolf,
Thanks, I am now trying the connect command.
That will perhaps make my script shorter, but
does it solve my problem of
selecting the same set of atoms in different frames?
Best regards
Anders
2014-09-12 11:40 GMT+02:00 Rolf Huehne :
> On 09/12/2014 09:55 AM, Anders Østergaard Madsen
On 09/12/2014 09:55 AM, Anders Østergaard Madsen wrote:
> Dear Robert,
>
> The atoms do not appear to have unique labels, only
> the numbers, i.e. #76 : clicking on the same atom in two
> different frames gives:
>
> C/1 #76 (and then the atomic coordinates in cartesian frame)
> C/2 #76 (and then
Dear Robert,
The atoms do not appear to have unique labels, only
the numbers, i.e. #76 : clicking on the same atom in two
different frames gives:
C/1 #76 (and then the atomic coordinates in cartesian frame)
C/2 #76 (and then the atomic coordinates in cartesian frame)
I have made a script that s
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