Bob wrote:
Sure, but -- you said you had the H atoms Are you saying you
might want
to move them?
On Thu, Nov 6, 2008 at 11:01 AM, David Leader
[EMAIL PROTECTED]wrote:
However I still might see if there is a student up to integrating
the C
code. My colleague tells me that this
Bob,
Sorry but I can't get the script line you sent to work.
To check it wasn't my version of Jmol I went to your tutorial site
and got the example page for connect. Then I:
1. Uploaded an example file with Hs: http://doolittle.ibls.gla.ac.uk/
top500H/1osaH.pdb
2. Pasted some script in
David,
connect 1.8 {H andetc.
is not correct; you need _H or hydrogen, not H
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Robert Hanson wrote:
On Mon, Nov 3, 2008 at 5:54 PM, [EMAIL PROTECTED] wrote:
Quoting Robert Hanson [EMAIL PROTECTED]:
So unfortunately the feature is rather useless except for special
purposes with experienced users aware of the problem and a lot of Java
memory.
I think it's certainly
Robert Hanson wrote:
On Fri, Nov 7, 2008 at 4:55 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
I think the scaled fonts are fixed. Label offset scaling is probably a
good
idea, but it's complicated because that's a 2D offset embedded in a 3D
zoom.
Not saying it's impossible; I just have to do
Sorry,
I lost a letter in the URL. the correct URL is:
http://www.imb-jena.de/cgi-bin/3d_mapping-rh.pl?CODE=1a5eVIEW=snp
Regards,
Rolf
Rolf Huehne wrote:
Robert Hanson wrote:
On Fri, Nov 7, 2008 at 4:55 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
I think the scaled fonts are fixed. Label offset
Angel/Bob
What version of Jmol would this script/command work with?
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE
Richard Steane
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On Fri, Nov 7, 2008 at 4:55 AM, Rolf Huehne [EMAIL PROTECTED] wrote:
I think the scaled fonts are fixed. Label offset scaling is probably a
good
idea, but it's complicated because that's a 2D offset embedded in a 3D
zoom.
Not saying it's impossible; I just have to do it right. Right now
Maybe 10.2 or 11.0
On Fri, Nov 7, 2008 at 9:59 AM, Richard Steane
[EMAIL PROTECTED]wrote:
Angel/Bob
What version of Jmol would this script/command work with?
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE
Richard Steane
On 7 Nov 2008 at 15:59, Richard Steane wrote:
What version of Jmol would this script/command work with?
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE
Not sure of the exact boundary, but I'd say any moderately recent.
However, I am still not familiar with the cruly
Sorry, I stand corrected
I mess up my test: both parentheses and braces work the same
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Angel wrote:
David,
connect 1.8 {H andetc.
is not correct; you need _H or hydrogen, not H
So I do. It works now. Many thanks!
I'm very curious to see whether it does the right thing with the
relevant motifs. But it's been a hard day in the bioinformatics lab,
so it will have to
OOPS! Thanks, Angel -- right, _H, not H. I was working too fast.
Bob
On Fri, Nov 7, 2008 at 11:27 AM, David Leader [EMAIL PROTECTED]wrote:
Angel wrote:
David,
connect 1.8 {H andetc.
is not correct; you need _H or hydrogen, not H
So I do. It works now. Many thanks!
I'm very
with that sample file, this looks better to me:
connect 2.5 {_H and connected(_O or _N)} {(_O or _N) and not within(group,
_1)} HBONDS CREATE
That last bit guarantees that the bonds are inter-residue bonds, not
intra-residue. It says, and not within the group of the atom selected
already
Bob
whew!
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OK. Keep me informed. The energy calculation that Jmol uses in general for
hydrogen bond calculation is specific to carbonylCO-amideNH interactions and
looks like the following. I'm sorry I don't have a literature reference to
this. If you know it, please let me know -- I'd like to add that as a
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