Bob wrote:
ah -- ok, I see. Well, that sounds terrific. I'd be interested just in
peeking at the C code, then, in that case. Just to see what sort of
considerations you made. Who knows. It might be an almost trivial
addition
to Jmol.
I'll send it you.
David
Bob wrote:
It might be interesting to see how the HBplus program works. I see
http://www.csb.yale.edu/userguides/datamanip/hbplus/algorithm.txt
but that suggests there is no energy calculation here, just a set of
angle/distance rules.
HOWEVER -- NOTE!!! The HBPlus program itself is not
ah -- ok, I see. Well, that sounds terrific. I'd be interested just in
peeking at the C code, then, in that case. Just to see what sort of
considerations you made. Who knows. It might be an almost trivial addition
to Jmol.
Bob
On Mon, Nov 10, 2008 at 11:36 AM, David Leader [EMAIL
right -- as I said in an earlier message, I used 2.5. Try this:
connect 2.5 {_H and connected(_O or _N)} {(_O or _N) and not within(group,
_1)} HBONDS CREATE
On Sun, Nov 9, 2008 at 2:54 PM, Angel Herráez [EMAIL PROTECTED] wrote:
David, have you measured the length of the Hbonds you want to
Angel wrote:
David, have you measured the length of the Hbonds you want to show up?
You might nedd some longer spec.
I've just tested
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE;
with
http://doolittle.ibls.gla.ac.uk/top500H/1osaH.pdb
and Jmol 11.6.3 and it creates and
David, have you measured the length of the Hbonds you want to show up?
You might nedd some longer spec.
I've just tested
connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE;
with
http://doolittle.ibls.gla.ac.uk/top500H/1osaH.pdb
and Jmol 11.6.3 and it creates and draws 12 new Hbonds
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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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
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
Bob wrote:
David -- none of the work I just did will be of help to you, since
you have
the H atoms already present. But I'm glad you started this discussion
anyway, because that will certainly be of interest to others.
I really think a simple command such as
connect 1.8 {H and connected(_O
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:
Bob wrote:
David -- none of the work I just did will be of help to you, since you have
the H atoms already present. But I'm glad
On Thu, November 6, 2008 12:01 pm, David Leader wrote:
However I still might see if there is a student up to integrating the
C code. My colleague tells me that this is quite sophisticated. For
example it calculates the H atoms and deals with the uncertainty in
serines and threonines, by
oops -- that didn't work -- will have this corrected later this morning.
Looks like 90 degrees is more reasonable -- 120 cuts out way too many.
On Tue, Nov 4, 2008 at 8:25 PM, Robert Hanson [EMAIL PROTECTED] wrote:
should be adjustable -- but I haven't actually tested it. Just thought I
would
OK, that's uploaded. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
On Wed, Nov 5, 2008 at 8:59 AM, Robert Hanson [EMAIL PROTECTED] wrote:
oops -- that didn't work -- will have this corrected later this morning.
That's very nice -- I'm quite pleased with that feature
Thanks Bob!
-Tom
On Wed, Nov 5, 2008 at 10:56 AM, Robert Hanson [EMAIL PROTECTED] wrote:
OK, that's uploaded. See
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
David -- none of the work I just did will be of help to you, since you have
the H atoms already present. But I'm glad you started this discussion
anyway, because that will certainly be of interest to others.
I really think a simple command such as
connect 1.8 {H and connected(_O or _N)} {_O or
I am not knowledgeable about the algorithms that are out there (perhaps
someone like Warren DeLano and others might chime in), but I'd like to throw
in my 2 cents (currently approaching the true value of my opinion with the
state of the US dollar!).
I'd rather see Jmol do *something *in this
For the angles, let me try to describe what I mean:
you have two hetero atoms, X and Y, located less than 3.4A from each other.
one of those atoms bears a hydrogen that is not present in the coordinate
file, let's not worry about which one.
each of X and Y are further covalently bonded to at
Possibly. Is that documented or discussed somewhere in the literature?
I could probably implement that tonight while watching the election returns
then let you try it out. I propose:
calculate hbonds {atomset1} {atomset2}
maybe with some settings for minimum and maximum distances.
Bob
--
I'd have to go dig in the literature for a referenceit's just my
personal guideline(s). I'll see what I can find -- most of that literature
is pretty old
-Tom
On Tue, Nov 4, 2008 at 3:23 PM, Robert Hanson [EMAIL PROTECTED] wrote:
Possibly. Is that documented or discussed somewhere
Thanks for the response to my message. I've been tied up with
something and now it's quite late in Europe so I'll just send a brief
reply to a couple of points and any further info later.
1. My interest is only in proteins where the hydrogens have been
added. The database of the proteins I
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