From owner-chemistry@ccl.net Sun Aug 30 07:38:01 2009
From: "Jose R. Valverde jrvalverde:_:cnb.csic.es" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: Steps of docking
Message-Id: <-40118-090830063546-7126-ETc9kVj+VqHwexQEb/3djg**server.ccl.net>
X-Original-From: "Jose R. Valverde" <jrvalverde]~[cnb.csic.es>
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Date: Sun, 30 Aug 2009 12:35:18 +0200
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Sent to CCL by: "Jose R. Valverde" [jrvalverde\a/cnb.csic.es]
(0) Understand what you are doing.

	If you don't, you can't be confident on your results.

	0.1 Docking in real life: what docks to what? Sometimes the
only relevant elements are one macromolecule and a small molecule. Others
you need more (adjuvants, water, etc..). If you want to mimic reality you
must do (i.e. ensure you include all relevant elements).

	0.2 Docking in real life: how does it happen? Sometimes the
molecules simply get together, others they change conformation in the
field of each other. Using flexible or rigid docking depends on that.

	0.3 Docking in real life: step by step. Sometimes molecules
simply get together, others they interact by successive steps each
dependent on the formers. Your need for molecular dynamics will depend
on that.

	0.4 etc...

	0.5 Docking in practice: most commonly you do not know in advance,
so you have two choices, one is to start with the cheaper (computationally)
methods (rigid docking, then flexible, then molecular dynamics, first
enzyme+substrate, then add water, then salts, then other molecules...) and
verify results experimentally, the other is to start with the most complex
methods in an attempt to be on the safe side. In any case that will depend
on previous knowledge of your problem and availability of computing power.


On Thu, 27 Aug 2009 12:43:41 -0700 (PDT)
"Basma Ghazal basmaghazal]~[ymail.com" <owner-chemistry_._ccl.net> wrote:
> Dear All:
> I am anewly user for docking I need some one who has experence on this fi=
eld to tell him If Iam true or not and to=A0see this step with me =A0:
> (1) dowenload the protien from the pdb=20
> (2) preparing it : removing water and adding hydrogen=20
> and why we remove the polar hydrogen
> (3)docking used arguslab and/or autodock
> ((4) and what after that
> Thanks

(4) look at the results, check binding energies and fitness to previous
knowledge (does it make sense?)

(5) Select a number of possibly significant results and verify experimental=
ly.

(6) start over if experiment does not confirm prediction.

As a corollary of (5) you may want to start with a known sample to check the
methodology (and what parameters need to be included).

--=20
	These opinions are mine and only mine. Hey man, I saw them first!

			    Jos=E9 R. Valverde

	De nada sirve la Inteligencia Artificial cuando falta la Natural


From owner-chemistry@ccl.net Sun Aug 30 10:39:01 2009
From: "Basma Ghazal basmaghazal],[ymail.com" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: Steps of docking
Message-Id: <-40119-090830103753-31434-j9VzQDQ0EKdLnWp51kBV4w*|*server.ccl.net>
X-Original-From: Basma Ghazal <basmaghazal[#]ymail.com>
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Date: Sun, 30 Aug 2009 07:37:41 -0700 (PDT)
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Sent to CCL by: Basma Ghazal [basmaghazal{}ymail.com]
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Hi:
Thanks for this result but I need to ask about somthing;
Why we remove water?
Thanks


      
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<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Hi:</DIV>
<DIV>Thanks for this result but I need to ask about somthing;</DIV>
<DIV>Why we remove water?</DIV>
<DIV>Thanks</DIV></td></tr></table><br>



      
--0-1360924395-1251643061=:63342--


From owner-chemistry@ccl.net Sun Aug 30 12:34:00 2009
From: "N. Sukumar nagams%x%rpi.edu" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: And now something completely different!
Message-Id: <-40120-090830122433-420-SILgWe0tlQOudVxlRewCAg],[server.ccl.net>
X-Original-From: "N. Sukumar" <nagams(~)rpi.edu>
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Date: Sun, 30 Aug 2009 12:24:17 -0400
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Sent to CCL by: "N. Sukumar" [nagams*rpi.edu]
On Sat, 29 Aug 2009 19:05:11 EDT "Kalju Kahn kalju^chem.ucsb.edu" wrote:


Coming back to where it all started, I see nothing wrong with using
oversimplified models with general audience in mind...

Best wishes,

Kalju

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Working chemists use oversimplified models all the time: e.g. molecular
orbitals, pushing electrons with arrows, harmonic oscillators,
hard-sphere or ribbon molecular models, ... The crucial point is: do we
recognize the limitations and domains of applicability of these
oversimplified models? Often pushing an analogy beyond reasonable limits
reinforces misconceptions, which can take years to dispel. Herein lies
the danger. What does it mean to show more than one pair of "electrons"
to be dancing in the same "orbit"? What does it mean to show a
"electron-photon" pair dancing in an "orbit"?

Dr. N. Sukumar
Rensselaer Exploratory Center for Cheminformatics Research
http://reccr.chem.rpi.edu/


From owner-chemistry@ccl.net Sun Aug 30 16:19:00 2009
From: "Kelly smilin_iis:+:yahoo.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: And now something completely different!
Message-Id: <-40121-090830145109-7196-T7yviSR9l3Pr14/KIyM1xQ]|[server.ccl.net>
X-Original-From: Kelly <smilin_iis(!)yahoo.com>
Content-Type: multipart/alternative; boundary="0-363034293-1251654656=:78134"
Date: Sun, 30 Aug 2009 10:50:56 -0700 (PDT)
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Sent to CCL by: Kelly [smilin_iis-,-yahoo.com]
--0-363034293-1251654656=:78134
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I can't resist joining the fray...=0A=0AWhen=A0i went back to college, 20 y=
rs after high school, i knew i wanted to be a chemist - mostly because i ha=
d a great chemistry teacher in high school.=A0 He had a knack for making co=
ncepts very clear,=A0using everyday analogies.=A0 =0A=0AHe explained that e=
lectrons always went into an empty orbital rather than pair up,=A0because t=
hey followed the sleeping bag rule:=A0 one person per sleeping bag, until y=
ou run out of sleeping bags, and then you pair up.=0A=0A20 yrs later i stil=
l remember that lecture.=0A=0AAnything that will broaden the base of chemis=
try and attract people not normally interested in the field is, in my opini=
on, a good thing.=0A=0AThere's no point in making chemistry (or anything) h=
arder than it has to be!=0A=0AYes, i have to explain to my 8 yr old that we=
 scientists can't make things as quickly as Jimmy Neutron, and that sometim=
es the Mythbuster's "scientific method" isn't very scientific, but it's get=
ting people involved in science and increasing the cool factor.=0A=0AMaybe =
we can attract more people who already have dates...=0A=0AThis is purely se=
lfish on my part=A0- the more diverse my labmates, the more angles our prob=
lems will be examined from, and the more our group can accomplish!=0A=A0=0A=
=0A=0A-Kelly=0A=A0=0A"Most folks are about as happy as they make up their m=
inds to be."=A0 - Abraham Lincoln
--0-363034293-1251654656=:78134
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<html><head><style type=3D"text/css"><!-- DIV {margin:0px;} --></style></he=
ad><body><div style=3D"font-family:garamond, new york, times, serif;font-si=
ze:14pt"><DIV></DIV>=0A<DIV>I can't resist joining the fray...</DIV>=0A<DIV=
>&nbsp;</DIV>=0A<DIV>When&nbsp;i went back to college, 20 yrs after high sc=
hool, i knew i wanted to be a chemist - mostly because i had a great chemis=
try teacher in high school.&nbsp; He had a knack for making concepts very c=
lear,&nbsp;using everyday analogies.&nbsp; </DIV>=0A<DIV>&nbsp;</DIV>=0A<DI=
V>He explained that electrons always went into an empty orbital rather than=
 pair up,&nbsp;because they followed the sleeping bag rule:&nbsp; one perso=
n per sleeping bag, until you run out of sleeping bags, and then you pair u=
p.</DIV>=0A<DIV>&nbsp;</DIV>=0A<DIV>20 yrs later i still remember that lect=
ure.</DIV>=0A<DIV>&nbsp;</DIV>=0A<DIV>Anything that will broaden the base o=
f chemistry and attract people not normally interested in the field is, in =
my opinion, a good thing.</DIV>=0A<DIV>&nbsp;</DIV>=0A<DIV>There's no point=
 in making chemistry (or anything) harder than it has to be!</DIV>=0A<DIV>&=
nbsp;</DIV>=0A<DIV>Yes, i have to explain to my 8 yr old that we scientists=
 can't make things as quickly as Jimmy Neutron, and that sometimes the Myth=
buster's "scientific method" isn't very scientific, but it's getting people=
 involved in science and increasing the cool factor.</DIV>=0A<DIV>&nbsp;</D=
IV>=0A<DIV>Maybe we can attract more people who already have dates...</DIV>=
=0A<DIV>&nbsp;</DIV>=0A<DIV>This is purely selfish on my part&nbsp;- the mo=
re diverse my labmates, the more angles our problems will be examined from,=
 and the more our group can accomplish!<BR>&nbsp;</DIV>=0A<DIV id=3DRTECont=
ent>=0A<DIV><FONT color=3Dblueviolet>=0A<DIV>&nbsp;</DIV>=0A<DIV><FONT colo=
r=3D#000000>-Kelly</FONT></DIV>=0A<DIV><FONT color=3D#000000></FONT>&nbsp;<=
/DIV></FONT></DIV>=0A<DIV><FONT color=3Dblueviolet>"Most folks are about as=
 happy as they make up their minds to be."&nbsp; <EM>- Abraham Lincoln</EM>=
</FONT></DIV>=0A<DIV>&nbsp;<BR><BR></DIV></DIV></div></body></html>
--0-363034293-1251654656=:78134--


From owner-chemistry@ccl.net Sun Aug 30 16:54:01 2009
From: "Kalju Kahn kalju() chem.ucsb.edu" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: Steps of docking
Message-Id: <-40122-090830162615-17130-7+/FsjijJ+2kxAHZs6YdbA*|*server.ccl.net>
X-Original-From: "Kalju Kahn" <kalju*_*chem.ucsb.edu>
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Date: Sun, 30 Aug 2009 13:26:01 -0700
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Sent to CCL by: "Kalju Kahn" [kalju]=[chem.ucsb.edu]
Basma,

One reason would be that the experimental structure was crystallized with
a small ligand in a larger pocket, and the voids of that pocket contain
water molecules.  But you may want these voids be accessible to ligand
atoms while docking.  With standard docking methods, the water will not be
"squeezed" out during binding, as would happen with real molecules, so you
need to remove them.  Of course, other times you may want to keep some of
these waters in order to benefit from solvent-mediated interactions.

Kalju


> Hi:
> Thanks for this result but I need to ask about somthing;
> Why we remove water?
> Thanks


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106


From owner-chemistry@ccl.net Sun Aug 30 18:18:01 2009
From: "Anatoli Korkin a_korkin_-_yahoo.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: And now something completely different!
Message-Id: <-40123-090830181710-10189-QUMMMr75MM7wzm02Pim1ig!=!server.ccl.net>
X-Original-From: Anatoli Korkin <a_korkin ~ yahoo.com>
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Date: Sun, 30 Aug 2009 15:16:56 -0700 (PDT)
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Sent to CCL by: Anatoli Korkin [a_korkin]![yahoo.com]
Dear CCLers,=0A=0AI plan to update a collection of references to video clip=
s at ASDN.NET:=0A=0Ahttp://asdn.net/asdn/links/videos.shtml=0A=0AReferences=
 to your own or your favourite clips, educational or simply fun science vid=
eos, preferably describing phenomena at atomic scale, will be higly appreci=
ated. They can be allocated at any server, not only at yuotube, as long as =
the server has a reasonable speed for download.=0A=0AThank you,=0AAnatoli K=
orkin =0A =0A=0A--- On Sun, 8/30/09, N. Sukumar nagams%x%rpi.edu <owner-che=
mistry(~)ccl.net> wrote:=0A=0A> From: N. Sukumar nagams%x%rpi.edu <owner-chem=
istry(~)ccl.net>=0A> Subject: CCL: And now something completely different!=0A=
> To: "Korkin, Anatoli " <a_korkin(~)yahoo.com>=0A> Date: Sunday, Aug=
ust 30, 2009, 9:24 AM=0A> =0A> Sent to CCL by: "N. Sukumar" [nagams*rpi.edu=
]=0A> On Sat, 29 Aug 2009 19:05:11 EDT "Kalju Kahn=0A> kalju^chem.ucsb.edu"=
 wrote:=0A> =0A> =0A> Coming back to where it all started, I see nothing wr=
ong=0A> with using=0A> oversimplified models with general audience in mind.=
..=0A> =0A> Best wishes,=0A> =0A> Kalju=0A> =0A> ~~~~~~~~~~~~~~~~~~~~~~~~~~=
~~~~~~~=0A> =0A> Working chemists use oversimplified models all the time:=
=0A> e.g. molecular=0A> orbitals, pushing electrons with arrows, harmonic=
=0A> oscillators,=0A> hard-sphere or ribbon molecular models, ... The cruci=
al=0A> point is: do we=0A> recognize the limitations and domains of applica=
bility of=0A> these=0A> oversimplified models? Often pushing an analogy bey=
ond=0A> reasonable limits=0A> reinforces misconceptions, which can take yea=
rs to dispel.=0A> Herein lies=0A> the danger. What does it mean to show mor=
e than one pair of=0A> "electrons"=0A> to be dancing in the same "orbit"? W=
hat does it mean to=0A> show a=0A> "electron-photon" pair dancing in an "or=
bit"?=0A> =0A> Dr. N. Sukumar=0A> Rensselaer Exploratory Center for Cheminf=
ormatics Research=0A> http://reccr.chem.rpi.edu/=0A> =0A> =0A> =0A> -=3D Th=
is is automatically added to each message by the=0A> mailing script =3D-=0A=
> To recover the email address of the author of the message,=0A> please cha=
nge=0A> the strange characters on the top line to the (~) sign. You=0A> can a=
lso=0A=0A> =0A> E-ma=
il to subscribers: CHEMISTRY(~)ccl.net=0A> or use:=0A> =A0 =A0 =A0 http://www=
.ccl.net/cgi-bin/ccl/send_ccl_message=0A> =0A> E-mail to administrators: CH=
EMISTRY-REQUEST(~)ccl.net=0A> or use=0A> =A0 =A0 =A0 http://www.ccl.net/cgi-b=
in/ccl/send_ccl_message=0A> =0A=0A> =A0 =A0 =A0 ht=
tp://www.ccl.net/chemistry/sub_unsub.shtml=0A> =0A> Before posting, check w=
ait time at: http://www.ccl.net=0A> =0A=0A> ==0A>=
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=0A> =0A=0A> =A0 =
=A0 =A0=0A> =0A> RTFI: http://www.ccl.net/c=
hemistry/aboutccl/instructions/=0A> =0A> =0A> =0A=0A=0A


From owner-chemistry@ccl.net Sun Aug 30 18:53:01 2009
From: "Basma Ghazal basmaghazal]-[ymail.com" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Steps of docking
Message-Id: <-40124-090830183221-16562-wWkWeZORACMkKWilqg8T0g||server.ccl.net>
X-Original-From: Basma Ghazal <basmaghazal##ymail.com>
Content-Type: multipart/alternative; boundary="0-144645533-1251671529=:71320"
Date: Sun, 30 Aug 2009 15:32:09 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Basma Ghazal [basmaghazal.]^[.ymail.com]
--0-144645533-1251671529=:71320
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Content-Transfer-Encoding: quoted-printable

Hi,
I know that some program involve the water molecule in there calculation bu=
t,
you said that some times we need to take some of water molecule in our calc=
ulation. =A0Could you tell me some of these cases?
Another help=20
I need some learning examples work with autodock ?
Thanks=A0=0A=0A=0A      
--0-144645533-1251671529=:71320
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Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><DIV><STRONG>Hi,</STRONG></DIV>
<DIV><STRONG>I know that some program involve the water molecule in there c=
alculation but,</STRONG></DIV>
<DIV><STRONG>you said that some times we need to take some of water molecul=
e in our calculation. &nbsp;</STRONG><STRONG><FONT style=3D"BACKGROUND-COLO=
R: #00ffff">Could you tell me some of these cases?</FONT></STRONG></DIV>
<DIV><STRONG>Another help </STRONG></DIV>
<DIV><STRONG><FONT style=3D"BACKGROUND-COLOR: #00ffff">I need some learning=
 examples work with autodock ?</FONT></STRONG></DIV>
<DIV><STRONG>Thanks&nbsp;</STRONG></DIV></td></tr></table><br>=0A=0A=0A=0A =
     
--0-144645533-1251671529=:71320--


From owner-chemistry@ccl.net Sun Aug 30 20:23:00 2009
From: "Gustavo Mercier gamercier * yahoo.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: Vibrational Frequencies Mn(III) (CN)_6 hi spin -thoughts?
Message-Id: <-40125-090830164652-27901-SD6n+YI/WZ0C5ccRzXd83A(a)server.ccl.net>
X-Original-From: Gustavo Mercier <gamercier]_[yahoo.com>
Content-Type: multipart/alternative; boundary="0-1598928466-1251665199=:99874"
Date: Sun, 30 Aug 2009 13:46:39 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Gustavo Mercier [gamercier_+_yahoo.com]
--0-1598928466-1251665199=:99874
Content-Type: text/plain; charset=us-ascii

Hi!

I am testing a method to compute redox potential. It requires doing some thermochemistry. For this I compute the frequency spectrum, etc.

However, in spite of multiple efforts, I keep getting 5 negative frequencies. This would suggest that I am in some saddle point and not a true minimum. They range from -50 to -20 cm-1.

I've done the following without much differences in the results:

Program: ADF 2008
Basis Sets: TZP and TZ2P
Functional: OPBE
Integration accuracy: 5 and 6
Geometry optimization: Energy: 10-3 (default) and 10-4 ; gradient 10-3 (default) and 10-4
Symmetry: No symmetry; Oh symmetry
Frequencies: Analytical
SCF Convergence: default

BTW: <S2> = 7.86 (expect 7.85)

Any
thoughts on how to reach the minimum? The output of the program states
that frequencies close to zero are not printed, so I am not willing to
dimiss them, yet. I've also viewed them and they do not correspond to
translations or  rotations of the whole complex. They correspond to
stretching along the Mn-C bonds.

Thanks for your help!
 --
Gustavo A. Mercier, Jr. MD,PhD
Boston Medical Center - Radiology
Chief of Molecular Imaging and Nuclear Medicine
Gustavo.Mercier|,|bmc.org
gamercier|,|yahoo.com
gumercie|,|bu.edu
cell: 469-396-6750; beeper: 3695
work: 617-414-6457, 617- 414-6440, 617-638-6610
fax: 617-414-4659
--0-1598928466-1251665199=:99874
Content-Type: text/html; charset=us-ascii

<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt;color:black;"><font><font style="font-family: Verdana,Arial,sans-serif; font-size: 13px; color: rgb(17, 17, 17);" face="Verdana,Arial,sans-serif" size="2" color="#111111">Hi!<br><br>I am testing a method to compute redox potential. It requires doing some thermochemistry. For this I compute the
 <span class="yshortcuts" id="lw_1251634677_0">frequency spectrum</span>, etc.<br><br>However, in spite of multiple efforts, I keep getting 5 <span class="yshortcuts" id="lw_1251634677_1">negative frequencies</span>. This would suggest that I am in some saddle point and not a true minimum. They range from -50 to -20 cm-1.<br><br>I've done the following without much differences in the results:<br><br>Program: ADF 2008<br>Basis Sets: TZP and TZ2P<br>Functional: OPBE<br>Integration accuracy: 5 and 6<br>Geometry optimization: Energy: 10-3 (default) and 10-4 ; gradient 10-3 (default) and 10-4<br>Symmetry: No symmetry; Oh symmetry<br>Frequencies: Analytical<br>SCF Convergence: default<br><br>BTW: &lt;S2&gt; = 7.86 (expect 7.85)<br><br>Any
thoughts on how to reach the minimum? The output of the program states
that frequencies close to zero are not printed, so I am not willing to
dimiss them, yet. I've also viewed them and they do not correspond to
translations or&nbsp; rotations of the whole complex. They correspond to
stretching along the Mn-C bonds.<br><br>Thanks
 for your help!</font></font><div>&nbsp;</div>--<br>Gustavo A. Mercier, Jr. MD,PhD<br>Boston Medical Center - Radiology<br>Chief of Molecular Imaging and Nuclear Medicine<br>Gustavo.Mercier|,|bmc.org<br>gamercier|,|yahoo.com<br>gumercie|,|bu.edu<br>cell: 469-396-6750; beeper: 3695<br>work: 617-414-6457, 617- 414-6440, 617-638-6610<br>fax: 617-414-4659<br><br><br><div><br></div></div></body></html>
--0-1598928466-1251665199=:99874--


From owner-chemistry@ccl.net Sun Aug 30 20:57:00 2009
From: "Kalju Kahn kalju-,-chem.ucsb.edu" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: And now something completely different!
Message-Id: <-40126-090830204654-16518-GVIAUuinoCohbJ/+hSItHA*server.ccl.net>
X-Original-From: "Kalju Kahn" <kalju()chem.ucsb.edu>
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Date: Sun, 30 Aug 2009 17:46:40 -0700
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Sent to CCL by: "Kalju Kahn" [kalju::chem.ucsb.edu]
Anatoli,

These are a bit more than fun video clips but feel free to link to these
animations:

Cooperativity in hemoglobin:
http://www.chem.ucsb.edu/~molvisual/Mov/142A/hemo_mov.mpg

Induced fit in hexokinase:
http://www.chem.ucsb.edu/~molvisual/Mov/142A/hexokinase_indfit.mpg

Structure of alpha helix:
http://www.chem.ucsb.edu/~molvisual/Mov/142A/alpha_helix_bckbone.mpg

Structure of DNA:
http://www.chem.ucsb.edu/~molvisual/Mov/142A/B_DNA_struct.mpg

There is no audio, unfortunately ... but if you are linking these into
your library I'll try come up with some text that briefly clarifies what's
being shown.  I use these when teaching intro biochem ... anyone here is
welcome to download and use these for teaching, of course.

Kalju

>
> Sent to CCL by: Anatoli Korkin [a_korkin]![yahoo.com]
> Dear CCLers,
>
> I plan to update a collection of references to video clips at ASDN.NET:
>
> http://asdn.net/asdn/links/videos.shtml
>
> References to your own or your favourite clips, educational or simply fun
> science videos, preferably describing phenomena at atomic scale, will be
> higly appreciated. They can be allocated at any server, not only at
> yuotube, as long as the server has a reasonable speed for download.
>
> Thank you,
> Anatoli Korkin
>
>
> --- On Sun, 8/30/09, N. Sukumar nagams%x%rpi.edu
> <owner-chemistry.:.ccl.net> wrote:
>
>> From: N. Sukumar nagams%x%rpi.edu <owner-chemistry.:.ccl.net>
>> Subject: CCL: And now something completely different!
>> To: "Korkin, Anatoli " <a_korkin.:.yahoo.com>
>> Date: Sunday, August 30, 2009, 9:24 AM
>>
>> Sent to CCL by: "N. Sukumar" [nagams*rpi.edu]
>> On Sat, 29 Aug 2009 19:05:11 EDT "Kalju Kahn
>> kalju^chem.ucsb.edu" wrote:
>>
>>
>> Coming back to where it all started, I see nothing wrong
>> with using
>> oversimplified models with general audience in mind...
>>
>> Best wishes,
>>
>> Kalju
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> Working chemists use oversimplified models all the time:
>> e.g. molecular
>> orbitals, pushing electrons with arrows, harmonic
>> oscillators,
>> hard-sphere or ribbon molecular models, ... The crucial
>> point is: do we
>> recognize the limitations and domains of applicability of
>> these
>> oversimplified models? Often pushing an analogy beyond
>> reasonable limits
>> reinforces misconceptions, which can take years to dispel.
>> Herein lies
>> the danger. What does it mean to show more than one pair of
>> "electrons"
>> to be dancing in the same "orbit"? What does it mean to
>> show a
>> "electron-photon" pair dancing in an "orbit"?
>>
>> Dr. N. Sukumar
>> Rensselaer Exploratory Center for Cheminformatics Research
>> http://reccr.chem.rpi.edu/
>>
>>
>>
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106