From owner-chemistry@ccl.net Wed Apr 11 08:13:01 2012 From: "Christopher Rinderspacher berend.c.rinderspacher.civ{}mail.mil" To: CCL Subject: CCL: SMILE from NBO Message-Id: <-46667-120411081011-15076-BpwcQ6LlZyfDMdTYWPo57g__server.ccl.net> X-Original-From: "Christopher Rinderspacher" Date: Wed, 11 Apr 2012 08:10:08 -0400 Sent to CCL by: "Christopher Rinderspacher" [berend.c.rinderspacher.civ:-:mail.mil] Dear CCLers, Is there a program that can produce a SMILE from an NBO calculation? Sincerely, Christopher From owner-chemistry@ccl.net Wed Apr 11 09:21:01 2012 From: "Geoffrey Hutchison geoffh:+:pitt.edu" To: CCL Subject: CCL:G: SMILE from NBO Message-Id: <-46668-120411091541-23880-p40o42lPdD+rB7F+FrnMQg ~~ server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Wed, 11 Apr 2012 09:15:32 -0400 MIME-version: 1.0 (Apple Message framework v1257) Sent to CCL by: Geoffrey Hutchison [geoffh() pitt.edu] > Is there a program that can produce a SMILE from an NBO calculation? If I understand the question, you want to use the bonding information from NBO to generate the SMILES line format? Haven't tried that, but if you send me an example NBO (or Gaussian / NBO or whatever) we can quickly patch Open Babel to do that. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh[-]pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Wed Apr 11 12:46:00 2012 From: "Jesse Gordon jesse.gordon=dotmatics.com" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46669-120410192115-29802-QZj2CAHtZ3QKbWW4Mo7tqQ_._server.ccl.net> X-Original-From: Jesse Gordon Content-Type: multipart/alternative; boundary=f46d0401fb2711600c04bd5b601c Date: Tue, 10 Apr 2012 19:20:58 -0400 MIME-Version: 1.0 Sent to CCL by: Jesse Gordon [jesse.gordon^^^dotmatics.com] --f46d0401fb2711600c04bd5b601c Content-Type: text/plain; charset=ISO-8859-1 I used the basic version of CLiDE -- one molecule at a time. But I believe the recognition algorithm is the same in all three versions -- just how it is applied differs. No, I don't think there are any systematic errors in CLiDE -- whether with vertical iodine groups vs vertical methyl groups or any other tricky situations. I think all of the the problems are inherent with automated chemical structure recognition, just like they are inherent with automated text recognition. I think CLiDE performs as well as any of them -- but of course none can be perfect. I cannot send the examples I had -- they were part of a video demonstration I made, to demonstrate the intergration of ChemDraw with CLiDE. Unfortunately, that video (and the supporting materials with positive and negative examples) were all removed from the ChemDraw video library because PerkinElmer, ChemDraw's new owner, also bought a CLiDE competitor product, and hence no longer wanted any association with CLiDE. So I have to work from memory -- the vertical iodine problem was one of them. Your examples actually HAVE vertical iodine -- that's less of a problem than having a vertical methyl group (with implicit carbon and implicit hydrogen, i.e. just a vertical line) misinterpreted as an iodo group, particularly when the vertical methyl group was a little shorter than IUPAC standards. Another problem I recall was dealing with crossed ring bonds, such as in morphine or any standard opiate drawing. Another problem was with resonant structures, for example a carboxylate group drawn in the standard "delocalized" manner with a floating negative sign and a curved dash line on O-C-O. Your example page has all benzene rings with Kekule structures -- I recall CLiDE has more difficulty with a delocalized benzene rendering. And of course the problems got worse when the quality of the original drawing was worse -- although I see in your bitmap examples that CLiDE handles at least SOME low quality pretty well! I certainly would recommend CLiDE to anyone -- it's as good as any structure recognition software -- but it's not magic, just like text OCR isn't magic either. ===================================== Jesse Gordon Application Scientist Dotmatics Inc. 400 West Cummings Park #5450, Woburn MA 01801 T: +1 781-305-3114 M: +1-617-320-6989 Email: jesse.gordon**dotmatics.com Skype: jessegordon ====================================== See the latest in Dotmatics Suite of Solutions at: Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade center, Boston, MA, www.bio-itworldexpo.com On 10 April 2012 12:21, Aniko Simon aniko ~~ simbiosys.ca < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "Aniko Simon" [aniko~~simbiosys.ca] > Hi Jesse, > > Thanks for taking the time to explain about different versions of CLiDE and > its similarity to OCR. You are absolutely right, the basic principles are > the > same, but while the OCR is using language dictionaries (e.g. one for > English > and a different one for German) CLiDE (or a chemical OCR) uses chemical > dictionaries or pre-coded-domain-knowledge to make its results better. The > broader the knowledge behind the program, the better the results are. > Certainly for CLiDE this body of knowledge expands systematically, along > with algorithmic improvements. > > I am not sure which version of CLiDE you tested, that gave you the > conclusions you listed below. I just did a quick substructure search on > ChemSpider for structures for iodine, one of the top ones (Diatrizoic acid) > had a vertical methyl group as well. Zoomed it, saved the image as PNG and > processed it with the latest version of CLiDE v5.2.3. Results in this > particular case: 100% accurate. See it in our gallery: > http://www.simbiosys.com/clide/gallery_clide.html > > Of course this does not mean that all images will be processed correctly > all > the time, but at least it shows that there is no systematic error with > iodine and vertical methyl groups. If you still have the images that caused > issues for you, please send them to us, it will be highly useful in > improving the program. > > We fully agree that no matter what version you use, as with any OCR, you > will require human inspection of the results. However, that is still > faster than redrawing multi-page documents structure by structure. > > Best wishes, > Aniko > > On April 6, 2012 08:00:45 am Jesse Gordon jesse.gordon{:}dotmatics.comwrote: > > Yes, I've used CLiDE to pull structures out of PDF files. There are three > > versions: > > - CLiDE standard is one-at-a-time; you draw a box around the structure > and > > CLiDE interprets it. > > - CLiDE pro version recognizes all the structures in a multi-page PDF and > > produces a list; > > - CLiDE batch version takes a whole stack of documents. > > > > The quality is comparable to OCR - optical character recognition - and > I've > > always called this method "Chemical OCR." If you're familiar with OCR, it > > makes a LOT of mistakes. For example, CLiDE almost always fails to > > recognize iodine, which it interprets as a methyl group with implicit > > carbon and hydrogen. Or vice versa -- if your methyl group happens to be > > vertical, it often gets misinterpreted as an iodine atom. Rings sometimes > > end up "broken", i.e. CLiDE interprets a 6-membered ring as a chain with > 6 > > atoms arranged in a hexagon. So it's not perfect. As with text OCR, you > > have to read the result and correct it manually. > > > > I found that using CLiDE, whether in one-at-a-time form or batch form, > > requires manually comparing the original with the > chemical-OCR-interpreted > > result (with text OCR you can usually skip referring back to the original > > since you know all the words in your head. But with chemical OCR, the two > > examples I gave above are obvious upon inspection, but many other errors > > are not). The best method to inspect is to assign names to the resulting > > structures using some automatic structure-to-name converter. That exposes > > any subtle issues like an atom being "close" to a methyl group when it > > should be an atom connected by a bond. Compare the automatically > generated > > name to your visual inspecction of the original, and the process is > pretty > > quick. > > > > > > > > On 5 April 2012 12:42, Alex Allardyce aa|a|chemaxon.com < > > owner-chemistry**ccl.net> wrote: > > > > > > > > Sent to CCL by: Alex Allardyce [aa : chemaxon.com] > > > ChemAxon supports text and scanned pdf (and doc, ppt, pptx etc). It is > > > integrated throughout our technology but probably easiest to try out in > > > MarvinView, (free for the desktop), just 'open' the pdf (or doc or ppt > etc) > > > and all extracted structures are shown. You also access all of the > > > functionality through the API/command line as well as KNIME and > Pipeline > > > Pilot nodes. > > > > > > Cheers > > > Alex > > > > > > On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=-=llnl.gov > > >> wrote: > > >> > > >>> Sent to CCL by: "Brian Bennion" [bennion1=llnl.gov] > > >>> Hello, > > >>> > > >>> Does anyone have/know of code to parse pdf tables for chemical > structure > > >>> and activity data? > > >>> > > >>> Searching the web did not result in much so I may not be searching > with > > >>> the correct terms. One interesting hit was the clide code from > simbiosis. > > >>> > > >>> Has anyone used this for pulling structures out of pdf files? > > >>> > > >>> I want to populate a repository with chemical structures and annotate > > >>> the entries with the activity data given in an associated table > located in > > >>> the same pdf document. > > >>> > > >>> Thanks > > >>> Brian> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message> > http://www.ccl.net/cgi-bin/**ccl/send_ccl_messagehttp://www.ccl.net/chemistry/**sub_unsub.shtml > http://server.ccl.net/** > > > chemistry/announcements/**conferences/< > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml< > http://www.ccl.net/chemistry/searchccl/index.shtml> > http://www.ccl.net/spammers.**txt > > > > > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/< > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > > > > > > > > > > > > > -- > > ===================================== > > Jesse Gordon > > Application Scientist > > Dotmatics Limited > > 400 West Cummings Park #5450, Woburn MA 01801 > > T: +1 781-305-3114 > > M: +1-617-320-6989 > > Email: jesse.gordon**dotmatics.com > > Skype: jessegordon > > ====================================== > > > > See the latest in Dotmatics Suite of Solutions at: > > Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San > > Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com > > Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade > > center, Boston, MA, www.bio-itworldexpo.com > > > > -- > > Disclaimer: This electronic mail and its attachments are intended solely > for > > the person(s) to whom they are addressed and contain information which is > > confidential or otherwise protected from disclosure, except for the > purpose > > for which they are intended. Dissemination, distribution, or > reproduction by > > anyone other than the intended recipients is prohibited and may be > illegal. > > If you are not an intended recipient, please immediately inform the > sender > > and return the electronic mail and its attachments and destroy any copies > > which may be in your possession. Dotmatics Limited screens electronic > mails > > for viruses but does not warrant that this electronic mail is free of any > > viruses. Dotmatics Limited accepts no liability for any damage caused by > > any virus transmitted by this electronic mail. Dotmatics Limited is > > registered in England & Wales No. 5614524 with offices at The Old > Monastery, > > Windhill, Bishops Stortford, Herts, CM23 2ND, UK.> > > -- -- Disclaimer: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. Dotmatics Limited screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. Dotmatics Limited accepts no liability for any damage caused by any virus transmitted by this electronic mail. Dotmatics Limited is registered in England & Wales No. 5614524 with offices at The Old Monastery, Windhill, Bishops Stortford, Herts, CM23 2ND, UK. --f46d0401fb2711600c04bd5b601c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
I used the basic version of CLiDE -- one molecule at a time. But I bel= ieve the recognition algorithm is the same in all three versions -- just ho= w it is applied differs.
=A0
No, I don't think the= re are any systematic errors in CLiDE -- whether with vertical iodine group= s vs vertical methyl groups or any other tricky situations. I think all of = the the problems are inherent with automated chemical structure recognition= , just like they are inherent with automated text recognition. I think CLiD= E performs as well as any of them -- but of course none can be perfect.
=A0
I cannot send the examples I had -- they were part of a = video demonstration I made, to demonstrate the intergration of ChemDraw wit= h CLiDE. Unfortunately, that video (and the supporting materials with posit= ive and negative examples) were all removed from the ChemDraw video library= because PerkinElmer, ChemDraw's new owner, also bought a CLiDE competi= tor product, and hence no longer wanted any association with CLiDE.
=A0
So I have to work from memory -- the vertical iodine pro= blem was one of them. Your examples actually HAVE vertical iodine -- that&#= 39;s less of a problem than having a vertical methyl group (with implicit c= arbon and implicit hydrogen, i.e. just a vertical line) misinterpreted as a= n iodo group, particularly when the vertical methyl group was a little shor= ter than IUPAC standards. Another problem I recall was dealing with crossed= ring=A0bonds, such as=A0in morphine or any standard opiate drawing. Anothe= r problem was with resonant structures, for example a carboxylate group dra= wn in the standard "delocalized" manner with a floating negative = sign and a curved dash line on O-C-O. Your example page has all benzene rin= gs with Kekule structures -- I recall CLiDE has more difficulty with a delo= calized benzene rendering.
=A0
And of course the problems got worse=A0when the quality = of the original drawing was worse -- although I see in your bitmap examples= that CLiDE handles at least SOME low quality pretty well! I certainly woul= d recommend CLiDE to anyone -- it's as good as any structure recognitio= n software -- but it's not magic, just like text OCR isn't magic ei= ther.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Jesse Gordon
App= lication Scientist
Dotmatics Inc.
400 West Cummings Par= k #5450, Woburn MA 01801
T: +1 781-305-3114
M: +1-617-3= 20-6989
Skype: jessegordon
=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D
=A0
See the latest in Dotmatics Suit= e of Solutions at:
Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San= Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com
Booth # 323 Bio= -IT World Conference, April 24-26, 2012, World Trade center,=A0 Boston,=A0 = MA, www.bio-itworldexpo.com<= /div>
=A0
On 10 April 2012 12:21, Aniko = Simon aniko ~~ simbiosys.ca <owner-chemistry**ccl= .net> wrote:

Sent to CCL by: "Aniko =A0Simon" [aniko~~simbiosys.ca]
Hi Jesse,

Thanks for taking the time to explain about different versions of CLiDE and=
its similarity to OCR. You are absolutely right, the basic principles are t= he
same, but while the OCR is using language dictionaries (e.g. one for Englis= h
and a different one for German) CLiDE (or a chemical OCR) uses chemical dic= tionaries or pre-coded-domain-knowledge to make its results better. The
broader the knowledge behind the program, the better the results are. =A0Ce= rtainly for CLiDE this body of knowledge expands systematically, along
with algorithmic improvements.

I am not sure which version of CLiDE you tested, that gave you the conclusi= ons you listed below. I just did a quick substructure search on ChemSpider = for structures for iodine, one of the top ones (Diatrizoic acid)
had a vertical methyl group as well. Zoomed it, saved the image as PNG and<= br> processed it with the latest version of CLiDE v5.2.3. Results in this parti= cular case: 100% accurate. See it in our gallery:
http://www.simbiosys.com/clide/gallery_clide.html

Of course this does not mean that all images will be processed correctly al= l
the time, but at least it shows that there is no systematic error with iodi= ne and vertical methyl groups. If you still have the images that caused
issues for you, please send them to us, it will be highly useful in improvi= ng the program.

We fully agree that no matter what version you use, as with any OCR, you will require human inspection of the results. However, that is still faster= than redrawing multi-page documents structure by structure.

Best wishes,
Aniko

On April 6, 2012 08:00:45 am Jesse Gordon jesse.gordon{:}dotmatics.com wrote:
> Yes, I've used CLiDE to pull structures out of PDF files. There ar= e three
> versions:
> - CLiDE standard is one-at-a-time; you draw a box around the structure= and
> CLiDE interprets it.
> - CLiDE pro version recognizes all the structures in a multi-page PDF = and
> produces a list;
> - CLiDE batch version takes a whole stack of documents.
>
> The quality is comparable to OCR - optical character recognition - and= I've
> always called this method "Chemical OCR." If you're fami= liar with OCR, it
> makes a LOT of mistakes. For example, CLiDE almost always fails to
> recognize iodine, which it interprets as a methyl group with implicit<= br> > carbon and hydrogen. Or vice versa -- if your methyl group happens to = be
> vertical, it often gets misinterpreted as an iodine atom. Rings someti= mes
> end up "broken", i.e. CLiDE interprets a 6-membered ring as = a chain with 6
> atoms arranged in a hexagon. So it's not perfect. As with text OCR= , you
> have to read the result and correct it manually.
>
> I found that using CLiDE, whether in one-at-a-time form or batch form,=
> requires manually comparing the original with the chemical-OCR-interpr= eted
> result (with text OCR you can usually skip referring back to the origi= nal
> since you know all the words in your head. But with chemical OCR, the = two
> examples I gave above are obvious upon inspection, but many other erro= rs
> are not). The best method to inspect is to assign names to the resulti= ng
> structures using some automatic structure-to-name converter. That expo= ses
> any subtle issues like an atom being "close" to a methyl gro= up when it
> should be an atom connected by a bond. Compare the automatically gener= ated
> name to your visual inspecction of the original, and the process is pr= etty
> quick.
>
>
>
> On 5 April 2012 12:42, Alex Allardyce aa|a|chemaxon.com <
> owner-chemistry**ccl.net<= /a>> wrote:
>
> >
> > Sent to CCL by: Alex Allardyce [aa : chemaxon.com]
> > ChemAxon supports text and scanned pdf (and doc, ppt, pptx etc). = It is
> > integrated throughout our technology but probably easiest to try = out in
> > MarvinView, (free for the desktop), just 'open' the pdf (= or doc or ppt etc)
> > and all extracted structures are shown. You also access all of th= e
> > functionality through the API/command line as well as KNIME and P= ipeline
> > Pilot nodes.
> >
> > Cheers
> > Alex
> >
> > =A0On Tue, Apr 3, 2012 at 17:55, Brian Bennion bennion1=3D-=3Dllnl.gov
> >> <owner-chemistry[*]ccl.net> =A0wrote:
> >>
> >>> Sent to CCL by: "Brian =A0Bennion" [bennion1=3D= llnl.gov]
> >>> Hello,
> >>>
> >>> Does anyone have/know of code to parse pdf tables for che= mical structure
> >>> and activity data?
> >>>
> >>> Searching the web did not result in much so I may not be = searching with
> >>> the correct terms. =A0One interesting hit was the clide c= ode from simbiosis.
> >>>
> >>> Has anyone used this for pulling structures out of pdf fi= les?
> >>>
> >>> I want to populate a repository with chemical structures = and annotate
> >>> the entries with the activity data given in an associated= table located in
> >>> the same pdf document.
> >>>
> >>> Thanks
> >>> Brian> =A0 =A0 http://www.ccl.net/cgi-bin/**ccl/s= end_ccl_message<http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 http://www.ccl.net/cgi-bin/**ccl/send_ccl_message&l= t;http://www.ccl.net/cgi-b= in/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/**sub_unsub.shtml&l= t;http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: <= a href=3D"http://server.ccl.net/**" target=3D"_blank">http://server.ccl.net= /**
> > chemistry/announcements/**conferences/<http://se= rver.ccl.net/chemistry/announcements/conferences/>
> >
> > Search Messages: http://www.ccl.net/chemistry/**searchccl= /index.shtml<http://www.ccl.net/chemistry/searchccl/index.shtm= l> =A0 =A0 http://www.ccl.net/spammers.**txt <http://www.ccl.net/spammers.txt>=
> >
> > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructio= ns/<http://www.ccl.net/chemistry/aboutccl/instructions/&g= t;
> >
> >
> >
>
>
> --
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> Jesse Gordon
> Application Scientist
> Dotmatics Limited
> 400 West Cummings Park #5450, Woburn MA 01801
> T: +1 781-3= 05-3114
> M: +1-617-320= -6989
> Email: jesse.gordon**dotmatics.com
> Skype: jessegordon
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
>
> See the latest in Dotmatics Suite of Solutions at:
> Booth # 11 CHI Drug Discovery Chemistry, April 17-19, 2012, Hilton San=
> Diego Resort & Spa, San Diego, CA, www.drugdiscoverychemistry.com
> Booth # 323 Bio-IT World Conference, April 24-26, 2012, World Trade > center, =A0Boston, =A0MA, www.bio-itworldexpo.com
>
> --
> Disclaimer: This electronic mail and its attachments are intended sole= ly for
> the person(s) to whom they are addressed and contain information which= is
> confidential or otherwise protected from disclosure, except for the pu= rpose
> for which they are intended. Dissemination, distribution, or reproduct= ion by
> anyone other than the intended recipients is prohibited and may be ill= egal.
> If you are not an intended recipient, please immediately inform the se= nder
> and return the electronic mail and its attachments and destroy any cop= ies
> which may be in your possession. Dotmatics Limited screens electronic = mails
> for viruses but does not warrant that this electronic mail is free of = any
> viruses. Dotmatics Limited accepts no liability for any damage caused = by
> any virus transmitted by this electronic mail. Dotmatics Limited is > registered in England & Wales No. 5614524 with offices at The Old = Monastery,
> Windhill, Bishops Stortford, Herts, CM23 2ND, UK.
>



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Disclaimer: This electronic mail and its attachments are intended solely =
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confidential or otherwise protected from disclosure, except for the purpo=
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If you are not an intended recipient, please immediately inform the sende=
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and return the electronic mail and its attachments and destroy any copies=

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viruses. Dotmatics Limited accepts no liability for any damage caused by
any virus transmitted by this electronic mail. Dotmatics Limited is =

registered in England & Wales No. 5614524 with offices at The Old Monaste=
ry, =

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--f46d0401fb2711600c04bd5b601c--


From owner-chemistry@ccl.net Wed Apr 11 13:38:01 2012
From: "Kira A Armacost kza0004^_^auburn.edu" 
To: CCL
Subject: CCL: Bio3D PCA
Message-Id: <-46670-120411133449-11324-PSdynCfptnDCkWeF/srY3A_._server.ccl.net>
X-Original-From: "Kira A Armacost" 
Date: Wed, 11 Apr 2012 13:34:45 -0400


Sent to CCL by: "Kira A Armacost" [kza0004(_)auburn.edu]
I'm having trouble figuring out how exactly to work PCA on Bio3D. I have been able to load my dcd and 
pdb file in, find the core, and set up the xyz, but when I go to do: pc.xray <- pca.xyz(xyz), I keep 
getting an error stating:

Error in var(xyz[subset, ]) : allocMatrix: too many elements specified

I have tried to reduce the volume of my system. It has 68,759 atoms, of which 19,000 are included as 
waters. I have removed the waters and still get the same error. My dcd file contains only 5ns of 
information, and is only for frames 0-250.

I'm not exactly sure if my system is too large and I need to continue to shrink it, or if there's something 
else i'm missing?
Thanks!


From owner-chemistry@ccl.net Wed Apr 11 18:38:01 2012
From: "Arturo Espinosa artuesp|*|um.es" 
To: CCL
Subject: CCL: energy for proton
Message-Id: <-46671-120411131218-9855-fBht3qFGN25AyEERTNH8gw[*]server.ccl.net>
X-Original-From: Arturo Espinosa 
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Date: Wed, 11 Apr 2012 19:12:07 +0200
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Sent to CCL by: Arturo Espinosa [artuesp(_)um.es]
Dear CCL users:

I am trying to compute ZPE-corrected dissociation energies for some 
particular bonds, in order to correlate these values with other 
properties computed at the same level (starting from, let's say, 
B3LYP-D/def2-TZVP). My problem (perhaps a bit stupid) comes when dealing 
with heterolytic dissociations of a A-H bond to give A- (anion) and H+ 
(a proton). Moreover I am intending to compare this dissociation with 
the other possible heterolytic dissociation and even with the homolytic 
one. Calculation of the A-H and A- species is straighforward (no matter 
what level of calculation), but the problem is what value (in atomic 
units) should I assign to the H+ species. No QC calculation is possible 
as there are no electrons. I recognize that I am a bit lost.
Suggestions are wellcome.
Thank you in advance and best regards,
Arturo