From owner-chemistry@ccl.net Tue Apr 10 10:21:01 2012 From: "Vera Cathrine vera.cathrine*yahoo.com" To: CCL Subject: CCL: G09 error: PGFIO-F-231/formatted read/internal file/error on data conv Message-Id: <-46661-120410101936-8296-Y9hWNwgDdo39wiKgbKz+LQ],[server.ccl.net> X-Original-From: "Vera Cathrine" Date: Tue, 10 Apr 2012 10:19:32 -0400 Sent to CCL by: "Vera Cathrine" [vera.cathrine|*|yahoo.com] Hello Everyone, I got the following error in a G09 ONIOM job. - PGFIO-F-231/formatted read/internal file/error on data conversion. In source file decaty.f, at line number 29 The G09 crashes without issuing any further message. I could not see any problem in the input file. I googled the error message. It is not clear to me why this error is happening? Could you please help me to find out the problem? Thanks you for your kind reply. Vera From owner-chemistry@ccl.net Tue Apr 10 11:08:01 2012 From: "Symon Gathiaka sgathiaka{}gmail.com" To: CCL Subject: CCL: Homology modeling of protein with more than one chain Message-Id: <-46662-120409152345-30683-GRN37/Jwo0g/DohHpkCG5g . server.ccl.net> X-Original-From: Symon Gathiaka Content-Type: multipart/alternative; boundary=f46d0444ee2d47944c04bd43f1b7 Date: Mon, 9 Apr 2012 14:23:35 -0500 MIME-Version: 1.0 Sent to CCL by: Symon Gathiaka [sgathiaka]~[gmail.com] --f46d0444ee2d47944c04bd43f1b7 Content-Type: text/plain; charset=ISO-8859-1 Hi, The project mode of the SWISS-MODEL workspace can also do it. It uses template-based approaches to model the structuraly conserved regions as well as loops. Modeller on the other hand uses *de novo* loop modeling techniques which can be less reliable depending on the biological question of interest you are trying to answer. You may consider using both modeller and the SWISS-MODEL workspace and see which one give a better quality model for your purposes. Consider checking the paper below: Nature Protocols 4, - 1 - 13 (2009). Symon On Sun, Apr 8, 2012 at 1:14 AM, Ben Webb ben++salilab.org < owner-chemistry[A]ccl.net> wrote: > > Sent to CCL by: Ben Webb [ben^^^salilab.org] > On 4/7/12 7:44 AM, Richard W Harper drrwharper%gmail.com wrote: > >> I am attempting to build a homology model of a protein with more than >> one chain. The only way I have discovered to accomplish this is to >> model the two chains independently and combine them by overlaying on >> the x-ray structure. Is there a better way? >> > > MODELLER can do this - it is very straightforward if your template also > has multiple chains. Simply proceed as per normal but add chain break > characters (/) between chains in your alignment for both template and model > sequence. > > Ben > -- > ben{:}salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > -- ** *As is a tale, so is life: not how long it is, but how good it is, is what matters.* ** ** ** ** --f46d0444ee2d47944c04bd43f1b7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
=A0
The project mode of the SWISS-MODEL workspace can also do it. It uses = template-based approaches to model the structuraly conserved regions as wel= l as loops. Modeller on the other hand uses de novo loop modeling = techniques which can be less reliable depending on the biological question = of interest you are trying to answer. You may consider using both modeller = and the SWISS-MODEL workspace and see which one give a better quality model= for your purposes.
=A0
Consider checking the paper below:
Nature Protocols = 4, - 1 - 13 (2009).

Symon


On Sun, Apr 8, 2012 at 1:14 AM, Ben Webb ben++salilab.org <owner-chemistry[A]ccl.net> = wrote:

Sent to CCL by: Ben Webb [ben^^^<= a href=3D"http://salilab.org/" target=3D"_blank">salilab.org]
On 4/7= /12 7:44 AM, Richard W Harper drrwharper%gmail.com wrote:
I am attempting to build a homology m= odel of a protein with more than
one chain. =A0The only way I have disco= vered to accomplish this is to
model the two chains independently and combine them by overlaying on
the= x-ray structure. =A0Is there a better way?

MODELLER ca= n do this - it is very straightforward if your template also has multiple c= hains. Simply proceed as per normal but add chain break characters (/) betw= een chains in your alignment for both template and model sequence.

=A0 =A0 =A0 =A0Ben
--
ben{:}salilab.org =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0http://salilab.org/~be= n/
"It is a capital mistake to theorize before one has data.&qu= ot;
=A0 =A0 =A0 =A0- Sir Arthur Conan Doyle



-=3D This is automat= ically added to each message by the mailing script =3D-
To recover the e= mail address of the author of the message, please change
the strange cha= racters on the top line to the [A] sign. You can also
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--
=A0As is a tale, so is life: not how long it is, = but how good it is, is what matters.
=A0
=A0
=A0
=A0

=A0
=A0

--f46d0444ee2d47944c04bd43f1b7-- From owner-chemistry@ccl.net Tue Apr 10 11:43:01 2012 From: "sobereva sobjubao###yahoo.com.cn" To: CCL Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file Message-Id: <-46663-120409164618-1018-KCVdPvWNKxrzHwq8SOACIw+/-server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 10 Apr 2012 04:46:06 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao]=[yahoo.com.cn] Hello, NLMOs (and NBOs, NHOs, NAOs) can be very conveniently visualized by Multiwfn, which can be freely download at http://multiwfn.codeplex.com. NBO plot files(.31~.40) and the .fch files containing NBOs/NLMOs are acceptable as input file. Please consult the tutorial given in Section 4.0.2 of the program manual for detail. Cube files of these orbitals can be generated by Multiwfn too by using its main function 5. Tian Lu --- On Thu, 4/5/12, Wilhelm Eger eger*theochem.tu-muenchen.de wrote: > From: Wilhelm Eger eger*theochem.tu-muenchen.de > Subject: CCL:G: Visualize NLMOs from Gaussian output/checkpoint file > To: "Lu, Tian " > Date: Thursday, April 5, 2012, 10:39 PM > > Sent to CCL by: Wilhelm Eger > [eger*o*theochem.tu-muenchen.de] > Dear all, > > In order to compare the shapes of a NLMO LP and its parent > NBO in regard to delocalization effects, I would like to > extract both as a cube file > > from a Gaussian calculation. > > I know the actual procedure consisting of: > > Run the NBO calculation with the POP=(SaveNBOs) keyword. > > Transform the resulting checkpoint file to a formatted > chechkpoint file using formchk. > > Look at the end of the calculation output file and get the > right position of the desired NBO. > > Extract the NBO with > > cubegen 0 mo=X file.fchk MOX.cube -3 h > > and all other related with > > cubegen 0 mo=Y file.fchk MOY.cube -3 h MOX.cube > > to ensure the same dimensions. > > However, if I run the calculation with POP=(SaveNLMOs), and > extract the related MO, I get exactly the same cube files as > for the NBO extraction method (e.g. diff results zero). The > Gaussian output tells me also of NBOs being stored in the > checkpoint file instead of NLMOs. Besides of 'SaveNLMOs' I > tried 'SaveMixed' and 'IOP=(6/7=3)', but still the same > result. Both G03 and G09 have been used. The desired NBO and > NLMO must be different due to significant delocalization of > the parent NBO into antibonds. > > Does anybody know how to reliably extract NLMOs to cube > files? > > Thanks in advance. > > Regards, > > Wilhelm > > -- > Dr. Wilhelm Eger > > Theoretische Chemie > Department Chemie > Technische Universitaet Muenchen > Lichtenbergstr. 4 > 85748 Garching > > Tel. 089/289-13605 > > > > -= This is automatically added to each message by the > mailing script =- > To recover the email address of the author of the message, > please change > the strange characters on the top line to the [-] sign. You > can also> > E-mail to subscribers: CHEMISTRY[-]ccl.net > or use: >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message > > E-mail to administrators: CHEMISTRY-REQUEST[-]ccl.net > or use >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message > > Subscribe/Unsubscribe:     >      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Tue Apr 10 12:18:01 2012 From: "Sreenithya A sreenithyanair\a/gmail.com" To: CCL Subject: CCL: ONIOM input Message-Id: <-46664-120410074113-10443-+IUk4gajK2KHf0bqgDy4jw .. server.ccl.net> X-Original-From: "Sreenithya A" Date: Tue, 10 Apr 2012 07:41:10 -0400 Sent to CCL by: "Sreenithya A" [sreenithyanair]_[gmail.com] Hi, I would like to do a two layer ONIOM calculation on a system having Pd. I am using B3LYP/6-31G(d,p) and Lanl2dz in high-level layer and HF/3-21G and Lanl2mb in low-lelvel layer. But I have problem in basis set specification. My attempt is listed below. How can I get rid of the error? Any advices will be greatly appreciated. %chk=checkponit file #oniom(b3lyp/genecp:hf/genecp) opt=calcfc freq=noraman comment line -1 1 cartesian coordinates c h n o 0 6-31g**:6-31g **** pd 0 lanl2dz:lanl2mb ***** pd 0 lanl2dz:lanl2mb Thank you, Sreenithya A IIT Bombay. From owner-chemistry@ccl.net Tue Apr 10 18:41:01 2012 From: "Aniko Simon aniko ~~ simbiosys.ca" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46665-120410122105-17349-t6uL18gDnaAK1vLV1zruCQ ~~ server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 10 Apr 2012 12:21:00 -0400 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.com wrote: > 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_message > chemistry/announcements/**conferences/ > > > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > > > RTFI: 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. > From owner-chemistry@ccl.net Tue Apr 10 19:16:01 2012 From: "Aniko Simon aniko(!)simbiosys.ca" To: CCL Subject: CCL: extract chemical information from PDF tables Message-Id: <-46666-120410164226-14631-uafE97op/TVUn4U1s3BiuA\a/server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 10 Apr 2012 16:42:22 -0400 Sent to CCL by: "Aniko Simon" [aniko*o*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.com wrote: > 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 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>