From owner-chemistry@ccl.net Tue Feb 5 01:51:01 2008 From: "gestionnaire licpro licpro.dechets^^^gmail.com" To: CCL Subject: CCL:G: Gaussian 03 compilation Message-Id: <-36225-080204132409-9424-7Zd+lArbnhN8SySZuWinfQ**server.ccl.net> X-Original-From: "gestionnaire licpro" Content-Type: multipart/alternative; boundary="----=_Part_7253_26901500.1202149033611" Date: Mon, 4 Feb 2008 19:17:13 +0100 MIME-Version: 1.0 Sent to CCL by: "gestionnaire licpro" [licpro.dechets(0)gmail.com] ------=_Part_7253_26901500.1202149033611 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Cclers, I am trying to compile Gaussian 03 (D02), on Xeon Emt64 machine with ifc (V 9.0) and mkl, based on the ia64.make file. However the compilation Stop with the following message : efc -L/usr/local/intel/fce/9.0/lib -WB -i8 -r8 -w -ftz -switch fe_new_cgoto -IPF_fp_relaxed -i-static -IPF_fp_speculation -openmp -fpp2 -auto -O3 -o g03 ml0.o util.a /home/jeff/lib/mkl/lib/em64t/libmkl_em64t.a IPO Error: unresolved : gauabt_ Referenced in ml0.o Referenced in util.a(prsarg.o) Referenced in util.a(lnk1e.o) Referenced in util.a(chain.o) Referenced in util.a(ntrerr.o) IPO Error: unresolved : fixinout_ Referenced in ml0.o IPO Error: unresolved : putenv_ Referenced in ml0.o IPO Error: unresolved : ggeten_ Referenced in ml0.o Referenced in util.a(getscd.o) IPO Error: unresolved : getexen_ Referenced in ml0.o IPO Error: unresolved : gaufls_ Referenced in ml0.o IPO Error: unresolved : gsyst_ Referenced in ml0.o IPO Error: unresolved : envfil_ Referenced in util.a(tstfil.o) Referenced in util.a(getatf.o) IPO Error: unresolved : gfree_ Referenced in util.a(chain.o) IPO Error: unresolved : gauexec_ Referenced in util.a(chain.o) IPO Error: unresolved : ntrbks_ Referenced in util.a(ntstat.o) IPO Error: unresolved : gfree1_ Referenced in util.a(ntrclo.o) IPO Error: unresolved : closwa_ Referenced in util.a(ntrclo.o) IPO Error: unresolved : ntrext1_ Referenced in util.a(ntrext.o) IPO Error: unresolved : ntrsiz_ Referenced in util.a(ntrext.o) Referenced in util.a(ntropn.o) IPO Error: unresolved : galloc1_ Referenced in util.a(ntrext.o) Referenced in util.a(ntropn.o) IPO Error: unresolved : writwa_ Referenced in util.a(ntrio.o) IPO Error: unresolved : readwa_ Referenced in util.a(ntrio.o) IPO Error: unresolved : waitwa_ Referenced in util.a(ntrwat.o) IPO Error: unresolved : openwa_ Referenced in util.a(ntropn.o) ml0.o(.text+0x2bb): In function `MAIN__': : undefined reference to `gauabt_' ml0.o(.text+0x40a): In function `MAIN__': : undefined reference to `fixinout_' ml0.o(.text+0xa81): In function `MAIN__': : undefined reference to `putenv_' ml0.o(.text+0xb35): In function `MAIN__': : undefined reference to `ggeten_' ml0.o(.text+0xba8): In function `MAIN__': : undefined reference to `getexen_' ml0.o(.text+0xeaf): In function `MAIN__': : undefined reference to `gaufls_' ml0.o(.text+0xebc): In function `MAIN__': : undefined reference to `gsyst_' ml0.o(.text+0xfa8): In function `MAIN__': : undefined reference to `gauabt_' ml0.o(.text+0x12ae): In function `MAIN__': : undefined reference to `gauabt_' ml0.o(.text+0x1353): In function `MAIN__': : undefined reference to `gauabt_' ml0.o(.text+0x13c9): In function `MAIN__': : undefined reference to `gauabt_' util.a(getscd.o)(.text+0x139): In function `getscd_': : undefined reference to `ggeten_' util.a(lnk1e.o)(.text+0xe4): In function `lnk1e_': : undefined reference to `gauabt_' util.a(prsarg.o)(.text+0x21e): In function `prsarg_': : undefined reference to `gauabt_' util.a(tstfil.o)(.text+0x756): In function `tstfil_': : undefined reference to `envfil_' util.a(tstfil.o)(.text+0x796): In function `tstfil_': : undefined reference to `envfil_' util.a(chain.o)(.text+0x81f): In function `chain_': : undefined reference to `gauabt_' util.a(chain.o)(.text+0x828): In function `chain_': : undefined reference to `gfree_' util.a(chain.o)(.text+0x87d): In function `chain_': : undefined reference to `gauexec_' util.a(getatf.o)(.text+0x243): In function `getatf_': : undefined reference to `envfil_' util.a(ntrclo.o)(.text+0x22f): In function `ntrclo_': : undefined reference to `gfree1_' util.a(ntrclo.o)(.text+0x2c1): In function `ntrclo_': : undefined reference to `closwa_' util.a(ntrerr.o)(.text+0x45): In function `ntrerr_': : undefined reference to `gauabt_' util.a(ntrext.o)(.text+0x15f): In function `ntrext_': : undefined reference to `ntrext1_' util.a(ntrext.o)(.text+0x19e): In function `ntrext_': : undefined reference to `ntrsiz_' util.a(ntrext.o)(.text+0x1d0): In function `ntrext_': : undefined reference to `galloc1_' util.a(ntrio.o)(.text+0x3cb): In function `ntrio_': : undefined reference to `writwa_' util.a(ntrio.o)(.text+0x400): In function `ntrio_': : undefined reference to `readwa_' util.a(ntrwat.o)(.text+0x79): In function `ntrwat_': : undefined reference to `waitwa_' util.a(ntstat.o)(.text+0x309): In function `ntstat_': : undefined reference to `ntrbks_' util.a(ntropn.o)(.text+0x309): In function `ntropn_': : undefined reference to `galloc1_' util.a(ntropn.o)(.text+0x34f): In function `ntropn_': : undefined reference to `openwa_' util.a(ntropn.o)(.text+0x441): In function `ntropn_': : undefined reference to `ntrsiz_' util.a(ntropn.o)(.text+0x5a0): In function `ntropn_': : undefined reference to `openwa_' util.a(ntropn.o)(.text+0x5f0): In function `ntropn_': : undefined reference to `openwa_' Can someone indicate me what going wrong with my options ? Thank you in advance, Jeff ------=_Part_7253_26901500.1202149033611 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi Cclers,
 
I am trying to compile Gaussian 03 (D02),  on Xeon Emt64 machine with ifc (V 9.0) and mkl, based on the ia64.make file.
 
However the compilation Stop with the following message :
 
 
efc -L/usr/local/intel/fce/9.0/lib -WB -i8 -r8 -w -ftz -switch fe_new_cgoto -IPF_fp_relaxed -i-static -IPF_fp_speculation -openmp -fpp2 -auto -O3 -o g03 ml0.o util.a /home/jeff/lib/mkl/lib/em64t/libmkl_em64t.a
 
IPO Error: unresolved : gauabt_
        Referenced in ml0.o
        Referenced in util.a(prsarg.o)
        Referenced in util.a(lnk1e.o)
        Referenced in util.a(chain.o)
        Referenced in util.a(ntrerr.o)
IPO Error: unresolved : fixinout_
        Referenced in ml0.o
IPO Error: unresolved : putenv_
        Referenced in ml0.o
IPO Error: unresolved : ggeten_
        Referenced in ml0.o
        Referenced in util.a(getscd.o)
IPO Error: unresolved : getexen_
        Referenced in ml0.o
IPO Error: unresolved : gaufls_
        Referenced in ml0.o
IPO Error: unresolved : gsyst_
        Referenced in ml0.o
IPO Error: unresolved : envfil_
        Referenced in util.a(tstfil.o)
        Referenced in util.a(getatf.o)
IPO Error: unresolved : gfree_
        Referenced in util.a(chain.o)
IPO Error: unresolved : gauexec_
        Referenced in util.a(chain.o)
IPO Error: unresolved : ntrbks_
        Referenced in util.a(ntstat.o)
IPO Error: unresolved : gfree1_
        Referenced in util.a(ntrclo.o)
IPO Error: unresolved : closwa_
        Referenced in util.a(ntrclo.o)
IPO Error: unresolved : ntrext1_
        Referenced in util.a(ntrext.o)
IPO Error: unresolved : ntrsiz_
        Referenced in util.a(ntrext.o)
        Referenced in util.a(ntropn.o)
IPO Error: unresolved : galloc1_
        Referenced in util.a(ntrext.o)
        Referenced in util.a(ntropn.o)
IPO Error: unresolved : writwa_
        Referenced in util.a(ntrio.o)
IPO Error: unresolved : readwa_
        Referenced in util.a(ntrio.o)
IPO Error: unresolved : waitwa_
        Referenced in util.a(ntrwat.o)
IPO Error: unresolved : openwa_
        Referenced in util.a(ntropn.o)
ml0.o(.text+0x2bb): In function `MAIN__':
: undefined reference to `gauabt_'
ml0.o(.text+0x40a): In function `MAIN__':
: undefined reference to `fixinout_'
ml0.o(.text+0xa81): In function `MAIN__':
: undefined reference to `putenv_'
ml0.o(.text+0xb35): In function `MAIN__':
: undefined reference to `ggeten_'
ml0.o(.text+0xba8): In function `MAIN__':
: undefined reference to `getexen_'
ml0.o(.text+0xeaf): In function `MAIN__':
: undefined reference to `gaufls_'
ml0.o(.text+0xebc): In function `MAIN__':
: undefined reference to `gsyst_'
ml0.o(.text+0xfa8): In function `MAIN__':
: undefined reference to `gauabt_'
ml0.o(.text+0x12ae): In function `MAIN__':
: undefined reference to `gauabt_'
ml0.o(.text+0x1353): In function `MAIN__':
: undefined reference to `gauabt_'
ml0.o(.text+0x13c9): In function `MAIN__':
: undefined reference to `gauabt_'
util.a(getscd.o)(.text+0x139): In function `getscd_':
: undefined reference to `ggeten_'
util.a(lnk1e.o)(.text+0xe4): In function `lnk1e_':
: undefined reference to `gauabt_'
util.a(prsarg.o)(.text+0x21e): In function `prsarg_':
: undefined reference to `gauabt_'
util.a(tstfil.o)(.text+0x756): In function `tstfil_':
: undefined reference to `envfil_'
util.a(tstfil.o)(.text+0x796): In function `tstfil_':
: undefined reference to `envfil_'
util.a(chain.o)(.text+0x81f): In function `chain_':
: undefined reference to `gauabt_'
util.a(chain.o)(.text+0x828): In function `chain_':
: undefined reference to `gfree_'
util.a(chain.o)(.text+0x87d): In function `chain_':
: undefined reference to `gauexec_'
util.a(getatf.o)(.text+0x243): In function `getatf_':
: undefined reference to `envfil_'
util.a(ntrclo.o)(.text+0x22f): In function `ntrclo_':
: undefined reference to `gfree1_'
util.a(ntrclo.o)(.text+0x2c1): In function `ntrclo_':
: undefined reference to `closwa_'
util.a(ntrerr.o)(.text+0x45): In function `ntrerr_':
: undefined reference to `gauabt_'
util.a(ntrext.o)(.text+0x15f): In function `ntrext_':
: undefined reference to `ntrext1_'
util.a(ntrext.o)(.text+0x19e): In function `ntrext_':
: undefined reference to `ntrsiz_'
util.a(ntrext.o)(.text+0x1d0): In function `ntrext_':
: undefined reference to `galloc1_'
util.a(ntrio.o)(.text+0x3cb): In function `ntrio_':
: undefined reference to `writwa_'
util.a(ntrio.o)(.text+0x400): In function `ntrio_':
: undefined reference to `readwa_'
util.a(ntrwat.o)(.text+0x79): In function `ntrwat_':
: undefined reference to `waitwa_'
util.a(ntstat.o)(.text+0x309): In function `ntstat_':
: undefined reference to `ntrbks_'
util.a(ntropn.o)(.text+0x309): In function `ntropn_':
: undefined reference to `galloc1_'
util.a(ntropn.o)(.text+0x34f): In function `ntropn_':
: undefined reference to `openwa_'
util.a(ntropn.o)(.text+0x441): In function `ntropn_':
: undefined reference to `ntrsiz_'
util.a(ntropn.o)(.text+0x5a0): In function `ntropn_':
: undefined reference to `openwa_'
util.a(ntropn.o)(.text+0x5f0): In function `ntropn_':
: undefined reference to `openwa_'
 
Can someone indicate me what going wrong with my options ?
 
Thank you in advance,
Jeff
------=_Part_7253_26901500.1202149033611-- From owner-chemistry@ccl.net Tue Feb 5 04:13:01 2008 From: "Pieter Stouten Pieter.Stouten .. glpg.com" To: CCL Subject: CCL: CRT monitors for hardware stereo - summary Message-Id: <-36226-080205041025-3518-s3aSFgcUJsmgpR/ci2TDgA++server.ccl.net> X-Original-From: "Pieter Stouten" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Feb 2008 10:12:54 +0100 MIME-Version: 1.0 Sent to CCL by: "Pieter Stouten" [Pieter.Stouten(-)glpg.com] I thank everybody for their answers. Finding 3D monitors has proven difficult. Several CRT monitors were recommended: Samsung SyncMaster 1100DF (21"), NEC-Mitsubishi FP2141SB (22"), IIYAMA Vision Master Pro 514 (22"), ViewSonic G225FB (21") and any old SGI monitor. The problem is that they have all been discontinued. Recommended glasses were NuVison 60GX. LCD screens don't have high refresh rates and often show ghost images, so alternating the left-eye and right-eye images does not seem an option. Therefore, statically polarized screens are the only option. They are typically very expensive. Recommended were Miracube 24" (3,995 Euro) and Planar SD2020 20" Stereoscopic Display (4,745 Euro). The latter has two polarised LCD screens and a half-mirror. Much cheaper is the Zalman ZM-M220W 22" Trimon 3D (639 Euro), but nobody seems to have any experience (good or bad) with it yet. I am not sure what I will be doing now as the responses have mostly confirmed what I already feared. If we go for LCD screens anyway, I'll let you know how we fare. Thanks again, Pieter PS: looking for a cool job with the company that is rapidly becoming Europe's leading biotech and the world's leading biotech/pharma service organization? Check out our job openings: http://www.biofocus.com/Jobs_at_BioFocus_DPI http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml --------------------- Original Message: I am looking for monitors for use with hardware stereo. I used to use the Samsung SyncMaster 1100DF and I was very happy with it. A colleague recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to have been discontinued. To have an adequate refresh rate and no ghost images, the rule of thumb was that only a CRT monitor would do. Is that still the case? If you have good hardware stereo experiences with a specific monitor (CRT or otherwise), could you please let me know? And what stereo-emitter and stereo-glasses work well for you? Any opinions, hints or pointers are much appreciated. And yes, in case you were wondering, we do have job openings: http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml Thanks, Pieter Pieter Stouten Group Leader Computational Chemistry Galapagos NV, Mechelen, Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. From owner-chemistry@ccl.net Tue Feb 5 06:13:01 2008 From: "Jamie Platts platts,,cardiff.ac.uk" To: CCL Subject: CCL: MGMS Spring meeting: 31st March - 2nd April 2008 Message-Id: <-36227-080205060833-9277-0JCig4MW94ZBbZC5m6SY/g . server.ccl.net> X-Original-From: "Jamie Platts" Date: Tue, 5 Feb 2008 06:08:29 -0500 Sent to CCL by: "Jamie Platts" [platts[-]cardiff.ac.uk] Dear CCL Registration is open now for the MGMS Spring meeting on Bio-Inorganic Chemistry, which will be held in Cardiff from 31st March to 1st April 2008. Early registration fees will apply until the end of the week, closing on 8th Feb. Thanks to generous sponsorship by CCG, travel bursaries for students and younger researchers will be available. We have an excellent line-up of speakers, all of whom have confirmed: * Dr. Frank Blaney - Cytochrome P450 2D6 - Recent Structural and Mechanistic Studies. * Prof. Jaroslav Burda - Physicochemical properties and reaction mechanisms of selected anticancer metallodrugs. * Prof. Paolo Carloni - Metal-based drugs/DNA interactions investigated by molecular simulation * Dr. Rob Deeth - Bridging Ligands at Multinuclear Metalloenzyme Active Sites: Novel Force Field Approaches for Dimanganese(II) and Dicopper(II) Systems * Dr. Jeremy Harvey - QM/MM Studies of Metalloprotein Structure and Reactivity * Prof. Fahmi Himo - On the Elusive Mechanism of Nitrile Hydratase * Prof. Nigel Richards - Fe-type nitrile hydratase: How does sulfur oxidation modulate metal chemistry? * Dr. Sam de Visser - Catalytic properties of oxygen activating non-heme enzymes In addition, Dr. Nick Besley will present the MGMS Silver Jubilee Prize lecture, titled: State-Selective Self-Consistent Field Calculations using the Maximum Overlap Method. More details on the meeting, including registration and accomodation details, can be found at URL: http://theory.chem.cf.ac.uk/~grant/conf Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts^cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy From owner-chemistry@ccl.net Tue Feb 5 10:58:00 2008 From: "Pascal Boulet pascal.boulet : univ-provence.fr" To: CCL Subject: CCL:G: pb to converge wavefunction with gaussian Message-Id: <-36228-080204165524-5329-lPUcNGyI31taDpz109UldA()server.ccl.net> X-Original-From: Pascal Boulet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 Feb 2008 22:55:09 +0100 MIME-Version: 1.0 Sent to CCL by: Pascal Boulet [pascal.boulet**univ-provence.fr] Dear Anthony, Thank you for your advice. I'm going to try this. Regards Pascal Debellis Anthony CE US anthony.debellis=-=ciba.com wrote: > Sent to CCL by: Debellis Anthony CE US [anthony.debellis*ciba.com] > Dear Pascal, > I assume you are using the SDD basis which places D95V on atoms up to > Ar. I would try to converge the SCF using the minimal LanL2MB basis > first, followed by guess=read with the larger basis. > Regards, > Anthony > > _________________________ > Dr. Anthony D. DeBellis > Research Fellow - Coating Effects Research > Ciba Specialty Chemicals Corp. > 540 White Plains Road > Tarrytown, NY 10591 > USA > Phone: 914 785 2949 > Fax: 914 785 3681 > E-mail: anthony.debellis#,#cibasc.com > Internet: www.ciba.com > > > > > Sent to CCL by: Pascal Boulet [pascal.boulet]~[univ-provence.fr] > > Dear CCL users, > > I am trying to optimize the structure of a cluster of zirconium oxide > with gaussian. I just cut a cluster from ZrO2 surface and saturated the > cluster with hydrogen atoms. I'm using the Stuttgart pseudopotential for > Zr and O. The SCF is not converging. I tried first the default > algorithm, then switched to Fermi, then to QC (which failed at some > point, for some obscur reasons) and now I'm using the combined keywords: > > cdiis, novaracc and vshift. Still no convergence. > > Does anyone know a way to make gaussian converge? > > Thank you for your help, > Regards > Pascal > > -- > Dr. Pascal Boulet, Computational Chemist University of Aix-Marseille I, > II and III, and CNRS > UMR6264: Laboratoire Chimie Provence > Centre Saint-Jerome, case MADIREL > F-13397 MARSEILLE Cedex 20, France > Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 > courriel: pascal.boulet-,-univ-provence.fr http://www.lc-provence.fr > http://allos.up.univ-mrs.fr/boulethttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > -=his is automatically added to each message by the mailing script =-> > > -- Dr. Pascal Boulet, Computational Chemist University of Aix-Marseille I, II and III, and CNRS UMR6264: Laboratoire Chimie Provence Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet]_[univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet From owner-chemistry@ccl.net Tue Feb 5 12:03:01 2008 From: "Pradeep Indrakanti vxi103()psu.edu" To: CCL Subject: CCL: NBO error Message-Id: <-36229-080205120128-3644-rqHyMoF11oPF6LdbF5wy0Q]*[server.ccl.net> X-Original-From: "Pradeep Indrakanti" Date: Tue, 5 Feb 2008 12:01:24 -0500 Sent to CCL by: "Pradeep Indrakanti" [vxi103.:.psu.edu] Kemi, If you were trying to use a ECP basis with P atoms (like LANL2DZ), you need to specify both the valence basis and the core potential expansion. The route keyword is GenECP and then the basis input section will look something like: P 0 LANL2DZ **** P 0 LANL2DZ **** Since the core potential was not specified, NBO gives this error. Hope this helps, Pradeep > "kemi oloba ooloba::uh.edu" wrote: > > Sent to CCL by: "kemi oloba" [ooloba[]uh.edu] > I am trying to run a NBO job and keep getting this error > > Subroutine NAOANL could not find a S-type core orbital on atom P 9. > ICORE : 2 1 0 0 M : 1 LA : 1 > > pls can someone help me > thanks > > From owner-chemistry@ccl.net Tue Feb 5 12:57:00 2008 From: "Ted Cabeen cabeen:-:chem.ucsb.edu" To: CCL Subject: CCL: CRT monitors for hardware stereo - summary Message-Id: <-36230-080205125518-2113-qAqr/j2YqMV0PfJ8v0t9Ng(~)server.ccl.net> X-Original-From: Ted Cabeen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 05 Feb 2008 09:18:20 -0800 MIME-Version: 1.0 Sent to CCL by: Ted Cabeen [cabeen.+*+.chem.ucsb.edu] Pieter Stouten Pieter.Stouten .. glpg.com wrote: > Sent to CCL by: "Pieter Stouten" [Pieter.Stouten(-)glpg.com] > I thank everybody for their answers. > > Finding 3D monitors has proven difficult. Several CRT monitors were > recommended: Samsung SyncMaster 1100DF (21"), NEC-Mitsubishi FP2141SB > (22"), IIYAMA Vision Master Pro 514 (22"), ViewSonic G225FB (21") and > any old SGI monitor. The problem is that they have all been > discontinued. Recommended glasses were NuVison 60GX. Try looking for any of these: http://www.reald-corporate.com/scientific/stereo_ready_monitors.asp A few of your monitors are still around just under newer model names. From RealD's page, CDW has one of the ViewSonics and one NEC in stock. --Ted From owner-chemistry@ccl.net Tue Feb 5 13:34:00 2008 From: "Igor Filippov Contr igorf]^[helix.nih.gov" To: CCL Subject: CCL: OSRA: Optical Structure Recognition Message-Id: <-36231-080205125410-1985-sXWv6zCFLUbBRLDabqUdVw:+:server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 05 Feb 2008 12:53:21 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf[]helix.nih.gov] Dear Colleagues, I would like to let you know that Optical Structure Recognition Application (OSRA) is now available for Windows platform as a compiled binary. The executable was generated by using MinGW compiler. You can download osra-mingw.zip from either http://cactus.nci.nih.gov/osra or http://osra.sf.net The archive includes: osra.bat - Windows batch file, sets the environment and calls osra.exe, osra.exe - main executable. It is recommended that you use osra.bat and not osra.exe directly, README - instructions on usage and compilation, delegates.xml - a configuration file for ImageMagick library, Read Image Document (OSRA).xml - a simple Scitegic Pipeline Pilot component to read in an image document using OSRA. To use: Make sure you have installed Ghostscript (32-bit executable) and edit if necessary osra.bat to have the correct PATH (by default it points to version 8.61) if you're planning to process PDF or PS files. Run osra.bat with the same options as for the Linux version. You can also run OSRA through Pipiline Pilot by using the included protocol. It runs osra.bat on the client by default but it's trivial to modify the component for "Run on Server" option. It is also possible to compile OSRA using Cygwin environment but I strongly recommend against it - the resulting executable is about 50 times slower than the equivalent Linux version and it is quite unpractical to use it. Read the README file included in the distribution for the detailed instructions if you would like to perform the compilation yourself. Sincerely, Igor Filippov From owner-chemistry@ccl.net Tue Feb 5 14:06:00 2008 From: "Frank Marchese ftmarchese,+,yahoo.com" To: CCL Subject: CCL: CRT monitors for hardware stereo - summary Message-Id: <-36232-080205104548-6131-c2sqHY18CXdcLDgThnYs2w[]server.ccl.net> X-Original-From: Frank Marchese Content-Type: multipart/alternative; boundary="0-290053829-1202222735=:59105" Date: Tue, 5 Feb 2008 06:45:35 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Frank Marchese [ftmarchese=yahoo.com] --0-290053829-1202222735=:59105 Content-Type: text/plain; charset=us-ascii Hi All, One other possibility for a 3D Stereo display is found in the new 3D DLP rear projection monitors manufactured by Samsung and Mitsubishi. http://www.mitsubishi-tv.com/j/i/18326/cid/5462/TelevisionDetails/WD57833.html http://product.samsung.com/dlp3d/3ddlps.html These systems are designed specifically for 3D content with a refresh rate of 120Hz. Shutter glasses are attached directly to a port on the rear of the TV. A PC is connected to the TV's HDMI port via a DVI (PC's video card) to HDMI cable. These TV's range in size from 50" (16:9, 720p) with a resolution of 1280 x 720 pixels (Samsung HLT5075S, street price less than $1500) to 1080p systems (1920 x 1080 pixels) that vary in size from 56" to 73" with prices ranging from about $2500 to $4000. I have seen a demo of a Samsung TV running a computer game using inexpensive ($100) shutter glasses. I was very impressed. Given the fact that many inexpensive video cards have dual DVI output and large LCD monitors have become inexpensive, the constuction of a two monitor shared/collaborative 3D visualization station is within the reach of more scientists. Frank Dr. Francis T. Marchese Professor Dept. of Computer Science Pace University New York, NY 10038 http://csis.pace.edu/~marchese email: fmarchese_._pace.edu phone: 212 346-1803 Director Pace Center for Advanced Media http://csis.pace.edu/~cam Co-director Pace Digital Gallery http://www.pace.edu/DigitalGallery ----- Original Message ---- > From: Pieter Stouten Pieter.Stouten .. glpg.com To: "Marchese, Francis T " Sent: Tuesday, February 5, 2008 4:12:54 AM Subject: CCL: CRT monitors for hardware stereo - summary Sent to CCL by: "Pieter Stouten" [Pieter.Stouten(-)glpg.com] I thank everybody for their answers. Finding 3D monitors has proven difficult. Several CRT monitors were recommended: Samsung SyncMaster 1100DF (21"), NEC-Mitsubishi FP2141SB (22"), IIYAMA Vision Master Pro 514 (22"), ViewSonic G225FB (21") and any old SGI monitor. The problem is that they have all been discontinued. Recommended glasses were NuVison 60GX. LCD screens don't have high refresh rates and often show ghost images, so alternating the left-eye and right-eye images does not seem an option. Therefore, statically polarized screens are the only option. They are typically very expensive. Recommended were Miracube 24" (3,995 Euro) and Planar SD2020 20" Stereoscopic Display (4,745 Euro). The latter has two polarised LCD screens and a half-mirror. Much cheaper is the Zalman ZM-M220W 22" Trimon 3D (639 Euro), but nobody seems to have any experience (good or bad) with it yet. I am not sure what I will be doing now as the responses have mostly confirmed what I already feared. If we go for LCD screens anyway, I'll let you know how we fare. Thanks again, Pieter PS: looking for a cool job with the company that is rapidly becoming Europe's leading biotech and the world's leading biotech/pharma service organization? Check out our job openings: http://www.biofocus.com/Jobs_at_BioFocus_DPI http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml --------------------- Original Message: I am looking for monitors for use with hardware stereo. I used to use the Samsung SyncMaster 1100DF and I was very happy with it. A colleague recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to have been discontinued. To have an adequate refresh rate and no ghost images, the rule of thumb was that only a CRT monitor would do. Is that still the case? If you have good hardware stereo experiences with a specific monitor (CRT or otherwise), could you please let me know? And what stereo-emitter and stereo-glasses work well for you? Any opinions, hints or pointers are much appreciated. And yes, in case you were wondering, we do have job openings: http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml Thanks, Pieter Pieter Stouten Group Leader Computational Chemistry Galapagos NV, Mechelen, Belgium -- This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently. Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising > from alteration of the contents of this message (by a third party) or as a result of a virus being passed on. - This is automatically added to each message by the mailing script -http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlIf your mail bounces > from CCL with 5.7.1 error, check:____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping --0-290053829-1202222735=:59105 Content-Type: text/html; charset=us-ascii
Hi All,

One other possibility for a 3D Stereo display is found in the new 3D DLP rear projection monitors manufactured by Samsung and Mitsubishi.
http://www.mitsubishi-tv.com/j/i/18326/cid/5462/TelevisionDetails/WD57833.html

http://product.samsung.com/dlp3d/3ddlps.html

These systems are designed specifically for 3D content with a refresh rate of 120Hz. Shutter glasses are attached directly to a port on the rear of the TV. A PC is connected to the TV's HDMI port via a DVI (PC's video card) to HDMI cable.

These TV's range in size from 50" (16:9, 720p) with a resolution of 1280 x 720 pixels (Samsung HLT5075S, street price less than $1500) to 1080p systems (1920 x 1080 pixels) that vary in size from 56" to 73" with prices ranging from about $2500 to $4000.

I have seen a demo of a Samsung TV running a computer game using inexpensive ($100) shutter glasses. I was very impressed.

Given the fact that many inexpensive video cards have dual DVI output and large LCD monitors have become inexpensive, the constuction of a two monitor shared/collaborative 3D visualization station is within the reach of more scientists.

Frank
 
Dr. Francis T. Marchese
Professor
Dept. of Computer Science
Pace University
New York, NY 10038
http://csis.pace.edu/~marchese
email: fmarchese_._pace.edu
phone: 212 346-1803
 
Director
Pace Center for Advanced Media
http://csis.pace.edu/~cam
 
Co-director
Pace Digital Gallery
http://www.pace.edu/DigitalGallery


----- Original Message ----
From: Pieter Stouten Pieter.Stouten .. glpg.com <owner-chemistry_._ccl.net>
To: "Marchese, Francis T " <marchesf_._pace.edu>
Sent: Tuesday, February 5, 2008 4:12:54 AM
Subject: CCL: CRT monitors for hardware stereo - summary


Sent to CCL by: "Pieter Stouten" [Pieter.Stouten(-)glpg.com]
I thank everybody for their answers.

Finding 3D monitors has proven difficult. Several CRT monitors were
recommended: Samsung SyncMaster 1100DF (21"), NEC-Mitsubishi FP2141SB
(22"), IIYAMA Vision Master Pro 514 (22"), ViewSonic G225FB (21") and
any old SGI monitor. The problem is that they have all been
discontinued. Recommended glasses were NuVison 60GX.

LCD screens don't have high refresh rates and often show ghost images,
so alternating the left-eye and right-eye images does not seem an
option. Therefore, statically polarized screens are the only option.
They are typically very expensive. Recommended were Miracube 24" (3,995
Euro) and Planar SD2020 20" Stereoscopic Display (4,745 Euro). The
latter has two polarised LCD screens and a half-mirror. Much cheaper is
the Zalman ZM-M220W 22" Trimon 3D (639 Euro), but nobody seems to have
any experience (good or bad) with it yet.

I am not sure what I will be doing now as the responses have mostly
confirmed what I already feared. If we go for LCD screens anyway, I'll
let you know how we fare.

Thanks again,

Pieter

PS: looking for a cool job with the company that is rapidly becoming
Europe's leading biotech and the world's leading biotech/pharma service
organization? Check out our job openings:

http://www.biofocus.com/Jobs_at_BioFocus_DPI
http://www.glpg.com/careers/openings.htm
http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml

---------------------

Original Message:

I am looking for monitors for use with hardware stereo. I used to use
the Samsung SyncMaster 1100DF and I was very happy with it. A colleague
recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to
have been discontinued.

To have an adequate refresh rate and no ghost images, the rule of thumb
was that only a CRT monitor would do. Is that still the case?

If you have good hardware stereo experiences with a specific monitor
(CRT or otherwise), could you please let me know? And what
stereo-emitter and stereo-glasses work well for you? Any opinions, hints
or pointers are much appreciated.

And yes, in case you were wondering, we do have job openings:

http://www.glpg.com/careers/openings.htm
http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml

Thanks,

Pieter

Pieter Stouten
Group Leader Computational Chemistry
Galapagos NV, Mechelen, Belgium

--
This e-mail and its attachment(s) (if any) may contain confidential and/or proprietary information and is intended for its addressee(s) only. Any unauthorized use of the information contained herein (including, but not limited to, alteration, reproduction, communication, distribution or any other form of dissemination) is strictly prohibited. If you are not the intended addressee, please notify the orginator promptly and delete this e-mail and its attachment(s) (if any) subsequently.

Galapagos nor any of its affiliates shall be liable for direct, special, indirect or consequential damages arising > from alteration of the contents of this message (by a third party) or as a result of a virus being passed on.



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Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. --0-290053829-1202222735=:59105-- From owner-chemistry@ccl.net Tue Feb 5 14:41:00 2008 From: "David P ccl_list{:}giantscience.com" To: CCL Subject: CCL: What happened to the docking program Flo-QXP ? Message-Id: <-36233-080205142801-353-+rWKkXBrzPIeh0pjOJhYaw-x-server.ccl.net> X-Original-From: "David P" Date: Tue, 5 Feb 2008 14:27:58 -0500 Sent to CCL by: "David P" [ccl_list^_^giantscience.com] Colin McMartin's program FLO-QXP has gotten a number of very positive mentions over the past few years in the various "we compare all the docking programs" surveys. However, as far as I can tell it is barely available, if at all. I've done as many smart Google searches as I can think of, and I come up pretty empty. Apparently, it used to be available from the link uwmml.pharmacy.wisc.edu/Flo/floindx.html, but that address is completely out of date/dead. Going to the U.Wisc website, I couldn't find an equivalent website. Supposedly, the software is also sold through "Thistlesoft" software, but they don't have a website, if they actually still exist. Does anyone know if this software is still being developed, and if so, from where? Is this software package still competitive with others? From owner-chemistry@ccl.net Tue Feb 5 18:26:01 2008 From: "Richard L. Wood woodx278:umn.edu" To: CCL Subject: CCL: Pipeline Pilot Question Message-Id: <-36234-080205182308-24971-zd5Ei9k+Niz3MufhMLxLzg**server.ccl.net> X-Original-From: "Richard L. Wood" Date: Tue, 5 Feb 2008 18:23:04 -0500 Sent to CCL by: "Richard L. Wood" [woodx278:-:umn.edu] Hi all, I've written a protocol in Pipeline Pilot that reads in a database in smiles format, coonverts it to 3D coordinates, then adds hydrogens and minimizes the structures. After this, I have it write the structures to an SDF file. The problem is that if there are a lot of molecules in the original database, this file will be very large. I've generated one that is 34 GB. I would like to be able to do something with this file, so I was wondering how or what I can do in Pipeline Pilot so that I can write out the molecules into multiple files that have fewer molecules per file? I'd like to be able to create something that I can use over and over, as opposed to just going in and having it write out x output files by having x output statements. I'm thinking that it has to be some kind of For Next loop, but I'm not sure how to write that in Pipeline Pilot. TIA, Richard Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 woodx278.:.umn.edu