From owner-chemistry@ccl.net Thu Mar 5 01:45:01 2009 From: "taner atalar taneratalar^gmail.com" To: CCL Subject: CCL:G: recommendations for computer hardware in windows Message-Id: <-38754-090305014116-7502-Mnthp+TvdBmDsvvzrnyGOQ]-[server.ccl.net> X-Original-From: taner atalar Content-Type: multipart/alternative; boundary=001485f631e0b03a4a0464597349 Date: Thu, 5 Mar 2009 08:41:02 +0200 MIME-Version: 1.0 Sent to CCL by: taner atalar [taneratalar#,#gmail.com] --001485f631e0b03a4a0464597349 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi David, thank you very much this s really very informative email for me i should use this information before buying my PC taner On Thu, Mar 5, 2009 at 1:39 AM, David Mannock dmannock(!)ualberta.ca < owner-chemistry|-|ccl.net> wrote: > > Sent to CCL by: David Mannock [dmannock(_)ualberta.ca] > Taner, I just purchased system components from Newegg.ca and Superbiiz.co= m. > I had thought of buying an AMD Phenom II system locally ($700CDN) with lo= ts > (8GB) of memory running under Vista 64 bit OS, but there is not much room > for upgrades with that platform unless you buy a DDR3 mobo and memory (+$= 500 > =3D$1200CDN) and Intel's new iC7 chips are faster, but all the components= are > very expensive, so an entry level system is $1500. After much searching I > found a Tyan S2912-E board on sale at Newegg for $90 CDN) and 2 quad-core > third generation socket F chips for $170US each at Superbiiz.com. As you = can > see from the totals below, I have a system which costs about $1100 CDN wi= th > 2 x Opteron socket F 3rd gen processors, 2 x 500GB HDs, 8GB DDR2 DRAM, an > ATI 3700 workstation video card and wireless PCI adapter. I will buy a KV= M > switch and use the monitor, keyboard and mouse from my desktop which has = a > good UPS back up. The new system will run Vista 64 ($75 CDN, Univ of Albe= rta > price), VMware (free) and Deep Freeze enterprise edition ($13) > http://www.faronics.com/html/deepfreeze.asp. > > Here is my Newegg.ca order: > 1 TYAN S2912G2NR Dual 1207(F) NVIDIA nForce Professional 3600 Extended A= TX > Server Motherboard - Retail > Item #: N82E16813151070 > $87.49 > Subtotal $87.49 > Handling $4.44 > UPS INTL CAN Standard (GND) $1.25 > Order Total $93.18 CAN $ > > > Qty Product Description Price > Shipped from CA, USA > 2 Seagate ST3640323AS 640GB 7200 RPM SATA 3.0Gb/s Hard Drive - OEM > Item #: N82E16822148335 > $159.98 CDN > ($79.99 ea) > 1 TP-LINK TL-WN651G 32bit PCI G & eXtended Range 108M Wireless Adapter= - > Retail > Item #: N82E16833704006 > $27.49 > 1 ATI 100-505564 FirePro V3700 256MB PCI Express 2.0 x16 Workstation > Video Card - OEM > Item #: N82E16814195073 > $106.49 CDN > 1 hec X-Power Pro 650 650W Continuous %% 40=B0C ATX12V / EPS12V SLI Re= ady > CrossFire Ready Power Supply - Retail > Item #: N82E16817339024 > $49.99 CDN > Shipped from NJ, USA > 8 Kingston 1GB 240-Pin DDR2 SDRAM DDR2 667 (PC2 5300) ECC Unbuffered > Intel Certified Server Memory Model KVR667D2E5/1GI - Retail > Item #: N82E16820134333 > $119.92 CDN > ($14.99 ea) > 1 HEC 69R5BB Black Steel ATX Full Tower Computer Case - Retail > Item #: N82E16811121018 > $58.74 CDN > Subtotal $522.61 > Handling $26.13 > UPS INTL CAN Standard (GND) $63.55 > Order Total $612.29 CAN$ > > > I used a purchase order to buy 2 AMD Opteron quad-core 2376 2.3 MHz > processors > http://products.amd.com/en-us/OpteronCPUDetail.aspx?id=3D489&f1=3DThird-G= eneration+AMD+Opteron%99&f2=3D&f3=3D&f4=3D512&f5=3D&f6=3D&f7=3D&f8=3D&f9=3D= &f10=3D4& > > for $170 USD each + $60 shipping. > > I purchased 2 new Dynatron A5MG's from an ebay seller for $20US each here= . > These are 4.1" sq for the 3rd generation Opteron chips. > http://stores.ebay.ca/UrCooler > > The new AMD price list for these chips is on their web site, but you have > to buy through a reseller. Contact Michelle Ousy (michelle%%ewiz.com) at > Superbiiz for processor availability. Tigerdirect also has these but for = an > extra $30 each. Also check out Starmicro. Make sure you are getting a new > cpu. Some are OEM, not boxed. A few may be tested pulls. Check this first= ! > > AMD reviews of servers with opteron chips > http://www.amd.com/us-en/Processors/ProductInformation/0,,30_118_8825_158= 85,00.html > > Notice the price difference vs Dell!! > > The benefits of this system are the dual processors, lower power > consumption (& thus heat) for the cpus vs Phenom II chips. The Phenom II > chips cannot be used on a 2 cpu board and from what I have read cannot be > used in this config for technical reasons. These socket F (1207) boards w= ill > support the new 6 core processors due in late 2009, so there is a process= or > upgrade possible although with this board, the DDR2 667MHz DRAM will not > change, you can expand the RAM up to 64GB full capacity. Basic graphics o= n > board, but workstation video card is better > http://ati.amd.com/products/firepro/index.html. It is a new design openGL > card. Lots of room for memory if you can afford it. I started at 8GB as i= t > was a reasonable price. I can wait for the chips to come down in price. T= he > 2 HDs mean that in principle, you could have one HD for Vista64 and the > other for LINUX. > > The down side. The mobo bios needs upgrading. This can be done through Ty= an > for $20 or you can get your tech department to do this via a CD or a USB > memory stick details at Tyan. The mobo designation S2912 and S2912-E are = not > the same (specs are at Tyan). Only the -E model will support QC processor= s. > The reviews at Newegg say that this is the -E version as many people have > done the bios upgrade to support third generation processors. There is so= me > speculation about whether you need a dual core or a quad core processor t= o > do this. A new cheap DC processor is under $100, but Tyan will do this fo= r > you in the USA. You need to upgrade to bios v4. Alternatively you can get= a > replacement bio chip > >> from Biosman. There was one problem noted at that >> > site for the S2912 mobo which was a question about shutting off the on > board graphics when using a graphics card. That may require a bios chip > modification. Prices are $27 . > > The choice of computer case is important. Most ATX cases built for gaming > have enough fans to cool everything, but these mobos are extended (E-ATX) > forms at 12"x13" , so you need to get a box 22x8x20". The Hec case is ide= al > and is well built and CHEAP. It must accommodate the cpu fans which are 2= U > (double height). I have tried to pick components, like the cpus, PS, etc > which put out less heat, but fast HDs produce more heat. The Seagates wer= e a > compromise between ultrafast drives and intelligent drives by Western > Digital whose speed varies with load. > > OK, well there is my input. All of the items will be here in a week and m= y > tech services shop will do the assembly and software installation for me. > This should give me a decent desktop workstation for $1100-1200CDN. Check > here for cpu benchmarks and go up one dir to see others. > http://www.cpubenchmark.net/high_end_cpus.html This set up (the dual cpu > Opteron 2354 processor info is provided) should be up there with the new > Intel i7 processors, but have a lot of upgrade potential in the future as > prices come down. AMD tends to incorporate this upgrade philosophy into > their designs, Intel do not! Last of all, with Sun, SGI and Dell asking > $10k+ for one of these you are getting a very good deal. If you can affor= d a > newer mobo spend the extra $300 now. Incidentally, these processors are > numbered as follows: 2 or 8 =3D no of processors per mobo. 1,2, or 3 =3D > generation of processor. I think you may be able to use 8000 series chips= on > 2000 series boards, but not the other way around, but I am not sure about > this. Also the lowest priced 4 cpu board I found was a Tyan board at > ~$350US, but the 8000 series chips cost too much for me. My department te= ch > guy is very interested in this little project and will help me with set u= p, > as there is the potential here to help crystallographers and NMR > spectroscopy people in our department and put together a multi-cpu QC > workstation farm for what would be considered to be peanuts. Then again w= ith > the recent interest in doing graphics work on multiple Sony PS3 's using > Yellow Dog Linux, maybe we are all wasting our time. > > Dave > > > At 05:48 AM 3/4/2009, you wrote: > > Sent to CCL by: "Taner Atalar" [taneratalar(-)gmail.com] >> I plan to buy a PC for moderate size organic compounds' calculations at >> DFT level. I plan to use Gaussian 03W and/or Spartan for this purpose. >> >> So I need a computer hardware recommendations. Thanks for help. >> >> Taner >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-Dr >> David Mannock >> > 339 Med Sci Bldg, > Dept of Biochemistry, > University of Alberta, > Edmonton, > Alberta, T6G 2H7 > Canada > > Tel: 1-780-492-2412 > FAX: 1-780-492-0886 > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --001485f631e0b03a4a0464597349 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi David,
=A0
thank you very much
this s really very informative email for me
i should use this information before buying my PC
=A0
taner

On Thu, Mar 5, 2009 at 1:39 AM, David Mannock dm= annock(!)ualberta.ca &= lt;owner-chemistry|-|ccl.net&g= t; wrote:

Sent to CCL by: David Mannoc= k [dmannock(_)ualberta.ca= ]
Taner, I just purchased system components from Newegg.ca and Superbiiz.com.= I had thought of buying an AMD Phenom II system locally ($700CDN) with lot= s (8GB) of memory running under Vista 64 bit OS, but there is not much room= for upgrades with that platform unless you buy a DDR3 mobo and memory (+$5= 00 =3D$1200CDN) and Intel's new iC7 chips are faster, but all the compo= nents are very expensive, so an entry level system is $1500. After much sea= rching I found a Tyan S2912-E board on sale at Newegg for $90 CDN) and 2 qu= ad-core third generation socket F chips for $170US each at Superbiiz.com. A= s you can see from the totals below, I have a system which costs about $110= 0 CDN with 2 x Opteron socket F 3rd gen processors, 2 x 500GB HDs, 8GB DDR2= DRAM, an ATI 3700 workstation video card and wireless PCI adapter. I will = buy a KVM switch and use the monitor, keyboard and mouse from my desktop wh= ich has a good UPS back up. The new system will run Vista 64 ($75 CDN, Univ= of Alberta price), VMware (free) and Deep Freeze enterprise edition ($13) = h= ttp://www.faronics.com/html/deepfreeze.asp.

=A0Here is my Newegg.ca order:
1 =A0TYAN S2912G2NR Dual 1207(F) NVID= IA nForce Professional 3600 Extended ATX Server Motherboard - Retail
Ite= m #: N82E16813151070
$87.49
Subtotal $87.49
Handling $4.44
=A0U= PS INTL CAN Standard (GND) $1.25
Order Total $93.18 CAN $


Qty Product Description Price
Shippe= d from CA, USA
=A0 2 =A0 Seagate ST3640323AS 640GB 7200 RPM SATA 3.0Gb/s= Hard Drive - OEM
Item #: N82E16822148335
$159.98 CDN
($79.99 ea)<= br> =A0 1 =A0TP-LINK TL-WN651G 32bit PCI G & eXtended Range 108M Wireless A= dapter - Retail
Item #: N82E16833704006
$27.49
=A0 1 =A0ATI 100-50= 5564 FirePro V3700 256MB PCI Express 2.0 x16 Workstation Video Card - OEMItem #: N82E16814195073
$106.49 =A0CDN
=A0 1 =A0hec X-Power Pro 650 650W Continuous %% 40=B0C AT= X12V / EPS12V SLI Ready CrossFire Ready Power Supply - Retail
Item #: N8= 2E16817339024
$49.99 CDN
Shipped from NJ, USA
=A0 8 =A0Kingston 1G= B 240-Pin DDR2 SDRAM DDR2 667 (PC2 5300) ECC Unbuffered Intel Certified Ser= ver Memory Model KVR667D2E5/1GI - Retail
Item #: N82E16820134333
$119.92 CDN
($14.99 ea)
=A0 1 =A0HEC 69R5B= B Black Steel ATX Full Tower Computer Case - Retail
Item #: N82E16811121= 018
$58.74 CDN
Subtotal $522.61
Handling $26.13
=A0UPS INTL CAN= Standard (GND) $63.55
Order Total $612.29 CAN$


I used a purchase order to buy 2 AMD Op= teron quad-core 2376 2.3 MHz processors http://products.amd.com/en-u= s/OpteronCPUDetail.aspx?id=3D489&f1=3DThird-Generation+AMD+Opteron%99&a= mp;f2=3D&f3=3D&f4=3D512&f5=3D&f6=3D&f7=3D&f8=3D&= ;f9=3D&f10=3D4&

for $170 USD each + $60 shipping.

I purchased 2 new Dynatron A5M= G's from an ebay seller for $20US each here. These are 4.1" sq for= the 3rd generation Opteron chips. =A0http://stores.ebay.ca/UrCooler

The new AMD price list for these chips is on their web site, but you ha= ve to buy through a reseller. Contact Michelle Ousy (michelle%%ewiz.com) at Superbiiz for processor= availability. Tigerdirect also has these but for an extra $30 each. Also c= heck out Starmicro. Make sure you are getting a new cpu. Some are OEM, not = boxed. A few may be tested pulls. Check this first!

AMD reviews of servers with opteron chips http://www.amd.com/us-en/Processors/ProductInformation/0,,30_11= 8_8825_15885,00.html

Notice the price difference vs Dell!!

The benefits of this syste= m are the dual processors, lower power consumption (& thus heat) for th= e cpus vs Phenom II chips. The Phenom II chips cannot be used on a 2 cpu bo= ard and from what I have read cannot be used in this config for technical r= easons. These socket F (1207) boards will support the new 6 core processors= due in late 2009, so there is a processor upgrade possible although with t= his board, the DDR2 667MHz DRAM will not change, you can expand the RAM up = to 64GB full capacity. Basic graphics on board, but workstation video card = is better http://ati.amd.com/products/firepro/index.html. It is a new= design openGL card. Lots of room for memory if you can afford it. I starte= d at 8GB as it was a reasonable price. I can wait for the chips to come dow= n in price. The 2 HDs mean that in principle, you could have one HD for Vis= ta64 and the other for LINUX.

The down side. The mobo bios needs upgrading. This can be done through = Tyan for $20 or you can get your tech department to do this via a CD or a U= SB memory stick details at Tyan. The mobo designation S2912 and S2912-E are= not the same (specs are at Tyan). Only the -E model will support QC proces= sors. The reviews at Newegg say that this is the -E version as many people = have done the bios upgrade to support third generation processors. There is= some speculation about whether you need a dual core or a quad core process= or to do this. A new cheap DC processor is under $100, but Tyan will do thi= s for you in the USA. You need to upgrade to bios v4. Alternatively you can= get a replacement bio chip
from Biosman. There was one prob= lem noted at that
site for the S2912 mobo which was a ques= tion about shutting off the on board graphics when using a graphics card. T= hat may require a bios chip modification. Prices are $27 .

The choice of computer case is important. Most ATX cases built for gami= ng have enough fans to cool everything, but these mobos are extended (E-ATX= ) forms at 12"x13" , so you need to get a box 22x8x20". The = Hec case is ideal and is well built and CHEAP. It must accommodate the cpu = fans which are 2U (double height). I have tried to pick components, like th= e cpus, PS, etc which put out less heat, but fast HDs produce more heat. Th= e Seagates were a compromise between ultrafast drives and intelligent drive= s by Western Digital whose speed varies with load.

OK, well there is my input. All of the items will be here in a week and= my tech services shop will do the assembly and software installation for m= e. This should give me a decent desktop workstation for $1100-1200CDN. Chec= k here for cpu benchmarks and go up one dir to see others. http://www.cpu= benchmark.net/high_end_cpus.html This set up (the dual cpu Opteron 2354= processor info is provided) should be up there with the new Intel i7 proce= ssors, but have a lot of upgrade potential in the future as prices come dow= n. AMD tends to incorporate this upgrade philosophy into their designs, Int= el do not! Last of all, with Sun, SGI and Dell asking $10k+ for one of thes= e you are getting a very good deal. If you can afford a newer mobo spend th= e extra $300 now. Incidentally, these processors are numbered as follows: 2= or 8 =3D no of processors per mobo. 1,2, or 3 =3D generation of processor.= I think you may be able to use 8000 series chips on 2000 series boards, bu= t not the other way around, but I am not sure about this. Also the lowest p= riced 4 cpu board I found was a Tyan board at ~$350US, but the 8000 series = chips cost too much for me. My department tech guy is very interested in th= is little project and will help me with set up, as there is the potential h= ere to help crystallographers and NMR spectroscopy people in our department= and put together a multi-cpu QC workstation farm for what would be conside= red to be peanuts. Then again with the recent interest in doing graphics wo= rk on multiple Sony PS3 's using Yellow Dog Linux, maybe we are all was= ting our time.

Dave=20



At 05:48 AM 3/4/2009, you wrote:

Sent to CCL by: "Taner =A0Atalar" [taneratalar(= -)gmail.com]
I plan = to buy a PC for moderate size organic compounds' calculations at DFT le= vel. I plan to use Gaussian 03W and/or Spartan for this purpose.

So I need a computer hardware recommendations. Thanks for help.

= Taner



-=3D This is automatically added to each message= by the mailing script =3D-Dr David Mannock
339 Med Sci Bld= g,
Dept of Biochemistry,
University of Alberta,
Edmonton,
Alberta, T6= G 2H7
Canada

Tel: 1-780-492-2412
FAX: 1-780-492-0886


- This is automatically added to each message by = the mailing script -
To recover the email address of the author of the m= essage, please change
the strange characters on the top line to the |-| si= gn. You can also
E-mail to subs= cribers: CHEMISTRY|-|c= cl.net or use:
=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_me= ssage

E-mail to administrators: CHEMISTRY-REQUEST|-|ccl.net or use
=A0 =A0 http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.s= html

Before posting, check wait time at: http://www.ccl.net

Job: http://www.c= cl.net/jobs Conferences: http://server.ccl.net/chemistry/= announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


--001485f631e0b03a4a0464597349-- From owner-chemistry@ccl.net Thu Mar 5 06:59:00 2009 From: "Peter Schmidtke pschmidtke^mmb.pcb.ub.es" To: CCL Subject: CCL: PDB file format : List of atom name / element type correspondance Message-Id: <-38755-090305065521-6383-ccJjf5hqMvIjVPZk7weT9Q(_)server.ccl.net> X-Original-From: "Peter Schmidtke" Date: Thu, 5 Mar 2009 06:55:18 -0500 Sent to CCL by: "Peter Schmidtke" [pschmidtke**mmb.pcb.ub.es] Dear CCL subscribers, I am looking for a list of atom names that occur in PDB files and their corresponding elements. Normally the PDB file convention says that the element has to be given explicitely in the column 77-78. Unfortunately, this is currently not systematically the case within the PDB and for PDB files saved with software packages (some commercial software I won't mention here and other packages). Last, Softwares often change atom names before output, in order to encode program internal atom types. Is there any way to guess the element from the atom name or is there any translation list out there? Thanks in advance. Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona From owner-chemistry@ccl.net Thu Mar 5 08:28:00 2009 From: "Marcel Swart marcel.swart++icrea.es" To: CCL Subject: CCL: PDB file format : List of atom name / element type correspondance Message-Id: <-38756-090305081933-6145-5XbS3XDiYTqxKukhpZvAbw=server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-9-253918195 Date: Thu, 5 Mar 2009 14:19:15 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart+/-icrea.es] --Apple-Mail-9-253918195 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed The complete description can be found for example at: http://www.wwpdb.org/documentation/format23/v2.3.html I remember that at this page there should also be a list of all "standard" residues/molecules that can be found in PDB files, such as ASP for aspartate, MOH for methanol, etc. But a quick look did not bring it forward On the "Coordinate section" of this page you can find for example the full format for the ATOM lines: Record Format COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------ 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 77 - 78 LString(2) element Element symbol, right-=20 justified. 79 - 80 LString(2) charge Charge on the atom. Unfortunately, not many PDB files in the PDB-database adhere to this =20 format. The pdb2adf program that is present within ADF also writes out a PDB =20 file with the complete structure that it made, and does write out the element =20 symbol at positions 77-78. So there are some software packages that do it =20 correctly. :-) On Mar 5, 2009, at 12:55 PM, Peter Schmidtke pschmidtke^mmb.pcb.ub.es =20= wrote: > Dear CCL subscribers, > > I am looking for a list of atom names that occur in PDB files and =20 > their corresponding elements. Normally the PDB file convention says =20= > that the element has to be given explicitely in the column 77-78. =20 > Unfortunately, this is currently not systematically the case within =20= > the PDB and for PDB files saved with software packages (some =20 > commercial software I won't mention here and other packages). > > Last, Softwares often change atom names before output, in order to =20 > encode program internal atom types. > > Is there any way to guess the element from the atom name or is =20 > there any translation list out there? > > Thanks in advance. > > Peter Schmidtke > > ---------------------- > PhD Student at the Molecular Modeling and Bioinformatics Group > Dep. Physical Chemistry > Faculty of Pharmacy > University of Barcelona =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 dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart(_)icrea.es marcel.swart(_)udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =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 --Apple-Mail-9-253918195 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

The complete description can be found for example = at:


I = remember that at this page there should also be a list of = all
"standard" residues/molecules that can be found in PDB = files,
such as ASP for aspartate, MOH for methanol, etc. But a = quick
look did not bring it = forward

On the "Coordinate section" of this = page you can find for example
the full format for the ATOM = lines:

Record Format

=
COLUMNS=A0 = =A0 =A0 DATA TYPE=A0 =A0 =A0 =A0 FIELD=A0 =A0 =A0 = DEFINITION
------------------------------------------------------
=
=A01 -=A0 = 6=A0 =A0 =A0 Record name=A0 =A0 =A0 "ATOM=A0 =A0 "
=
=A07 - 11=A0 = =A0 =A0 Integer=A0 =A0 =A0 =A0 =A0 serial =A0 =A0 Atom serial = number.
13 - 16=A0 =A0 =A0 Atom =A0 =A0 =A0 =A0 =A0 =A0 = name =A0 =A0 =A0 Atom name.
17 =A0 =A0 =A0 =A0 =A0 = Character=A0 =A0 =A0 =A0 altLoc =A0 =A0 Alternate location = indicator.
18 - 20=A0 =A0 =A0 Residue name =A0 =A0 resName=A0 = =A0 Residue name.
22 =A0 =A0 =A0 =A0 =A0 Character=A0 =A0 =A0 =A0 = chainID=A0 =A0 Chain identifier.
23 - 26=A0 =A0 =A0 = Integer=A0 =A0 =A0 =A0 =A0 resSeq =A0 =A0 Residue sequence = number.
27 =A0 =A0 =A0 =A0 =A0 AChar=A0 =A0 =A0 =A0 =A0 =A0= iCode=A0 =A0 =A0 Code for insertion of residues.
=
31 - 38=A0 = =A0 =A0 Real(8.3)=A0 =A0 =A0 =A0 x=A0 =A0 =A0 =A0 =A0 Orthogonal = coordinates for X in=A0
=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Angstroms
39 - 46=A0 =A0 =A0 = Real(8.3)=A0 =A0 =A0 =A0 y=A0 =A0 =A0 =A0 =A0 Orthogonal coordinates for = Y in=A0
=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Angstroms
47 - 54=A0 =A0 =A0 = Real(8.3)=A0 =A0 =A0 =A0 z=A0 =A0 =A0 =A0 =A0 Orthogonal coordinates for = Z in=A0
=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Angstroms
55 - 60=A0 =A0 =A0 = Real(6.2)=A0 =A0 =A0 =A0 occupancy=A0 Occupancy.
61 - 66=A0 =A0 =A0 = Real(6.2)=A0 =A0 =A0 =A0 tempFactor Temperature factor.
=
77 - 78=A0 = =A0 =A0 LString(2) =A0 =A0 =A0 element=A0 =A0 Element symbol, = right-justified.
79 - 80=A0 =A0 =A0 LString(2) =A0 =A0 =A0 charge = =A0 =A0 Charge on the = atom.

Unfortunately, not many PDB files = in the PDB-database adhere to this format.

The = pdb2adf program that is present within ADF also writes out a PDB file = with
the complete structure that it made,=A0and does write out = the element symbol=A0
at positions 77-78. So there are some = software packages that do it = correctly.
:-)

On Mar 5, = 2009, at 12:55 PM, Peter Schmidtke pschmidtke^mmb.pcb.ub.es = wrote:

Dear CCL = subscribers,


I am looking for a list of atom names that occur in PDB = files and their corresponding elements. Normally the PDB file convention = says that the element has to be given explicitely in the column 77-78. = Unfortunately, this is currently not systematically the case within the = PDB and for PDB files saved with software packages (some commercial = software I won't mention here and other packages).


Last, Softwares often change atom names before output, in order = to encode program internal atom types.=A0


Is there any = way to guess the element from the atom name or is there any translation = list out there?


Thanks in advance.


Peter Schmidtke


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

PhD Student at the Molecular Modeling and Bioinformatics = Group

Dep. Physical = Chemistry

Faculty of = Pharmacy

University of = Barcelona


dr. Marcel = Swart

ICREA = researcher=A0at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
17003 Girona
Catalunya = (Spain)

tel
marcel.swart(_)udg.edu



=

= --Apple-Mail-9-253918195-- From owner-chemistry@ccl.net Thu Mar 5 09:46:01 2009 From: "Konrad Hinsen hinsen*_*cnrs-orleans.fr" To: CCL Subject: CCL: PDB file format : List of atom name / element type correspond Message-Id: <-38757-090305092846-3734-c6ALrj/CA4OxMQHqHT4q1A_._server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Thu, 5 Mar 2009 09:28:42 -0500 Sent to CCL by: "Konrad Hinsen" [hinsen^^cnrs-orleans.fr] On 05.03.2009, at 12:55, Peter Schmidtke pschmidtke^mmb.pcb.ub.es wrote: > I am looking for a list of atom names that occur in PDB files and their corresponding elements. For files that fully respect the PDB conventions, you can find all the information you need in the PDB format definition: http://www.wwpdb.org/docs.html As you noted, recent versions of the PDB format conventions state that the element should be given explicitly in columns 77-78. For files conforming to older versions of the PDB format, you can obtain the element as the first two letters of the atom name. If the first letter is a digit, then you should use only the second letter (which must then be H). However, the real problem is that the vast majority of programs write PDB files that do not fully respect the PDB file format conventions. The summary of my ten-year experience in dealing with PDB files of various origins is that you can't rely on anything concerning atom and residue names. There is no way to avoid special treatments for files produced by specific programs. My advice is: 1) If you only need to handle PDB files from a specific source, write code specifically for that variety of the PDB format and get on with your science. 2) If you want to write a general tool that can handle a large variety of PDB files, use existing PDB parser and support libraries that do at least part of the nasty work. In the category of existing libraries, I'll mention my own which are written in Python: - Module Scientific.IO.PDB in Scientific Python: http://dirac.cnrs-orleans.fr/ScientificPython/ - Modules MMTK.PDB and MMTK.PDBMoleculeFactory in the Molecular Modelling Toolkit: http://dirac.cnrs-orleans.fr/MMTK/ -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen|cnrs-orleans.fr --------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Mar 5 11:11:00 2009 From: "Farhan Pasha pashafa(-)yahoo.co.in" To: CCL Subject: CCL:G: IRC calculation Message-Id: <-38758-090304201638-19433-AJAakw+wBsa54VUjlc9XyA%%server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-1957794508-1236212180=:91046" Date: Thu, 5 Mar 2009 05:46:20 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa(!)yahoo.co.in] --0-1957794508-1236212180=:91046 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable hi =A0 If you using gaussian=A0 just do two seprate calculation using following ke= yword irc=3D(rcfc,forward) irc=3D(rcfc,reverse) it will work =A0 cheers pasha Correspondence Address Dr. Syed Farhan Ahmad Pasha Room No. 5202 Institut de Biologie Structurale Laboratoire de Dynamique Moleculaire 41 rue Jules Horowitz 38027 Grenoble cedex France tel : =0A=0A=0A Connect with friends all over the world. Get Yahoo! In= dia Messenger at http://in.messenger.yahoo.com/?wm=3Dn/ --0-1957794508-1236212180=:91046 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
Add more friends to your messenger= and enjoy! Invite them now. --0-1957794508-1236212180=:91046-- From owner-chemistry@ccl.net Thu Mar 5 11:50:00 2009 From: "Thomas Patko tpatko(~)gmail.com" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38759-090304230737-584-COmjWFLZ3IKrUuLc0CO1gw[]server.ccl.net> X-Original-From: Thomas Patko Content-Type: multipart/alternative; boundary=0016e64f683aebcd3f0464574df5 Date: Wed, 4 Mar 2009 20:07:19 -0800 MIME-Version: 1.0 Sent to CCL by: Thomas Patko [tpatko++gmail.com] --0016e64f683aebcd3f0464574df5 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Chemcraft has a feature that allows you to create GIF animations of you molecule rotating. Just go to Tools -> Create Animation -> Molecule rotation. There are number of options although GIF worked fine for me. The result should work in a PowerPoint presentation on Mac or Windows (I use both). Good luck, Thomas On Wed, Mar 4, 2009 at 3:54 PM, Anandarup Goswami ananda1911[A]gmail.com < owner-chemistry**ccl.net> wrote: > Hi all, > I am using powewrpoint in my mac to make presentation. I have to put some > calculated structures in my slides. I have been using chemcraft and > gaussview to make the picture. But it would have been much better if I could > allow some of my structures to rotate freely (like a movie file) during my > presentation. I am relatively new to this field and have no experience in > this kind of 3D effect particularly in mac. Any help regarding this would be > highly appreciated. > Thanks, > Anandarup Goswami > --0016e64f683aebcd3f0464574df5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Chemcraft has a feature that allows you to create GIF animations of you mol= ecule rotating.=A0 Just go to Tools -> Create Animation -> Molecule r= otation.=A0 There are number of options although GIF worked fine for me.=A0= The result should work in a PowerPoint presentation on Mac or Windows (I u= se both).

Good luck,

Thomas

On Wed, Mar = 4, 2009 at 3:54 PM, Anandarup Goswami ananda1911[A]gmail.com <owner-chemistry**ccl.net> wrote:
Hi all,
I am u= sing powewrpoint in my mac to make presentation. I have to put some calcula= ted structures in my slides. I have been using chemcraft and gaussview to m= ake the picture. But it would have been much better if I could allow some o= f my structures to rotate freely (like a movie file) during my presentation= . I am relatively new to this field and have no experience in this kind of = 3D effect particularly in mac. Any help regarding this would be highly appr= eciated.
Thanks,
Anandarup Goswami

--0016e64f683aebcd3f0464574df5-- From owner-chemistry@ccl.net Thu Mar 5 12:22:01 2009 From: "Hannes Loeffler hannes.loeffler=-=stfc.ac.uk" To: CCL Subject: CCL: PDB file format : List of atom name / element type correspondance Message-Id: <-38760-090305093748-5709-OTHfpc18JIMSvql3MpGjaw . server.ccl.net> X-Original-From: Hannes Loeffler Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 05 Mar 2009 13:57:32 +0000 Mime-Version: 1.0 Sent to CCL by: Hannes Loeffler [hannes.loeffler#stfc.ac.uk] On Thu, 2009-03-05 at 06:55 -0500, Peter Schmidtke pschmidtke^mmb.pcb.ub.es wrote: > Sent to CCL by: "Peter Schmidtke" [pschmidtke**mmb.pcb.ub.es] > Dear CCL subscribers, > > I am looking for a list of atom names that occur in PDB files and > their corresponding elements. Normally the PDB file convention says > that the element has to be given explicitely in the column 77-78. I am not quite sure about this but I think metals may be indicated by different alignment. CA=C-alpha for example starts at column 14 whereas a CA=calcium starts from column 13. But this may be just a convention followed by some and not in the standard... From owner-chemistry@ccl.net Thu Mar 5 12:56:00 2009 From: "Antonio G. De Crisci antonio.decrisci]^[utoronto.ca" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38761-090305121755-14676-D8BDHbpVel+OanK1CUvgGg(!)server.ccl.net> X-Original-From: "Antonio G. De Crisci" Date: Thu, 5 Mar 2009 12:17:49 -0500 Sent to CCL by: "Antonio G. De Crisci" [antonio.decrisci]=[utoronto.ca] I would recommend that you do a video capture using this free video capturing program from Microsoft called Windows Media Encoder 9 Series: http://www.microsoft.com/downloads/details.aspx?FamilyID=5691ba02-e496-465a-bba9-b2f1182cdf24&displaylang=en The advantage of this software is that you wont run into 3rd party software incompatibilities (if any) when using PowerPoint and you can use your favourite computational viewer/builder to animate the motion. There are various levels of video (and audio) quality that you can use when performing a video capture. Then just import the movie into PPT as *.wmv (a native windows format). You can also 'square-in' the portion of the screen that you want to capture with the crop like tool in this program or select the entire window from a list. Thanks, Anthony > "Anandarup Goswami ananda1911[A]gmail.com" wrote: > > Sent to CCL by: Anandarup Goswami [ananda1911*gmail.com] > --001517573dd08ba2be046453c5ed > Content-Type: text/plain; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > > Hi all, > I am using powewrpoint in my mac to make presentation. I have to put some > calculated structures in my slides. I have been using chemcraft and > gaussview to make the picture. But it would have been much better if I could > allow some of my structures to rotate freely (like a movie file) during my > presentation. I am relatively new to this field and have no experience in > this kind of 3D effect particularly in mac. Any help regarding this would be > highly appreciated. > Thanks, > Anandarup Goswami > > --001517573dd08ba2be046453c5ed > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > > Hi all,
I am using powewrpoint in my mac to make presentation. I have to= > put some calculated structures in my slides. I have been using chemcraft a= > nd gaussview to make the picture. But it would have been much better if I c= > ould allow some of my structures to rotate freely (like a movie file) durin= > g my presentation. I am relatively new to this field and have no experience= > in this kind of 3D effect particularly in mac. Any help regarding this wou= > ld be highly appreciated.
> Thanks,
Anandarup Goswami
> > --001517573dd08ba2be046453c5ed-- > > From owner-chemistry@ccl.net Thu Mar 5 13:31:00 2009 From: "John McKelvey jmmckel__gmail.com" To: CCL Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? Message-Id: <-38762-090305121223-10659-upGBhozGR69XWydT51LP5g(~)server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=000e0cd2e33e83257e046462449a Date: Thu, 5 Mar 2009 12:12:05 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel!=!gmail.com] --000e0cd2e33e83257e046462449a Content-Type: text/plain; charset=ISO-2022-JP Content-Transfer-Encoding: 7bit Is the possibility of finding a symmetry of lower energy _*all that* *bad*_? I can think of an obvious reason why it would be beneficial.... Cheers, John McKelvey On Wed, Mar 4, 2009 at 11:19 PM, Johannes Hachmann jh388 ~~ cornell.edu < owner-chemistry a ccl.net> wrote: > > Sent to CCL by: "Johannes Hachmann" [jh388_._cornell.edu] > Hi Ding, > > sorry, never ran into this problem. Note that you might have to try a > number of orbital swaps to get to the wavefunction irrep you want. Also, in > case you use the STABLE keyword, DO NOT use STABLE=OPT because that will > likely bring you back to a more stable wavefunction of different symmetry. > > Hope that helps > > Best > > Johannes > > --------------------------------------------------------------- > Johannes Hachmann > (Dipl.-Chem., M.Sc.) > > Chan Research Group > 140D Baker Laboratory > Department of Chemistry and Chemical Biology > Cornell University > Ithaca, NY 14853-1301 > USA > --------------------------------------------------------------- > > > -----Original Message----- > > From: owner-chemistry+jh388==cornell.edu]|[ccl.net > > [mailto:owner-chemistry+jh388 ==cornell.edu]|[ > ccl.net] On Behalf > > Of xunlei ding dingxunlei:_:gmail.com > > Sent: Wednesday, March 04, 2009 5:12 AM > > To: Hachmann, Johannes > > Subject: CCL:G: G- How to retain the symmetry in a SCF calculation ? > > > > > > Sent to CCL by: xunlei ding [dingxunlei|gmail.com] Dear Johannes, > > > > Sometimes scf=QC works but not always. > > I hope there be a better way for this problem. > > > > It seems that we can use IOP, as is described as: > > > > IOp(5/15) > > Apply Abelian symmetry constraints on orbitals. > > > > 0 Default (1 for L502, 2 for L501 and L506). > > 1 No. > > 2 Yes, keep occupation of each irrep the same as the > > initial guess. > > 3 Yes, keep overall wavefunction the same as the initial guess, > > but doing the minimal amount > > of orbital switching to accomplish this. > > 00 Default (use Abelian symmetry in diagonalization). > > 10 Use Abelian symmetry in diagonalization. > > 20 Do not use Abelian symmetry in diagonalization. > > > > But in my test, iop(5/15=2) doesn't work. > > > > Any more suggestions? > > > > Thanks a lot! > > > > Best regards, > > Ding > > > > > > > > 2009/2/13 Johannes Hachmann jh388[*]cornell.edu > > : > > > > > > Sent to CCL by: "Johannes Hachmann" [jh388!A!cornell.edu] Hi Ding, > > > > > > use SCF=QC (however quadratically convergent SCF is a bit > > costy...). > > > See description under > > http://www.gaussian.com/g_ur/k_guess.htm on the > > > bottom together with GUESS=ALTER. This is not a > > particularly elegant > > > way to do things (compared to just specifying the state symmetry in > > > e.g. MOLPRO) but it works. You might want to use the STABLE > > option so > > > that you know whether you have instabilities to which other > > states and > > > which additional MO swaps you might want to perform. > > > > > > Best > > > > > > Johannes > > > > > > --------------------------------------------------------------- > > > Johannes Hachmann > > > (Dipl.-Chem., M.Sc.) > > > > > > Chan Research Group > > > 140D Baker Laboratory > > > Department of Chemistry and Chemical Biology Cornell University > > > Ithaca, NY 14853-1301 USA > > > --------------------------------------------------------------- > > >> -----Original Message----- > > >> From: owner-chemistry+jh388==cornell.edu[]ccl.net > > >> [mailto:owner-chemistry+jh388 ==cornell.edu > []ccl.net] On Behalf Of > > >> xunlei ding dingxunlei::gmail.com > > >> Sent: Friday, February 13, 2009 3:42 AM > > >> To: Hachmann, Johannes > > >> Subject: CCL:G: G- How to retain the symmetry in a SCF > > calculation ? > > >> > > >> > > >> Sent to CCL by: xunlei ding [dingxunlei.:.gmail.com] Dear CCLers, > > >> > > >> In the manual of G03, the key word "SCF= Symm" is > > discribed as below: > > >> Retain all symmetry constraints: make the number of > > occupied orbitals > > >> of each symmetry type (abelian irreducible > > >> representation) match that of the initial guess. Use this > > option to > > >> retain a specific state of the wavefunction throughout the > > >> calculation. It is the default only for GVB calculations. > > >> > > >> But sometimes it doesn't work and the last state is different from > > >> the initial state. > > >> > > >> Could you give me more suggestions on how to retain the > > symmetry in a > > >> SCF calculation? > > >> > > >> Thanks! > > >> > > >> Best regards, > > >> Ding > > >> > > >> > > >> > > >> -= 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> > > >> Conferences: > > >> http://server.ccl.net/chemistry/announcements/conferences/ > > >> > > >> Search Messages: http://www.ccl.net/htdig (login: ccl, > > >> Password: search)> > > >> > > > > > > > > > > > > -= This is automatically added to each message by the > > mailing script > > > =-> Search Messages: http://www.ccl.net/htdig (login: ccl, > > Password: > > > search)> > > > > > > > > > > > > > > -- > > ------------------------------------------------------ > > Xun-Lei Ding > > Associate Research Professor of Physical Chemistry State Key > > Lab for Struct. Chem. of Unstable and Stable Species > > Institute of Chemistry, The Chinese Academy of Sciences > > Zhongguancun North First Street 2， > > Beijing 100190, P. R. China > > Phone 86-10-62568330 > > Fax 86-10-62559373 > > > > > > > > -=his is automatically added to each message by the mailing script = > > To recover the email address of the author of the message, > > please change> > Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > > > > > > > > - This is automatically added to each message by the mailing script -> > > --000e0cd2e33e83257e046462449a Content-Type: text/html; charset=ISO-2022-JP Content-Transfer-Encoding: base64 SXMgdGhlIHBvc3NpYmlsaXR5IG9mIGZpbmRpbmcgYSBzeW1tZXRyeSBvZiBsb3dlciBlbmVyZ3kg XzxpPmFsbCB0aGF0PC9pPiA8aT5iYWQ8L2k+Xz8mbmJzcDsgSSBjYW4gdGhpbmsgb2YgYW4gb2J2 aW91cyByZWFzb24gd2h5IGl0IHdvdWxkIGJlIGJlbmVmaWNpYWwuLi4uPGJyPjxicj5DaGVlcnMs PGJyPjxicj5Kb2huIE1jS2VsdmV5PGJyPjxicj48YnI+PGRpdiBjbGFzcz0iZ21haWxfcXVvdGUi PgpPbiBXZWQsIE1hciA0LCAyMDA5IGF0IDExOjE5IFBNLCBKb2hhbm5lcyBIYWNobWFubiBqaDM4 OCB+fiA8YSBocmVmPSJodHRwOi8vY29ybmVsbC5lZHUiPmNvcm5lbGwuZWR1PC9hPiA8c3BhbiBk 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dGFyZ2V0PSJfYmxhbmsiPmh0dHA6Ly93d3cuY2NsLm5ldC9jaGVtaXN0cnkvYWJvdXRjY2wvaW5z dHJ1Y3Rpb25zLzwvYT48YnI+Cjxicj4KPGJyPgo8L2Jsb2NrcXVvdGU+PC9kaXY+PGJyPgo= --000e0cd2e33e83257e046462449a-- From owner-chemistry@ccl.net Thu Mar 5 14:21:01 2009 From: "Andrew Orry andy]~[molsoft.com" To: CCL Subject: CCL: Rotating a structure during the presentation in powerpoint in mac Message-Id: <-38763-090305141828-12183-FghTnz87uRThZEpb/aHNEA(~)server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Mar 2009 10:04:03 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy%x%molsoft.com] Anandarup It is very easy to insert fully interactive, annotated 3D objects into PowerPoint using MolSoft's ICM software (www.molsoft.com) Step1: Download ICM-Browser Pro here http://www.molsoft.com/icm_browser_pro.html Step 2: Make one or more fully-interactive slides of your molecule(s). See a video on how to do this here: http://www.molsoft.com/video-activeicm1.html Step 3: Download free ActiveICM here http://www.molsoft.com/activeicm.html Step 4: Insert into PowerPoint. See a video on how to do this here: http://www.molsoft.com/video-activeicm2.html Or alternatively you can skip PowerPoint altogether and present using ICM-Browser-Pro directly - for examples see how the the Structural Genomics Consortium present their data using MolSoft's ICM here: http://www.sgc.ox.ac.uk/iSee/ ActiveICM is free and Browser-Pro is only $99 for a perpetual student license. Andy Anandarup Goswami ananda1911[A]gmail.com wrote: > Hi all, > I am using powewrpoint in my mac to make presentation. I have to put > some calculated structures in my slides. I have been using chemcraft > and gaussview to make the picture. But it would have been much better > if I could allow some of my structures to rotate freely (like a movie > file) during my presentation. I am relatively new to this field and > have no experience in this kind of 3D effect particularly in mac. Any > help regarding this would be highly appreciated. > Thanks, > Anandarup Goswami -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From owner-chemistry@ccl.net Thu Mar 5 17:41:00 2009 From: "David A. Mannock dmannock|*|ualberta.ca" To: CCL Subject: CCL:G: recommendations for computer hardware in windows Message-Id: <-38764-090305144400-10342-8HnALMx1b9pubuSC/3FIbw~!~server.ccl.net> X-Original-From: "David A. Mannock" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 05 Mar 2009 12:43:53 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Mannock" [dmannock|*|ualberta.ca] Tanar, Also, I noticed that Dell has a Poweredge server model 605 which you can custom build. Their price for a similarly equipped system was close to $3K CDN. I have heard bad things about their PC mobos, so check that first. Dave At 05:48 AM 04/03/2009, you wrote: >Sent to CCL by: "Taner Atalar" [taneratalar(-)gmail.com] >I plan to buy a PC for moderate size organic compounds' calculations >at DFT level. I plan to use Gaussian 03W and/or Spartan for this purpose. > >So I need a computer hardware recommendations. Thanks for help. > >Taner From owner-chemistry@ccl.net Thu Mar 5 21:09:00 2009 From: "Jing Kong jkong\a/q-chem.com" To: CCL Subject: CCL: Q-Chem Workshop at PSC. Last reminder. Online broadcast. Message-Id: <-38765-090305210732-16955-wqbBvo1KvyyKDN6vxFYqyQ^^server.ccl.net> X-Original-From: "Jing Kong" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Mar 2009 21:07:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong*_*q-chem.com] Dear colleague, We would like to inform you that the registration for the Workshop entitled "Quantum leap into the future: advances in methods and applications of electronic structure calculations", will be closed on Monday, March 9. The details of the workshop can be found here (http://www.q-chem.com/ws_hh.html). We will also provide an online live broadcast of the Workshop. If you are interested, please sign up here (http://www.q-chem.com/ws_regi.html). Detailed instructions will be sent to you by an email once you sign up. The registration for the live broadcast is free of charge. We apologize if you have received multiple copies of this email. Sincerely, Jing Kong, Ph.D. CEO & Chief Scientist, Q-Chem Inc.
hi
 
If you using gaussian  just do two seprate calculation using foll= owing keyword
irc=3D(rcfc,forward)
irc=3D(rcfc,reverse)
it will work
 
cheers
pasha


Correspondence Address
Dr. Syed Farhan Ahmad PashaRoom No. 5202
Institut de Biologie Structurale
Laboratoire de Dynam= ique Moleculaire
41 rue Jules Horowitz
38027 Grenoble cedex
France=
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fax : (+33) (0)4 38 78 54 94
fpasha/./rediff= mail.com
URL:www.geocities.com/pashafa
www.ibs.fr

--- On We= d, 4/3/09, Sriraj Srinivasan ss537%a%drexel.edu <owner-chemistry/./ccl.= net> wrote:

From: Sriraj Srinivasan ss537%a%drexel.edu <ow= ner-chemistry/./ccl.net>
Subject: CCL:G: IRC calculation
To: "Pasha,= Frahan Ahmad " <pashafa/./yahoo.co.in>
Date: Wednesday, 4 M= arch, 2009, 10:10 PM


-----Inline Attachment Follows-----


Sent to CCL by: Sriraj Srinivasan [ss537:_:drexe= l.edu]

Hi Kavitha,

Make sure that your hessian is correct eno= ugh to go in both directions. This is critical for an IRC calculation to su= cceed. I do DFT calculations and have found no problems as such.

Sri= raj



----- Original Message -----
> From: "Justin Finne= rty justin.finnerty~~uni-oldenburg.de" <owner-chemistry/./ccl.net>
Date: Wednesday, Marc= h 4, 2009 8:12 am
Subject: CCL:G: IRC calculation

>
> S= ent to CCL by: Justin Finnerty [justin.finnerty*_*uni-oldenburg.de]
>=
> On Tue, 2009-03-03 at 09:48 -0500, Kavitha Velappan
> kavit= ha.velappan(a)gmail.com wrote:
> > Sent to CCL by: "Kavitha  = Velappan" [kavitha.velappan_-_gmail.com]
> > Hi all,
> >
> > I tried to do IRC calculation to follow the reaction path fo= r
> conformer interconversion (Dimethoxymethane G+G- to G-G- conform= er
> - rotation around OCH3 bond). The route section looks like this= :
> >
> > #N RB3LYP/6-31++G** IRC=3D(CalcFC,maxpoints=3D= 12)
>
> I have had this issue whenever I do an IRC with DFT in= gaussian.  The
> problems are as you see, the IRC only goes in = one direction and
> doesn'treach maxpoints.
>
> I found= that the best solution to this is to reduce the STEPSIZE. The
> defa= ult is 10 and I have had much success with STEPSIZE=3D4 or 3.  (You> have to increase MAXPOINTS accordingly!)  Using this I have
= > successfullyused IRC to go from the TS to close to the ground
>= state.  Using a small
> stepsize will increase the length of th= e calculation but not as
> much as
> it first appears because the previous step of the IRC is now much
> closerto the new step so= each step converges in two or three cycles.
>
> The other iss= ue is getting both the forward and reverse directions to
> work. I ha= ve found no reliable way to do this automatically in
> gaussianusing= DFT - gaussian always seems to go in one direction!
> My normal
= > solution is to manually modify the TS structure in the direction
&g= t; gaussian didn't go and start the IRC from the modified structure.  =
> How I
> modify the structure is of course based on the motio= n vectors of the
> imaginary frequency.
>
> PS Your inpu= t uses CALCFC, surely you could use READFC from the freq
> calculatio= n for the TS?
>
> Cheers
>     Justin
= >
> --
> Dr Justin Finnerty
> Rm W3-1-165  &nbs= p;      Ph  49&n= bsp;(441) 798 3726 
> = Carl von Ossietzky Universit=E4t Oldenburg
>
>
>
> -=3D This is automatically ad= ded to each message by the mailing
> script =3D-
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