[PyMOL] Pymol on MacMini: performances
Hi everyone, I'm thinking of buying a Mac mini to use as minimal computer for home, and will need it to run pymol smoothly. is this the case, or the little machine doesn't have enough juice to handle, let's say, visualisation of a protein active site and ligand docked into it, with different level of transparence and such? I need pymol essentially to look at my structure and generate pretty pictures for my phD thesis... many thanks to anyone can give insights... luca -- S for stupendous! T for Tiger, ferocity of! U for Underwear, red! P for Power, incredible! E for Excellent physique! N for ...um... something... hmm, well I'll come back to that... D for Determination! U.. for... wait, how do you spell this? Is it 'I'?
Re: [PyMOL] Pymol on MacMini: performances
Hi, I can run pymol smoothly on my celeron-m 1.3ghz laptop with intel i855gmch embedded graphics chip. This has no dedicated memory and uses a portion of the 512MB system ram for graphics processing. The specs say that mac mini's come standard with ati r9200 with 32mb *dedicated* ram for graphics so you should have no problems. In general a dedicated ati or nvidia chip has more opengl capabilities than embedded intel or sis graphics chips. A $50 upgrade to 512MB would help tremendously however. Hope that helps, Sabuj Pattanayek Luca Fenu wrote: > Hi everyone, > > I'm thinking of buying a Mac mini to use as minimal computer for home, > and will need it to run pymol smoothly. is this the case, or the little > machine doesn't have enough juice to handle, let's say, visualisation of > a protein active site and ligand docked into it, with different level of > transparence and such? I need pymol essentially to look at my structure > and generate pretty pictures for my phD thesis... many thanks to anyone > can give insights... > >luca
Re: [PyMOL] Pymol on MacMini: performances
Thanks Sabuj, I thought so, but couldn't be sure, as a lot depends on the quality of the drivers... w/o Direct Rendering (ATI drivers sucks!), my ath64 laptop with R9700 only manages to give me some 4 fps... that makes it all but unusable. so i was afraid to find myself in an even worst situation... Hopefully, PyMol takes advantage of Altivec... I'll give it a try. thanks again... luca Sabuj Pattanayek wrote: Hi, I can run pymol smoothly on my celeron-m 1.3ghz laptop with intel i855gmch embedded graphics chip. This has no dedicated memory and uses a portion of the 512MB system ram for graphics processing. The specs say that mac mini's come standard with ati r9200 with 32mb *dedicated* ram for graphics so you should have no problems. In general a dedicated ati or nvidia chip has more opengl capabilities than embedded intel or sis graphics chips. A $50 upgrade to 512MB would help tremendously however. Hope that helps, Sabuj Pattanayek Luca Fenu wrote: > Hi everyone, > > I'm thinking of buying a Mac mini to use as minimal computer for > home, and will need it to run pymol smoothly. is this the case, or > the little machine doesn't have enough juice to handle, let's say, > visualisation of a protein active site and ligand docked into it, > with different level of transparence and such? I need pymol > essentially to look at my structure and generate pretty pictures > for my phD thesis... many thanks to anyone can give insights... > > luca --- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- S for stupendous! T for Tiger, ferocity of! U for Underwear, red! P for Power, incredible! E for Excellent physique! N for ...um... something... hmm, well I'll come back to that... D for Determination! U.. for... wait, how do you spell this? Is it 'I'?
Re: [PyMOL] Pymol on MacMini: performances
Dear Luca, I own a current G4 iBook, and the Mac mini is in principle an iBook in cubuoid form (but without display and keyboard). I don't know how demanding your pymol sessions are, but I'm quite happy with the MacPyMOL version on my iBook, which seems to be subjectively a little bit faster than the X11 version (via fink). Make sure that you have enough memory (at least 512 MB), otherwise this will be the bottleneck. Maybe, you find among your colleages somebody who owns an iBook and try your pymol tasks there? Best regards, Dirk Kostrewa. Luca Fenu wrote: Hi everyone, I'm thinking of buying a Mac mini to use as minimal computer for home, and will need it to run pymol smoothly. is this the case, or the little machine doesn't have enough juice to handle, let's say, visualisation of a protein active site and ligand docked into it, with different level of transparence and such? I need pymol essentially to look at my structure and generate pretty pictures for my phD thesis... many thanks to anyone can give insights... luca -- Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch
RE: [PyMOL] Pymol on MacMini: performances
Hi Luca, I'm using MacPymol on an old blue and white G3, and it works fine. Einat To reply, please change the mmm in the reply-to address to hotmail _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
RE: [PyMOL] Pymol on MacMini: performances
Luca, We bought a Mini here in the office to use as an inexpensive, secure, stable, & hassle-free CVS server. I hadn't tried running PyMOL on it until today... In a very small set of tests with surfaces, a $600 1.42 Ghz G4 Mini (ATI) has about 25% of the OpenGL performace and 60% of the ray-tracing performance of a $1800 1.8 Ghz iMac G5 (nVidia). For comparison, a $450 eMachines 2.8 Ghz Celeron (Intel Graphics) has about 80% of the OpenGL performace and 40% of the ray-tracing performance of the iMac. In other words, the Mini's CPU performance is great; the graphics performance isn't. However, if you just stick to displaying lines, then the Mini does very well -- as good as the iMac. You can display transparent surfaces of active sites just fine, but complete protein surfaces will seem rather slow. 512 MB RAM is a minimum recommendation for ray-tracing with PyMOL. 784MB or 1GB is better. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Luca Fenu > Sent: Tuesday, June 14, 2005 10:25 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Pymol on MacMini: performances > > Hi everyone, > > I'm thinking of buying a Mac mini to use as minimal computer > for home, and will need it to run pymol smoothly. is this the > case, or the little machine doesn't have enough juice to > handle, let's say, visualisation of a protein active site and > ligand docked into it, with different level of transparence > and such? I need pymol essentially to look at my structure > and generate pretty pictures for my phD thesis... many thanks > to anyone can give insights... > > luca > -- > S for stupendous! T for Tiger, ferocity of! U for Underwear, > red! P for Power, incredible! E for Excellent physique! N for > ...um... something... > hmm, well I'll come back to that... D for Determination! U.. for... > wait, how do you spell this? Is it 'I'? > > > > --- > SF.Net email is sponsored by: Discover Easy Linux Migration > Strategies from IBM. Find simple to follow Roadmaps, > straightforward articles, informative Webcasts and more! Get > everything you need to get up to speed, fast. > http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Pymol on MacMini: performances
Luca, I've been using a eMac with similar specs to the MacMini and it works fine. The only major change I see between the G5 in my lab and the eMac at home is the surface calculations and ray tracing. For what you want, my guess is it will be fine. Dan -- Dr. Daniel Moriarty Siena College Chemistry and Biochemistry Dept. 515 Loudon Road Loudonville, NY 12211 (518) 783-2472 fax: (518) 276-4887 > From: Luca Fenu > Organization: university of southampton > Reply-To: > Date: Tue, 14 Jun 2005 17:24:32 + > To: > Subject: [PyMOL] Pymol on MacMini: performances > > Hi everyone, > > I'm thinking of buying a Mac mini to use as minimal computer for home, > and will need it to run pymol smoothly. is this the case, or the little > machine doesn't have enough juice to handle, let's say, visualisation of > a protein active site and ligand docked into it, with different level of > transparence and such? I need pymol essentially to look at my structure > and generate pretty pictures for my phD thesis... many thanks to anyone > can give insights... > > luca > -- > S for stupendous! T for Tiger, ferocity of! U for Underwear, red! P for > Power, incredible! E for Excellent physique! N for ...um... something... > hmm, well I'll come back to that... D for Determination! U.. for... > wait, how do you spell this? Is it 'I'? > > > > --- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Pymol on MacMini: performances
On Jun 15, 2005, at 9:13, Luca Fenu wrote: I thought so, but couldn't be sure, as a lot depends on the quality of the drivers... w/o Direct Rendering (ATI drivers sucks!), my ath64 laptop with R9700 only manages to give me some 4 fps... that makes it all but unusable. so i was afraid to find myself in an even worst situation... Hopefully, PyMol takes advantage of Altivec... I'll give it a try. thanks again... There's no Altivec in the G4 processor that drives the mac mini. Apple has always had good graphics drivers, I wouldn't worry about that. My iBook (whose hardware is very similar to the mini) has much better PyMol performance than some of my Linux boxes whose hardware (both CPU and graphics) is more powerful in theory. However, nothing beats real-life experience. Pack PyMOL and your data on a CD and go visit your nearest Apple vendor! Konrad. -- - Konrad Hinsen Laboratoire Léon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khin...@cea.fr -
RE: [PyMOL] Pymol on MacMini: performances
> There's no Altivec in the G4 processor that drives the mac mini. According to Apple, the mini's do have a "Velocity Engine" aka Altivec. However, PyMOL doesn't itself use it, though we seriously considering writing some Ativec code for MacPyMOL back when the G5 came out. With Apple now going to Intel chips, I'm glad now that we didn't waste our time on that. -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > konrad.hin...@cea.fr > Sent: Friday, June 17, 2005 9:14 AM > To: l.a.f...@soton.ac.uk > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Pymol on MacMini: performances > > On Jun 15, 2005, at 9:13, Luca Fenu wrote: > > > I thought so, but couldn't be sure, as a lot depends on the > quality of > > the drivers... w/o Direct Rendering (ATI drivers sucks!), my ath64 > > laptop with R9700 only manages to give me some 4 fps... > that makes it > > all but unusable. so i was afraid to find myself in an even worst > > situation... Hopefully, PyMol takes advantage of Altivec... > I'll give > > it a try. thanks again... > > There's no Altivec in the G4 processor that drives the mac mini. > > Apple has always had good graphics drivers, I wouldn't worry > about that. My iBook (whose hardware is very similar to the > mini) has much better PyMol performance than some of my Linux > boxes whose hardware (both CPU and graphics) is more powerful > in theory. > > However, nothing beats real-life experience. Pack PyMOL and > your data on a CD and go visit your nearest Apple vendor! > > Konrad. > -- > - > Konrad Hinsen > Laboratoire Léon Brillouin, CEA Saclay, > 91191 Gif-sur-Yvette Cedex, France > Tel.: +33-1 69 08 79 25 > Fax: +33-1 69 08 82 61 > E-Mail: khin...@cea.fr > - > > > > --- > SF.Net email is sponsored by: Discover Easy Linux Migration > Strategies from IBM. Find simple to follow Roadmaps, > straightforward articles, informative Webcasts and more! Get > everything you need to get up to speed, fast. > http://ads.osdn.com/?ad_idt77&alloc_id492&op=ick > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
