I never thought I would agree with Tassos :-) But same experience 3D and wiggling with a snaked ligand makes live so much easier. It helps to have a fast graphics card though. Jürgen
...................... Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Mar 23, 2011, at 4:21, Anastassis Perrakis <[email protected]> wrote: > To add my two cents, I am not at all a fun of stereo for routine use, but I > appreciate it if I have to look at a long ligand bent 90 deg in the middle to > bury in my protein, and all that at 3.0-3.5 A resolution ... So, I must have > both types of brain damage that Jan refers to. No surprises here I guess. > > A. > > On Mar 23, 2011, at 3:16, Phoebe Rice wrote: > >> My 2 cents worth on the stereo-dependent: >> >> 1) They have carpal tunnel syndrome that makes it painful to keep the >> molecule in motion while rebuilding it (NOTE: enough constant mouse-wiggling >> and you will get carpal tunnel problems if you don't have them yet!) >> >> 2) They work on big, low-resolution structures where you need to see a >> bigger-picture view. I've had people tell me that can fit 3-3.5A maps just >> fine without stereo, but having viewed their work, I beg to differ. >> >> Phoebe >> >> ---- Original message ---- >>> Date: Tue, 1 Mar 2011 22:30:54 +0000 >>> From: CCP4 bulletin board <[email protected]> (on behalf of Jan Löwe >>> <[email protected]>) >>> Subject: Re: [ccp4bb] while on the subject of stereo >>> To: [email protected] >>> >>> Ah! The question of to stereo or not to stereo! There has to be a >>> scientific reason why this question is more popular than asking for what >>> Linux distro is more fashionable this spring or why an Rmerge of 0.90 in >>> the outermost shell is good for you and your structure. >>> >>> I am offering my two (conflicting) theories (and apologies that both >>> seem to imply some problem): >>> >>> A) people who do use stereo have a problem with their brain because they >>> cannot produce three dimensional vision from depth cues alone. >>> >>> B) people who do not use stereo have a problem with their brain because >>> they cannot see properly in three dimensions and rely on depth cues alone. >>> >>> I personally prefer people with A) when I am their passenger in a car >>> since they do not need to rotate by 90° to see how far the braking >>> lights of the car in front are away :-) >>> >>> jan >>> >>> >>> >>> On 01/03/2011 21:35, Jim Pflugrath wrote: >>>> I will offer my view. >>>> >>>> I hate stereo glasses and hate stereo in general. >>>> >>>> One should be able to see 3D from the depth-cueing and by keeping the view >>>> in motion. For fitting, I like to flip the view by 90 degrees. I know I >>>> am >>>> going to move in displayX and displayY, but never in displayZ. I then >>>> rotate the view around the vertical axis so thatn the old displayZ becomes >>>> displayX. >>>> >>>> Furthermore, I don't waste too much time fitting. I know the software can >>>> fit the map better than me, so I let it do its job. I only need to get the >>>> coordinates within the radius of convergence of the refinement program. I >>>> also know that 9 times out of 10, the displayed electron density is >>>> probably >>>> suspect, so I believe in stereochemistry more than I believe in the map. >>>> >>>> The main trick is to realize that as a human being, you really are not that >>>> good at fitting the map or that it is unnecessary to waste your time since >>>> the software is really so much better than you. Refinement is quick enough >>>> that you can try various hypotheses as in: "If I move this here, then >>>> refinement will do the trick" and "Well, that didn't work, so I will move >>>> that over there and see if refinement will do the trick." >>>> >>>> As for stereo figures, you should be able to convey what you want to say >>>> from a good figure with depth-cueing, shadows, etc. Don't ever use stereo >>>> glasses in a public seminar. Maybe my opinion will change with better >>>> stereo technology. >>>> >>>> OK, I know quite a lot of people will disagree with me. :) >>>> >>>> Jim >>>> >>>> -----Original Message----- >>>> From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of David >>>> Roberts >>>> Sent: Tuesday, March 01, 2011 10:29 AM >>>> To: [email protected] >>>> Subject: [ccp4bb] while on the subject of stereo >>>> >>>> Hi again, >>>> >>>> I'd like to ask a question about the pedagogy of stereo. That is, using >>>> stereo with students in the classroom. >>>> >>>> Do you all find that, after setting up these elaborate stereo devices, >>>> students really use the stereo or do they tend not to? >>>> >>>> I am a huge fan of stereo - and frankly here we have quite a few options >>>> for >>>> doing stereo - from the active Nvidia systems that people have recently >>>> been >>>> discussing to passive zalmans. ... >>>> >>>> As I mentioned, I like stereo a lot, but really projecting on a nice bright >>>> lcd monitor also has it's advantages, and with the ease of moving things >>>> using the mouse (or whatever device you use), the overall need for stereo >>>> seems to be decreasing. I don't know - I just wonder what peoples views >>>> are >>>> out there for the actual "need" for stereo. It's incredibly cool - and I >>>> think is a very powerful way to show things - but I'm wondering if we focus >>>> too much on it because it's cool and not because it's pedagogically >>>> necessary. >>>> >>>> Just wondering, no worries. Thanks >>>> >>>> Dave > > P please don't print this e-mail unless you really need to > Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member > Department of Biochemistry (B8) > Netherlands Cancer Institute, > Dept. B8, 1066 CX Amsterdam, The Netherlands > Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 > > > >
