[ccp4bb] New crystal screening analysis web server...

Hi all, I've recently set up a web server to help in the initial crystal screening process, and thought it might be useful for other people too. It allows one to point-and-click to catalog and analyze the results of initial screens to help see what your protein does and doesn’t like, as well a

[ccp4bb] Stereo graphics on Head Mounted Displays

Hi All, I am thinking about buying a HMD for stereo graphics and was wondering if anyone has had any success running Xtallographic software with any of the following models using a Nvidia quad-buffered stereo card. In particular, I would like to know if they are relatively easy to set up and i

[ccp4bb] Survey on computer usage in crystallography

Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html Its point-and-click, with 10 short questions, and should take under 2 minutes to complete. You are not requested to enter you

Re: [ccp4bb] Survey on computer usage in crystallography

be greatly appreciated. Paul From: "David J. Schuller" <[EMAIL PROTECTED]> Reply-To: "David J. Schuller" <[EMAIL PROTECTED]> To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Survey on computer usage in crystallography Date: Wed, 20 Jun 2007 10:18:44 -0400 On Tue, 2007-0

Re: [ccp4bb] Survey on computer usage in crystallography

nt lots of time in the library reading while your rigid body refinement was chewing on the next cycle is long gone. Bart David J. Schuller wrote: On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be

[ccp4bb] Popularity of Stereo graphics in crystallography

hing. If I needed the performance, it would be a 5 minute job to install the drivers, but I haven't needed it. Kevin P Hubbard wrote: I am sorry you are unhappy with the questions, David. As I am sure you know, I half-decent system with stereo graphics doesn't come cheap, and if y

[ccp4bb] Stereo grpahics and Virtual Reality

Hi, Thank you for all the comments and to those to completed the survey (it is still open, in case you hadn't had chance to do it yet). Just a quick comment on stereo graphics and VR... I think for people to take full advantage of auto-refinement/building routines which speed up model buildi

Re: [ccp4bb] Flat Screen and Stereo

Hi, The following web page should answer your question: http://pymol.sourceforge.net/stereo3d.html On a related note, I recently came across a new 22" LCD stereo system which is below $1000 and requires polarized glasses ($10 each). It doesn't seem to be set up for OpenGL yet, so isn't suitab

[ccp4bb] Data mining using consensus sequences

Hi all, I'm certain this can be done, but I figure it would be much easier asking the news group than spending hours trawling though random web pages: Does anyone know how to search protein sequence databases using a consensus sequence which allows varying gap sizes, and homologous amino acid

[ccp4bb] Protein models in Blender

Hi all, I've had some spare time to teach myself blender, which seems to me to be a powerful model editing and animation tool. However, I've not found any python scripts or software to convert objects such as ribbons mesh made in ccp4mg or pymol into something that blender can use (I know its

Re: [ccp4bb] Protein models in Blender

s possible to generate a povray input file from molecule objects, it should be possible to generate a VRML file which blender can open. If I'm not mistaken, Mike Carson's Ribbons is able to write VRML files. /Michel On Thu, 2007-09-13 at 12:23 -0700, P Hubbard wrote: > Hi all, &g

[ccp4bb] Crystal Screening and Analysis web server

Hi All, I've rewitten the code for the Crystal Screen Wizard web server. The original aim of this home project was to analyze drop appearance patterns from initial screening in order to find "ideal" storage buffers for unstable proteins; however, I've modified it to include other useful featur

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

Hi, I've played around with the VR920 - and have used it with WinCoot using GlovePIE for head tracking. It's fun to fly round your protein but the screen judder(?) hurts your brain after a few minutes (low quality accelerometers?). There are people developing Linux drivers; you can contact the

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

Hi, Just an FYI you can build those yourself at a fraction of the price! You just need the special piece of glass, two identical LCD monitors, and an edited X config file. They are still bulky though! AGS > Date: Mon, 4 Feb 2008 10:46:45 + > From: [EMAIL PROTECTED] > Subject: Re: [cc

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

:24:32 + > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional > To: CCP4BB@JISCMAIL.AC.UK > > P Hubbard wrote: > > > Just an FYI you can build those yourself at a fraction of the price! > > You just need the special piece of

Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

s case needs to be polarized vertically, since the reflected polarized light will be horizontal. No idea where you can buy large sheets of Polaroid™ though. IMWBW, though... On 4 Feb 2008, at 11:30, P Hubbard wrote: Hi Andrew, Just like the commercial systems, the glass is the

Re: [ccp4bb] 3D Glasses

Below is a good discussion about different DLPs which are supposed to work in stereo. Some models listed would appear to me to give high levels or flicker so you may want to double check; however, there are people who see stereo fine with refresh rates of much less than 120 Hz. Anyway, it seems

[ccp4bb] drag-and-drop (custom condition order) option in Crystal Screen Wizard

Hi all, To respond to a users suggestion, I've added drag-and-drop boxes to the crystal screen wizard, so now you can now set up your screening conditions in any order you want (web 2.0-ified if you will). You can also mix and match different kits from different manufacturers in the same tray.

Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments

What about Dennis Madsen et al's "Indonesia"? http://xray.bmc.uu.se/dennis/ I don't think it's been updated in years (or I have a old link), but it's still quite nice as it runs locally using java. AGS > Date: Tue, 4 Mar 2008 12:02:20 -0800 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] mu

[ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs

Hi, I could be wrong, but I’m not aware of any servers that have tray inspection web pages designed for iPhones and Pocket-PCs, so I thought I’d try and make a web page with simple scoring sheets for such devices. I don’t own an iPhone myself, but the following web page seems to work well on a

Re: [ccp4bb] Crystal scoring sheets for iPhones/Pocket-PCs

. > > This of course also suggests that iPod touch is a valid research > expense ... > > > William G. Scott > > Contact info: > http://chemistry.ucsc.edu/~wgscott/ > > > On Mar 19, 2008, at 8:59 AM, P Hubbard wrote: > > > > > Hi, > > &g

Re: [ccp4bb] Co-expression plasmids

Hi, If you are expressing just two proteins, you could try a single pET vector with a pCDF vector. The only reason I'm suggesting this is that I had trouble with pET-Duet, but doing each one separately worked first time (plasmid size issue?). I used pET24-a and pCDF-1b - so I had one construct

Re: [ccp4bb] Co-expression plasmids

) A. On 2 Apr 2008, at 19:39, P Hubbard wrote:Hi, If you are expressing just two proteins, you could try a single pET vector with a pCDF vector. The only reason I'm suggesting this is that I had trouble with pET-Duet, but doing each one separately worked first time (plasmid size issue?).

Re: [ccp4bb] projecting 3d stereo

Hi, Below is what I've thought would make a good, but inexpensive, 3D system (not had the opportunity to try all the parts out though): Edimensional glasses (not compatible with the old Stereographics goggles and emitters - dunno the exact wavelengths, but from visual appearance of the LEDs

[ccp4bb] Off topic: McDonalds Happy Meal and Crystallography

I took my 5 year old niece to a McDonald's (in England) for a happy meal today - Spiderwick Chronicles promotion. The toy's light effect reminded me of a visual aid I saw to help introduce X-ray diffraction and the crystal lattice to students. My niece was more interested in using the visual ef

[ccp4bb] Ionic strength reduction by PEG

Hi all, Does someone have a table, or a web link to a table of dielectric constants for solubilized states of all PEGs (and related compounds) commonly used in macromolecular crystallography? Non-Merck Index suggestions please. A related question: can anyone recommend any freely available arti

[ccp4bb] Specific conductivities of crystal screen conditions

Hi all, I am looking for a list of specific conductivities for commercial screens. If anyone has one (even if measured in the lab) and wouldn’t mind sharing, please let me know. Thanks, AGS _ It’s easy to add contacts from Faceb

[ccp4bb] Google maps and X-Ray Facilities/Equipment

Hi all, I’ve wondered what use a Google Maps mashup would be to the structural biology community, so for some fun I set up the following web page (please let me know if something like it already exists)… http://www.pageforaday.com/xtalwizard/maps/ It’s aimed at new PIs at small research insti

Re: [ccp4bb] interface

The way I look at it; BSA the the total surface area defined within two bisecting 3D curves, interface area is the minimum surface area that can be that can be produced by interpolation between regions at bisect each other. Probably not the best definition. On a side note: can one really use th

Re: [ccp4bb] foam dewar usage ?

A side note about ice formation... This might have already been mentioned, but I have personally used a shower cap over cryo-bowls and it seems to do a reasonable job - ice seems to form quicker on the shower cap than in the bowl. Covering the bowl with an old Styrofoam lid from a spare shippi

[ccp4bb] Crystal Screen Optimization Server

Hi all, I’ve written a GUI to calculate 2D gradients for crystal screen optimization that people might find useful (much like a web 2.0 version of Hampton’s “Make Tray” utility). It’s intended to write scripts for a liquid handling robot our lab uses, but I’ve set up a public version up that g

Re: [ccp4bb] Na/K Phosphate

On a side note, I have created a web server that, based on your sample buffer, makes a crude attempt at prediciting conditions within a screen that may form salt crystals (though this probably should be taken with a grain of. salt, ahem!). http://www.pageforaday.com/xtalwizard/salt.php

[ccp4bb] Sumo protease (Ulp) expression vector

Hi all, I've had a Google around, but can't find anywhere on the net that sells a sumo protease (Ulp) expression vector. Does anyone know any different? As an alternative, does anyone recommend a company that sells inexpensive sumo protease. Thanks! __

Re: [ccp4bb] Sumo protease (Ulp) expression vector

s for expression of SUMO fusions." Protein Expr Purif. 2007 May;53(1):40-50.We express the Ud1 domain of the yeast hydrolase. Contact me off-line if you're interested. Pat On 12 Aug 2009, at 4:51 PM, P Hubbard wrote:Hi all, I've had a Google around, but can't find anywhere on

[ccp4bb] Off topic: Question about CD spectrum

Hi all, I've limited experience interpreting CD spectra, so I might be missing something, but I've collected CD data for a hydrophobic 15-mer peptide that forms a putative alpha-helix. I get a region of strong negative ellipticity, bottoming out at ~222nm; however, I also get a strong positive

[ccp4bb] Off topic - nickel magnetic beads

Hi all, I'm looking at getting some nickel magnetic beads. I've never used them before, and they seem pretty expensive. Does anyone know of a good inexpensive supplier? Thanks in advance for any replies! __