Re: [ccp4bb] Popularity of Stereo graphics in crystallography

P Hubbard wrote: ... Thanks for the e-mail. The current results of the survey would certainly put you in the minority! Stereo graphics are not dead after all. I have used systems with and without stereo graphics. I personally prefer them, and think they are great for helping newbies refine, an

Re: [ccp4bb] Survey on computer usage in crystallography

I find that in a large proportion of cases depth-cued graphics without stereo are enough (e.g. quickly examining a structure, rebuilding in a refined map, tracing at 2.4 A), and indeed I do most of my graphics work on a laptop. But, when you are lost in a poorly-phased 3.5 A map of a structure yo

Re: [ccp4bb] Popularity of Stereo graphics in crystallography

I haven't used stereo since the last millenium - I don't miss it. You don't really need it and it's not worth the expense/hassle to set up. In my opinion it's just something to impress visitors! Dave --- Dr. David M. Lawson Biological Chemistry Dept., John Innes C

Re: [ccp4bb] mac pro configuration for crystallographic computing

I should apology for my unqualified remark (initiated by a personal note to me). I do appreciate and like grasp. >From my experience, though, the appearance of an electrostatic surface representation is so much dependent on the parameters, on the input PDB-file (presence of ligands, waters,

Re: [ccp4bb] Popularity of Stereo graphics in crystallography

I have found stereo essential for building low resolution structures where data beyond 3.3A is not available, I must also say that I have found it unnecessary for any structures which there is data (with decent phases) to 3A and beyond. The question is, is it worth spending a substantial amoun

Re: [ccp4bb] Popularity of Stereo graphics in crystallography

It seems not so long ago that people were interested not only in stereo graphics, but also in research into interactive gloves etc. for maximal virtual reality in manipulating protein structures, "feeling" forces, etc. To simulate depth by rendering solvent accessible surfaces with shadows and ref

[ccp4bb] eCheminfo Autumn Meeting Program available

Schedule, Abstracts and Biographies for the eCheminfo Autumn Community of Practice meeting program at Bryn Mawr College, Philadelphia in October on "Latest Advances in Drug Discovery & Development" are now available through the eCheminfo website: http://echeminfo.colayer.net/COMTY_conferencesprog0

[ccp4bb] Research Fellow in Structural Biology of Tuberculosis

Research Fellow School of Biosciences University of Birmingham We seek a highly motivated Research Fellow to join an interdisciplinary research team working on structural and biochemical aspects of cell wall synthesis in the pathogen Mycobacterium tuberculosis, in a thriving research enviro

[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] Stereo grpahics and Virtual Reality

Full VR systems with motion tracking and are now affordable to most labs (~$2500 for all the peripherals). Nintendo Wii remotes are about £25 and they do 3-dimensional motion tracking. Perhaps we should by trying to use them for refinement instead? They communicate via the Bluetooth protocol (

Re: [ccp4bb] Stereo grpahics and Virtual Reality

For the benefit of overworked and stressed-out graduate students and post-docs, funding agencies need to be convinced that the remotes cannot be bought without the console. Andreas Stephen Graham wrote: Full VR systems with motion tracking and are now affordable to most labs (~$2500 for all

[ccp4bb] Fitting molecule B7G or B8G using COOT

Hi everybody, I am trying to short out to fit a molecule into a density but having problem. It is n-beta-octyl-glucopyranoside into a electron density of my structure. The coordinate of this molecule I got from different from PDB. n-beta-octyl-glucopyranoside was present in the crystallization c

Re: [ccp4bb] Stereo grpahics and Virtual Reality

And obviously, each crystallography lab should invest in a Wii station with a full complement of games - for training purposes. Artem -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Stephen Graham Sent: Thursday, June 21, 2007 10:46 AM To: CCP4BB@JISCMA

[ccp4bb] Save image in Postscript format from PYMOL

Hi, all I am drawing some stereo images with label by PYMOL. But the label interfere with protein. I try to output to Postscript format so that I can change the position of label. However, I can't output the image to Postscript format in Pymol. Is there anyboy know how to save image in Postscr

Re: [ccp4bb] Fitting molecule B7G or B8G using COOT

> I am trying to short out to fit a molecule into a density but having problem. > It is n-beta-octyl-glucopyranoside into a electron density of my structure. > The coordinate of this molecule I got from different from PDB. > n-beta-octyl-glucopyranoside was present in the crystallization conditio

[ccp4bb] Ligand fitting in COOT and SHELX refinement

Hi I would like to know following issue for a ligand. A ligand of a long alkyl chain can have multiple conformation. In coot in order to fit any protein residues into "difference Density", we can select a specific "rotamer" conformation and refine. For fitting ligand of above kind, how does it wor

Re: [ccp4bb] Ligand fitting in COOT and SHELX refinement

My following question relates to the fitting and refinemt of a ligand, n-octyl-beta-D-glucopyranoside. Sam > Date: Fri, 22 Jun 2007 06:27:45 + > From: [EMAIL PROTECTED] > Subject: [ccp4bb] Ligand fitting in COOT and SHELX refinement > To: CCP4BB@JISCMA