My first attempt of a cover design

I was recently part of a project that got a publication accepted in PNAS and therefor I decided to try and make a cover design just for fun, but with the hopes that the editor would put it on the cover

Anyway the final design ended up like his:

Continue reading My first attempt of a cover design

The power of jiggle fit in low resolution data

At the homepage for Garib Murshudov’s lab, there is a page dedicated to EM fitting tools and scripts. Among these scripts are some for Coot which adds jiggle-fit, morph modeling  and user-define restraints capabilities to Coot (you can read a bit about them here).

If you have not used Jiggle-fit yet, I can highly recommend it, especially for low resolution de-novo building.

Here is an example I did using jiggle-fit in Coot using my own map and a Coot generated ideal RNA double helix. Continue reading The power of jiggle fit in low resolution data

Converting cryo-EM map to mtz

As I have not been able to find basic newbee information anywhere regarding how to convert a Cryo-EM map to mtz, I will just note down what I did. I have no idea if it is the “correct”way or not, but it works.

Basically I just used the phenix program: phenix.map_to_structure_factors with my EM map (in mrc or ccp4 format, they are normally identical formats) as input together with a resolution constant (d_min) e.g.

phenix.map_to_structure_factors CrappyEMmap.mrc d_min=4.4

and out comes a mtz file for you.

Increasing grid points in your EM map

If you want to make your crappy EM map look better( with look being the operative word, as the quality of the map is unchanged) when using e.g. coot, you might want to consider increasing the grid spacing, that is the number of sampling divisions along any of the axis.  It is basically the same process you use in PyMol when generating figures with a very fine mesh density, there it is just called map double . Continue reading Increasing grid points in your EM map

Cryo-EM

cryo_em_progress

So I have ventured into the Cryo-EM field recently, as so many others have done as well. This means that this page will see a bunch of small updates with stuff related to Cryo-EM (primarily de-novo model building, and refinement etc.) and not so much on molecular visualization. Not that I updated this page every week/month any way, so no big changes.

Nenad Ban and the Ribosome

Atomic Models of the 60S and 40S Eukaryotic Ribosomal Subunits in Complex with Initiation Factors 6 and 1 respectively Photograph: Katharina Bohm and Felix Voigts-Hoffmann

From a ribosome and PyMol point of view, Professor Nenad Bans lab page is simply a must read as they summarize a lot of useful information. Continue reading Nenad Ban and the Ribosome

QuteMol tutorial – how to make realistic looking figures in 1 min

Just a short introduction to what could have become the perfect tool for generating high quality realistic renderings of PDB files, QuteMol.

QuteMol is an open source program for high quality molecular visualizations of PDB files only. QuteMol mainly differentiates itself from PyMol by its use of real time ambient occlusion and a incredible intuitive user interface.

As a token of just how easy QuteMol actually is to use, I created the below GIF on my own desktop computer in about 1 min. Continue reading QuteMol tutorial – how to make realistic looking figures in 1 min

PyMol tips: batch mode

I personally think  that the most efficient way to do large amounts of high quality and processor demanding renderings with PyMol is to do it in batch mode.

Continue reading PyMol tips: batch mode

Advanced Pymol Movie

Here I will give a shortish guide to how I made this ribosome movie  with Pymol.

Continue reading Advanced Pymol Movie

segid vs chain ID’s using the ribosome as an example

UPDATE: found this command in pymol

set ignore_case, 0

Which, when set to 0, activates the recognition and differentiation of lowercase and uppercase chain IDs in Pymol thereby circumventing some of the problems working with large molecules in PyMol!

Continue reading segid vs chain ID’s using the ribosome as an example

An amateurish molecular visualization blog