[ccp4bb] adjusting bad Ramachandran angles

Does anyone know of a way to adjust Ramachandran angles so that they fall within the preferred range? Either in Coot or possibly some online server? I have been trying to do it manually without much success, I was wondering whether there might another way to do it. -Thanks

[ccp4bb] problem with phenix refine and non bonded interactions

I am using Phenix 1.8-1069. I am having a problem with phenix refine terminating with an error message. I added several solvent molecules, MPD and bicarbonate in Coot, and ran Phenix ReadySet to generate restraints for them and applied those restraints to all future jobs in that project. When I

[ccp4bb] comparing differences across multiple structures of the same protein

I am trying to compare structures of the same protein in the apo form and when bound to several different ligands. There are differences, but they are subtle and I am unsure whether they are actually significant or just do to coordinate error or something similar. Is there a theoretical minimum

Re: [ccp4bb] getting larger protein crystals

If you have found a condition that is yielding crystals, but they are either too many/too small or do not have a very optimal shape, I have found varying the drop sizes and/or ratios of protein:precipitant solutions can make a big difference On Wed, Jul 4, 2012 at 5:33 AM, REX PALMER

[ccp4bb] how to install coot on ubuntu 11.10

I am trying to install Coot on a laptop that runs Ubuntu. Following the instructions on the CCp4wiki http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 1DC81A57 sudo add-apt-repository ppa:mok0/ppa

[ccp4bb] bug in Coot when saving coordinates

I am adding solvent molecules into unmodelled blobs of density in Coot. When I am finished, I merge molecules, then save my coordinates. For some reason Coot is saving two copies of each molecule that I have modelled and assigns them different chain ID's. I notice this when I open it in PyMol and

[ccp4bb] fixing the slab view in Coot

Hi All, Does anyone know how to fix the default view mode in Coot, where things disappear from your view when you zoom in on them?

[ccp4bb] problem with PyMol on Ubuntu

I running Ubuntu on a laptop (Toshiba Satellite L505 ATI/AMD FGLRX graphics driver). I downloaded and installed PyMol but it runs poorly. For some reason, it runs fine the very first time I use it after I login, but every time I launch it after that all of the buttons and text of the the PyMol

Re: [ccp4bb] problem with PyMol on Ubuntu

to download any files from the pymol website. Best regards, Claudio Shah Am Mittwoch, den 15.12.2010, 10:50 -0500 schrieb Michael Murphy: I running Ubuntu on a laptop (Toshiba Satellite L505 ATI/AMD FGLRX graphics driver). I downloaded and installed PyMol but it runs poorly. For some reason