[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] 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 a

[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 View

Re: [ccp4bb] problem with PyMol on Ubuntu

oad 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 PyM

[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] renumbering amino acid residues in a pdb file

Hi All, I have a pdb file of a single domain from a protein. The amino acid residues are numbered based on their position in the full length protein, so they do not start at 1, but I would like them to. Coot has a Renumber Residues feature under the Calculate menu, but it does not appear t

[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

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 wrote: > Doe

[ccp4bb] is it valid to compare the B factors of corresponding domains or regions of molecules from different crystal structures

I am looking to compare the B-factors of a particular stretch of DNA bases when bound by several different proteins. I have crystal structures for each, but the structures are of different resolutions and also then different Wilson B-factors. Is it valid to compare those B-factors directly? (probab

[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 (in

[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 try