[ccp4bb] Launching COOT "Stepped Refine" from terminal/script

Hi All, I’m working with many different structures at the same time and I want to speed up opening the structures in COOT buy using the terminal but then launching the usually, menu activated Stepped Refine option at the same time. Normally I would have to manually select Calculate • All

[ccp4bb] Job Offer: Structural Biologist-Membrane Proteins, Vertex Pharmaceuticals UK

Structural Biologist-Membrane Proteins Structural Biology and Biophysics (UK) Abingdon, Oxon, UK Full-Time Job Description Summary: Vertex Pharmaceuticals (Europe) Ltd has an immediate opening for a talented membrane protein structural biologist in the Structural Biology and Biophysics

[ccp4bb] Empty CORRECT.LP file

Hello, I have a question regarding the XDS output file CORRECT.LP. I have a dataset collected on a Pilatus which has 4960 frames. XDS ran over night to process the data with the ALL job activated and terminated successfully but the output CORRECT.LP file contains ZERO bytes, no data. I ran XDS

[ccp4bb] Adding ligand to crystallization drop

concentrated ligand and this method would not work…? Thanks, Chris -- Christopher Browning, Ph. D Vertex Pharmaceuticals (Europe) Ltd 86-88 Jubilee Avenue Milton Park Abingdon Oxfordshire OX14 4RW United Kingdom Tel +44 (0) 1235 438327 christopher_b_brown...@vrtx.com www.vrtx.comhttp

Re: [ccp4bb] Adding ligand to crystallization drop

conc. being added. I'll co-crystallize just to have a backup! Cheers C -- Christopher Browning, Ph. D Vertex Pharmaceuticals (Europe) Ltd 86-88 Jubilee Avenue Milton Park Abingdon Oxfordshire OX14 4RW United Kingdom Tel +44 (0) 1235 438327 christopher_b_brown...@vrtx.com www.vrtx.comhttp

Re: [ccp4bb] Adding ligand to crystallization drop

, Chris -- Christopher Browning, Ph. D Vertex Pharmaceuticals (Europe) Ltd 86-88 Jubilee Avenue Milton Park Abingdon Oxfordshire OX14 4RW United Kingdom Tel +44 (0) 1235 438327 christopher_b_brown...@vrtx.com www.vrtx.comhttp://www.vrtx.com/ From: Bosch, Juergen jubo...@jhsph.edumailto:jubo

[ccp4bb] Joining two atoms to display in pymol

file with something like CONNECT or JOIN or LINK? These are the two atoms I'd like to join. ATOM 19317 C2 SIA Y 1 20.503 35.557 43.691 1.00 22.97 C ATOM 19387 O9 SLB Z 1 21.630 36.539 45.311 1.00 28.53 O Thanks, Chris -- Dr. Christopher Browning Post-Doctor to Prof

Re: [ccp4bb] Joining two atoms to display in pymol

line, pymol should draw a bond between them (if they are in the same object that is). Sabine On 09/25/2012 06:36 PM, Christopher Browning wrote: Hi, I have a question about how to join two atoms together so that in Pymol a bond is drawn between them. I have 2 sugar molecules

[ccp4bb] Hydrogens added when using Phenix Readyset for ligands

molecules. As a test, I removed the hydrogens added to the ligands and the refined protein coordinates are way different than when the hydrogens are left in? Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04

Re: [ccp4bb] Hydrogens added when using Phenix Readyset for ligands

-bumping restraints. Tim On 05/07/12 15:07, Christopher Browning wrote: Hi, I've generally used PRODRG to create paramater files for any ligands I add during refinement with CCP4 and/or PHENIX. I've been trying READYSET from PHENIX as it greatly helps refining some metal ion positions

[ccp4bb] COOT Real Space Refinement keyboard shortcut??

. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40

Re: [ccp4bb] Problem with COOT and MSE (SeMET ) residues

Hi Laurie, Not much, I did not get any useful feedback so I emailed Paul Emsley directly. Chris On Tue, 2012-02-14 at 22:43 -0500, Laurie Betts wrote: Problem with COOT and MSE (SeMET ) residues -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne

[ccp4bb] Problem with COOT and MSE (SeMET ) residues

of the residues next to the MSE) are not fitted at all. I use COOT 0.6.2 and refine my structure with the latest PHENIX edition. Can anybody help Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40

Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled

if the Rfree was created with PHENIX. Both maps now look the same, and it indeed looks like the protein in the crystal is different from the sequence. Cheers, Chris -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40

[ccp4bb] PHENIX vs REFMAC refinement had me fooled

this be and what causes this? Link for the pictures: Both maps are at identical Sigma levels in both pictures. PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png Cheers, Chris Browning -- Dr. Christopher Browning Post-Doctor

Re: [ccp4bb] sealing slides on VDX plates?

. Continue until you're. Should take no more than a few seconds to do the whole plate. Cheers, Chris Browning -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Tel: 0041 (0) 02 16 93 04 40

Re: [ccp4bb] Precipitating Crystallization Condition

-- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Tel: 0041 (0) 02 16 93 04 40 -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40

[ccp4bb] Pymol question

yellow, (HISA and elem S) set stick_radius=0.20, HISA #hide everything, HISA -- Dr. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40

Re: [ccp4bb] Glutathione sepharose

. Christopher Browning Post-Doctor to Prof. Petr Leiman EPFL BSP-416 1015 Lausanne Switzerland Tel: 0041 (0) 02 16 93 04 40