Re: [ccp4bb] Protein crosslinking before crystallization

2011-08-15 Thread Jason C Porta
I found this paper to be very helpful for a similar experiment. "Elucidation of the mechanism and end products of glutaraldehyde cross-linking reaction by x-ray structure analysis". Wine et al. Biotechnology & Engineering, Vol. 98, No. 3, October 15, 2007. -CCP4 bulletin board wrote: ---

Re: [ccp4bb] Error in LABIN

2011-04-30 Thread Jason C Porta
It was a permissions problem with the tmp directory. I thought I changed it, but alas it was set to root. Thanks for your help! Jason -Bruno Matias wrote: - To: Jason C Porta From: Bruno Matias Date: 04/30/2011 07:21AM Subject: Re: [ccp4bb] Error in LABIN Jason, I think you shoud

Re: [ccp4bb] Error in LABIN

2011-04-29 Thread Jason C Porta
Here is more information on my problem: I installed ccp4i in /usr/local as root using the automated install.sh script. I then sourced the ccp4.setup and ccp4-others.setup for the proper shell, making sure the environment variables were pointing in the right direction. Now, if I run ccp4i as a

Re: [ccp4bb] fink update

2010-04-09 Thread Jason C Porta
Hi Raja,I assume you are running OS X?I had this same problem since I was running xcode v3.0. The new compiler (the one its complaining about) should be packaged with the xcode on the snow leopard disc, which I believe is the most recent version. I could be wrong, since I haven't yet fixed my own p

Re: [ccp4bb] Refining residues as rigid bodies

2009-12-01 Thread Jason C Porta
Basically my reasoning for doing this is a low data-to-parameter ratio, which makes B-factor refinement unfeasible. So far I have had nice results with breaking the complex into rigid subdomains. So i was basically just thinking of a way I could refine the structure best, without using too many par

[ccp4bb] SA composite omit maps in Phenix

2009-10-06 Thread Jason C Porta
After searching the documentation and archives, I could not find an answer to a question regarding Phenix maps. I am trying to make an Fo-Fc composite omit map of a structure that has the solvent deleted. I want to create a map using Fo-Fc as the coefficient and with composite omit phases.How would

Re: [ccp4bb] Phoenix robot

2008-09-09 Thread Jason C Porta
Does anyone have the experience of using Phoenix robot automatically setup thecrystal? We have had a Phoenix in our lab for about 2 years now, and have been very pleased with the performance. Other users I spoke with have also expressed the same satisfaction.Which plate the Phoenix could use such a

[ccp4bb] How to change R-free set?

2008-06-17 Thread Jason C Porta
Hi all,I am currently refining a high-resolution structure that has many reflections (~180,000). I would like to halve the R-free set from 5% to 2.5%, and am unsure how to do so. Any advice will be greatly appreciated.Jason PortaGraduate StudentDept. Biochemistry and Molecular BiologyUniversity of