[ccp4bb] fsck problem.

Hi, everyone. My linux workstation(rhel4) is giving following errors, when i am trying to boot. here is what i get. Starting undev: [ok] Initializing hardware... storage network audio done [ok] mount: mount: can't find /dev/pts in /etc/fstab or /etc/mtab Setting clock (localtime): Thu Jul 1 12:

Re: [ccp4bb] UV microscope

I used a Korima a few times and didn't like it. Poor image quality and you have to worry about nuking your crystals with UV. However, I haven't tried any other UV microscopes to compare. For most purposes outside of high throughput imaging, I'd rather just shoot the mystery crystals with xrays. Yo

Re: [ccp4bb] vacuum adapter for Dry shipper Cryo Dewar

Thank you everyone that replied ! I got some excellent answers! Cheers! Gunnar :^) On Tue, Jun 29, 2010 at 3:32 PM, James Holton wrote: > > The part you are looking for is known as a "valve operator", at least in > the parlance of our supplier. Here's a cut & paste of the item we

Re: [ccp4bb] UV microscope

Hi there. I don't know how much it costs, but I've used a Korima PRS-1000 serval times, and it appears to be fairly good. Although the image quality isn't great and there is still a bit of a learning curve for identifying small crystals and/or crystals buried

[ccp4bb] Bioinformatics Job Posting - Charleston, SC

This position may be of interest to someone currently associated with a structural biology group. Please apply directly to www.jobs.musc.edu Thanks! Chris Davies The Medical University of South Carolina (w

Re: [ccp4bb] TLS refinement in phenix

On Wednesday 30 June 2010 11:57:45 am Pavel Afonine wrote: > Hi Ethan, > > On 6/30/10 11:43 AM, Ethan Merritt wrote: > > On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote: > > > >> Just a remark/precaution: if you remove ANISOU records then you will > >> basically invalidate the refine

Re: [ccp4bb] TLS refinement in phenix

Hi Ethan, On 6/30/10 11:43 AM, Ethan Merritt wrote: On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote: Just a remark/precaution: if you remove ANISOU records then you will basically invalidate the refinement results (the refined model). If that is true then I would say there i

Re: [ccp4bb] TLS refinement in phenix

On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote: > Just a remark/precaution: if you remove ANISOU records then you will > basically invalidate the refinement results (the refined model). If that is true then I would say there is a deeper problem. The description of the TLS groups in th

Re: [ccp4bb] TLS refinement in phenix

Just a remark/precaution: if you remove ANISOU records then you will basically invalidate the refinement results (the refined model). Make sure you recompute the R-factors after removing ANISOU and be prepared to see (much) higher values. Pavel. On 6/30/10 11:09 AM, Nat Echols wrote: On Wed,

Re: [ccp4bb] TLS refinement in phenix

On Wed, Jun 30, 2010 at 10:59 AM, Pavel Afonine wrote: > I am refining a structure at 2.25 A using Phenix.refine. I am using TLS > parameters for refinement but as i use TLS, phenix does individual > anisotropic refinemnt also. > > No, it doesn't: it does not do "individual anisotropic refinement

Re: [ccp4bb] TLS refinement in phenix

Hi Mirage, I am refining a structure at 2.25 A using Phenix.refine. I am using TLS parameters for refinement but as i use TLS, phenix does individual anisotropic refinemnt also. No, it doesn't: it does not do "individual anisotropic refinement" unless you specifically asked for this. Let m

Re: [ccp4bb] Wilson B and Mean B factors

Usually, this means that the linear fit of a straight line to the automatically-selected "good" region of your Wilson plot produced a slope that was ... well. wrong. Have a look at your Wilson plot (graph log(mean(Intensity)) vs (0.5/d-spacing)^2) in your favorite graphing program, and then

[ccp4bb] TLS refinement in phenix

Dear all, I am refining a structure at 2.25 A using Phenix.refine. I am using TLS parameters for refinement but as i use TLS, phenix does individual anisotropic refinemnt also. Is there some setting by which i can close anisotropic refinment? Looking forward for your answers. Regards Mirage sin

[ccp4bb] Wilson B and Mean B factors

Dear all, If one could find a difference of more than 15 between Wilson B factor of the data ( 55) and Mean B factor of the structure, (30) what could be the possible reasons? I am seeing it in my structure. Could someone tell me why it could be?? Thanks in advance. Yours faithfully, Murug

Re: [ccp4bb] density quiz

My best guess would be acetylation/propionylation with the oxygen pointing into the top small green density. cheers Ajit B. - Original Message - From: Christian Biertuempfel Date: Tuesday, June 29, 2010 2:54 pm Subject: [ccp4bb] density quiz To: CCP4BB@JISCMAIL.AC.UK > Dear all, >

Re: [ccp4bb] Programs to detwin.

Hmm - detwinning is difficult - problematic , because you need to give a fixed twin fraction, which you may have estimated wrongly. both SHELX (I think) and REFMAC (I know) will refine with multiple twin operators, improve the twin fraction estimates, and output an "fobs" which is a detwinned F

[ccp4bb] Phased translation in MOLREP question

Dear All, I use MOLREP to fit my structure into various EM maps using phased rotation/translation. It works perfectly for some maps while for others it gets stuck in the translation search with the message : ERROR: in STRPACK: problem with memory allocation The EM maps that create this problem a

[ccp4bb] Postdoctoral Position in Structural Biology/Biophysics

Postdoctoral Position in Structural Biology Applicants are invited to apply for a postdoctoral position in the area of structural biology and signal transduction. We are seeking enthusiastic, well-trained and self-motivated scientists with excellent organizational and communication skills to jo

[ccp4bb] PiMS tutorial 13th July

INSTRUCT will be hosting a workshop on the PIMS laboratory information management system. PiMS supports the recording and organisation of data generated during the multi-stage process from the selection of a Target to its purification, in readiness for structure determination. The workshop wil

Re: [ccp4bb] problem with coot

Dear Munan, this is a question that should better go to the Coot mailing list. Anyway - it is difficult to say what the problem is, without more informations. It could be an X11 problem or a Coot installation problem. Generally, on Mac OS X, you don't have to start X11 manually or at login -

Re: [ccp4bb] Programs to detwin.

Hi, Why detwin a-periori ? I think the advice usually given on the bb is to let Refmac do this for you internally (and yes, it can handle multiple twin operators). I'm not sure about whether Phenix can handle multiple twin operators as of now. I'm sure it's in the works.   Cheers,           

[ccp4bb] problem with coot

Dear BB I have a problem with coot opening, i tried to open but its not opended. Then I found some other problem, X11 terminal is not opened on login (even its in the list on login items), if I open X11 and then tried to open coot still not working, I am using Macbook and the OS X is 10.6.1. (c

[ccp4bb] post doc position at NCMM in Olso, Structural Biology of membrane proteins

Postdoctoral Research Fellow - (Membrane Proteins Structural Biology) Position as Postdoctoral Research Fellow - in membrane proteins structural biology Ref.no.: 2010/ 8649 Available at the Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo. A post-

Re: [ccp4bb] Difficult to solve MR - A mysterious case

Chen, The first of your diffraction patterns looks streaky and I'm wondering whether your intensities carry a significant error due to poor peak profiles. I know you used already two alternative data processing programs, but I'd recommend to give XDS a try. When dealing with poor peak pro