[ccp4bb] Postdoctoral Positions of Structural Biology, SUSTech, Shenzhen, China

Dear all, Two postdoctoral positions are currently available in the structural biology laboratory of Dr. Zhiyi Wei (http://bio.sustc.edu.cn/en/?p=189) at Department of Biology, Southern University of Science and Technology (SUSTech, Shenzhen, China). Our research interests is to uncover

Re: [ccp4bb] manipulation of water molecules in pdb files

to continue refinement? Eleanor On 30 Jul 2012, at 09:27, Zhiyi Wei wrote: Dear all, I have a refine structure with 8 ncs copies and several hundreds of water molecules (which was put in one chain). Now I try to separate these molecules by renaming to the chain id of each adjacent protein

[ccp4bb] manipulation of water molecules in pdb files

Dear all, I have a refine structure with 8 ncs copies and several hundreds of water molecules (which was put in one chain). Now I try to separate these molecules by renaming to the chain id of each adjacent protein molecule. I know RCSB can do this during deposition process. Do anyone know a

Re: [ccp4bb] an ambiguous result of molecular replacement

Hi Leonid, Thank you for your valuable suggestion. It is exactly the case. When I tried P21, it works well. The solution is now very clear. Best, Zhiyi On 3/31/12, Leonid Sazanov saza...@mrc-mbu.cam.ac.uk wrote: Hi, we had the same case in apparent C2221, with many similarly shifted Phaser

[ccp4bb] an ambiguous result of molecular replacement

Dear all, I got a weird solution from Phaser. The background is that, space group C2221, resolution ~4A, in complex with a peptide, and having a apo form structure as the search model. Phaser gave two rotation function peaks with Z 7. But when searching translation function peaks, Phaser gave

Re: [ccp4bb] Structure Determination combining X-ray Data and NMR

Hi Yuan, Bad geometry is a general issue for most low resolution structure refinement. There are quite a lot papers discussing it. I think you can try to set a reference structure or set high restrain in refinement, which should be easily achieved in Phenix. How did you know the B-factors are too

Re: [ccp4bb] From non-twinned to twinned?

domains are collected. The same applies if you apply translations at the crystal (to collect data from fresh crystal regions to decrease the radiation damage effect). Hope it helps, cheers, Carlos Zhiyi Wei wrote: Thank you for all the quick reply. Here are the additional information about

[ccp4bb] From non-twinned to twinned?

Dear all, I recently collected a dataset (~2000 frames) from a single crystal. If merge first 600 frames (sca1) or last 600 frames (sca2), Rmerge values from scalepack seem to be ok (~10%) though rejection ratios are high (~5%). But if I merge all frames together, Rmerge value goes up to ~20% and

Re: [ccp4bb] From non-twinned to twinned?

+0800, Zhiyi Wei wrote: Dear all, I recently collected a dataset (~2000 frames) from a single crystal. If merge first 600 frames (sca1) or last 600 frames (sca2), Rmerge values from scalepack seem to be ok (~10%) though rejection ratios are high (~5%). But if I merge all frames together, Rmerge

[ccp4bb] Local refinement strategy

Dear all, I am trying to refine a structure with two domains. The electron density of one domain is reasonable, but that of the other domain is poor. So, I am wondering whether the refinement by Phenix or Refmac can be done locally with two parts, the first domain is refined with normal

[ccp4bb] Change cell parameter

Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi

Re: [ccp4bb] Change cell parameter

! Zhiyi On Wed, Jun 8, 2011 at 11:20 AM, Clemens Vonrhein vonrh...@globalphasing.com wrote: Hi, try  reindex hklin in.mtz hklout out.mtz e  REIN HKL -h,-k,l  END  e Cheers Clemens On Wed, Jun 08, 2011 at 11:14:03AM -0400, Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset

[ccp4bb] Off topic: Bruker Microstar

Dear all, Our group plan to buy a X-ray diffraction system. We found Bruker provide a new X-ray generator called Microstar, which they claim is better than traditional rotating anode tube. Because we did not use Microstar before, we do not know whether this new generator is indeed good choice in

Re: [ccp4bb] Crystal rescue

but diffraction pattern is similar. On Tue, Jan 26, 2010 at 10:42 AM, Zhiyi Wei ustcwebri...@gmail.com wrote: Dear all, I got a problem with my crystals. I have two total different proteins that both can be crystallized in the condition with PEG3350 and Tacsimate (although the concentrations are different

Re: [ccp4bb] Crystal rescue

of different compounds - but the smears are too close together to be a small salt crystal on top... Good luck, Ezra On 1/26/2010 10:42 AM, Zhiyi Wei wrote: Dear all, I got a problem with my crystals. I have two total different proteins that both can be crystallized in the condition with PEG3350