[ccp4bb] Ramachandran plot difference between Coot and Morprobity (or Phenix)

Dear all, I just notified that there is a big difference between the Ramachandran plot analysis results produced by Coot and Morprobity (or Phenix). For the structure I am working now, Phenix(Morprobity) gives out Ramachandran outliers 0.2%, favored 95.2%, whileas Coot gives out Outliers 1.24%,

Re: [ccp4bb] help me to determine ligand's b fator?

I made a simple script for this, perhaps you can edit it for your case. Just save it as baverage.sh, then run it as ./baverage.sh your.pdb. #!/bin/bash echo "--" grep '^ATOM' $1|cut -b61-66|cat |awk '{sum+=$1} END { print " Protein Average B =",sum/NR;print

Re: [ccp4bb] help me after several refmac

Dear Yuri, Could you give out the details? Such as how you found the twins? 2-Could have twinning? I recently just got done working on a structure that could be scaled in C 2 2 21 but turned out to really be an almost perfect P21 twin. (of course in monoclinic there are certain conditions for tw

Re: [ccp4bb] RNA polymerase purification

Which RNA polymerase are you working? xiaopeng - 原始邮件 - 发件人: "Appu kumar" 收件人: CCP4BB@JISCMAIL.AC.UK 发送时间: 星期五, 2011年 11 月 25日 上午 2:04:39 主题: [ccp4bb] RNA polymerase purification Hello every one, Sorry for asking off topic question, I have purified different subunit of RNA polymerase

[ccp4bb] Space group and R/Rfree value

, Xiaopeng Hu

Re: [ccp4bb] Space group and R/Rfree value

3.5, while with P212121, the Z score is high (>10). I didn't go further. The maps look just the same between the two space groups. - 原始邮件 - 发件人: "Kelly Daughtry" 收件人: "Xiaopeng Hu" 发送时间: 星期四, 2010年 12 月 02日 上午 12:05:08 主题: Re: [ccp4bb] Space group and R/Rfre

[ccp4bb] Off topic: How to identify a unknown ligand

Dear all, Sorry for this off topic question. We are working on protein/inhibitor complex structure although we can not get our inhibitors in. However, we did find a strange density at the active site, it looks really like GSH, the natural co-enzyme of thiis protein.We tried to use very simple

[ccp4bb] step refine speed of wincoot

Dear all, I found the step refine speed of wincoot is much slower than that of linux coot (with the same pc). Is it normal or I need to configure something with the wincoot? best, Xiaopeng Hu

Re: [ccp4bb] Question about TEV cleavage

Our experience is do not shake the tube during TEV cleavage,I dont know why, but it does help. xiaopeng

[ccp4bb] About NCS and inhibitors

else observed this before? Thanks for any help and suggestion! Best, Xiaopeng Hu