Re: [ccp4bb] No improvement in R-factor after Refmac.

Hi, We ran Scala program with 2 A resolution cut-off and it gave mean I / sig I value as follows Overall: 7.3 OuterShell: 2.0 InnerShell: 16.5 CC(1/2) : Overall: 0.994 OuterShell: 0.665 InnerShell: 0.997 We also tried Scala with 2.33 A resolution cut-off and the statistics are as

Re: [ccp4bb] No improvement in R-factor after Refmac.

Hi, We checked all possible space groups of orthorhombic crystal system using Scala and Pointless but the statistics show that P212121 is the possible space group. Thank You, Satya Dev On Fri, Mar 17, 2017 at 8:03 PM, Teplyakov, Alexey [JRDUS] < atepl...@its.jnj.com> wrote: > Check the space

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Pymol alignment command grammar help

The “name” means atom names, e.g. n for nitrogen (backbone), yes, you would use “name” (or n. in short) in your command. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Alex Lee Sent: Friday, March 17, 2017 2:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb]

[ccp4bb] Pymol alignment command grammar help

Dear CCP4BB members, I tried to use pymol command to align two proteins, I read the pymol wiki and I could not understand the command grammars (I am not computer major and not familiar with machine language). For example pymol wiki says as below: Furthermore, you may wish to restrict the

Re: [ccp4bb] ITC question

I recall a case of this a few years ago where it had to do with the relative concentration of the protein to the buffer/salt molecules (can't remember which anymore), which ended up being important in the binding that was observed. So it was entirely a concentration effect that caused the

Re: [ccp4bb] ITC question

Le Vendredi 17 Mars 2017 16:07 CET, Nicholas Larsen a écrit: Do you mean that the affinity from ITC is 100-fold weaker ? Which would mean that the Kd values from ITC are 100-fold larger (in the range 0.1-1 µM) ? If this is the case, it makes me think to a

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[ccp4bb] ITC question

Dear colleagues, We have a target where people have measured Kd's for ligands using radioligand binding assays. Several publications report Kd's of single digit nanomolar and we are able to reproduce that data using this assay format. When we try to do the same measurement using ITC, we generate

[ccp4bb] Positive densities map on selective residues on Coot or Pymol

Dear All, In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, but I'd like to show the density on selective residues, not on the unselected part of structure, is there a way to do it? I am using WinCoot 0.81. In addition, could Pymol do it? Thanks ahead!

Re: [ccp4bb] No improvement in R-factor after Refmac.

One way is to refine the best chain out of four, first and then generate a seperate pdb for that chain only and use molecular replacement to find the rest of the three chains. It does help with improving map to certain extent. Also delete the missing residues one by one and then run refmac to see

[ccp4bb] No improvement in R-factor after Refmac.

Dear all, I solved a structure at 2.0 A resolution with R-work and R-free values 0.25 and 0.32 respectively and I am stuck at Refmac step where there is no further reduction in R-factor. The above stated values were obtained after several rounds of manual refinement followed by refmac. There are

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