atom selection in phenix.pdbtools
Hi, I want to calculate the mean b-value for all atoms of a specific ligand in my structure. I tried: phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and residue 400" , but it still prints out all b-values including solvent etc. any ideas? thanks Michael
Hi Michael, this will be available as part of phenix.model_vs_data output in one of the next PHENIX versions. Currently you can do it as following: step 1: phenix.pdbtools model.pdb keep="chain A and residue 400" step 2: phenix.pdbtools --show-adp-statistic model_chainA_residue400.pdb Pavel. On 9/1/10 3:02 PM, Michael Hothorn wrote:
Hi,
I want to calculate the mean b-value for all atoms of a specific ligand in my structure. I tried:
phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and residue 400"
, but it still prints out all b-values including solvent etc.
any ideas?
thanks Michael _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
You can just do this grep 'A 400' structure.pdb | grep -v REMARK | cut -c 61-66 | awk '{s+= $1} END {print s/NR}' On Wed, 2010-09-01 at 15:02 -0700, Michael Hothorn wrote:
Hi,
I want to calculate the mean b-value for all atoms of a specific ligand in my structure. I tried:
phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and residue 400"
, but it still prints out all b-values including solvent etc.
any ideas?
thanks Michael _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Cool! That's for few of those who can solve a structure with a pencil and a sheet of paper -:) Sometimes I wish I'm 10 years older so I'm not spoiled with the technology and understand these "hieroglyphs". Thanks Ed, it's always good to know a backdoor! Pavel. On 9/1/10 6:49 PM, Ed Pozharski wrote:
You can just do this
grep 'A 400' structure.pdb | grep -v REMARK | cut -c 61-66 | awk '{s+= $1} END {print s/NR}'
On Wed, 2010-09-01 at 15:02 -0700, Michael Hothorn wrote:
Hi,
I want to calculate the mean b-value for all atoms of a specific ligand in my structure. I tried:
phenix.pdbtools --show-adp-statistic model.pdb keep="chain A and residue 400"
, but it still prints out all b-values including solvent etc.
any ideas?
thanks Michael
participants (3)
-
Ed Pozharski -
Michael Hothorn -
Pavel Afonine