Number of atoms and average b-factors for specific chain IDs (with the option of specifying multiple chain IDs).
Is there anyway to get this quickly? Either by phenix util, web util, or whatever? Thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Francis, What about Baverage in CCP4i or you can use 'act' (CCP4 supported program for analysing co-ordinates), I believe it is not in ccp4 GUI. And Moleman (Uppsalla SF software). On 12 Mar 2010, at 16:43, Francis E Reyes wrote:
Is there anyway to get this quickly? Either by phenix util, web util, or whatever?
Thanks! FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
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8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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Vinothkumar K.R. Structural Studies Division MRC-Laboratory of Molecular Biology Hills Road, Cambridge. CB2 0QH Tel: 44-1223-402405
Is there anyway to get this quickly? Either by phenix util, web util, or whatever?
Number of atoms is easy: phenix.pdb_atom_selection your.pdb 'chain A or chain B' For the average B-factor you'll have to go to Python: import iotbx.pdb from cctbx.array_family import flex import sys pdb_inp = iotbx.pdb.input(file_name=sys.argv[1]) hierarchy = pdb_inp.construct_hierarchy() sel = hierarchy.atom_selection_cache().selection("chain A or chain B") print "number of atoms:", sel.count(True) print "mean b:", flex.mean(hierarchy.select(sel).atoms().extract_b()) Save to a file and run with "phenix.python". Ralf
While I realize this is not a Phenix solution and this is a Phenix bb I have to suggest: You could just import your coordinates into a spreadsheet and ask for the number of rows and the average of the B factor column. On the other hand, I've never understood why the PDB requires us to enter information that they could easily calculate from the model for themselves... Dale Tronrud Ralf W. Grosse-Kunstleve wrote:
Is there anyway to get this quickly? Either by phenix util, web util, or whatever?
Number of atoms is easy:
phenix.pdb_atom_selection your.pdb 'chain A or chain B'
For the average B-factor you'll have to go to Python:
import iotbx.pdb from cctbx.array_family import flex import sys pdb_inp = iotbx.pdb.input(file_name=sys.argv[1]) hierarchy = pdb_inp.construct_hierarchy() sel = hierarchy.atom_selection_cache().selection("chain A or chain B") print "number of atoms:", sel.count(True) print "mean b:", flex.mean(hierarchy.select(sel).atoms().extract_b())
Save to a file and run with "phenix.python".
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
It's for NSMB, they actually ask for this stuff in their table 1 x-ray template. FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D On Mar 13, 2010, at 12:26 PM, [email protected] wrote:
While I realize this is not a Phenix solution and this is a Phenix bb I have to suggest: You could just import your coordinates into a spreadsheet and ask for the number of rows and the average of the B factor column.
On the other hand, I've never understood why the PDB requires us to enter information that they could easily calculate from the model for themselves...
Dale Tronrud
Ralf W. Grosse-Kunstleve wrote:
Is there anyway to get this quickly? Either by phenix util, web util, or whatever? Number of atoms is easy: phenix.pdb_atom_selection your.pdb 'chain A or chain B' For the average B-factor you'll have to go to Python: import iotbx.pdb from cctbx.array_family import flex import sys pdb_inp = iotbx.pdb.input(file_name=sys.argv[1]) hierarchy = pdb_inp.construct_hierarchy() sel = hierarchy.atom_selection_cache().selection("chain A or chain B") print "number of atoms:", sel.count(True) print "mean b:", flex.mean(hierarchy.select(sel).atoms().extract_b()) Save to a file and run with "phenix.python". Ralf
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Hi,
I will add it to phenix.model_vs_data tool once I get a chance sometime next week.
Pavel.
----- Original Message -----
From: "Ralf W. Grosse-Kunstleve"
Is there anyway to get this quickly? Either by phenix util, web util, or whatever?
Number of atoms is easy:
phenix.pdb_atom_selection your.pdb 'chain A or chain B'
For the average B-factor you'll have to go to Python:
import iotbx.pdb from cctbx.array_family import flex import sys pdb_inp = iotbx.pdb.input(file_name=sys.argv[1]) hierarchy = pdb_inp.construct_hierarchy() sel = hierarchy.atom_selection_cache().selection("chain A or chain B") print "number of atoms:", sel.count(True) print "mean b:", flex.mean(hierarchy.select(sel).atoms().extract_b())
Save to a file and run with "phenix.python".
Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi, phenix.pdbtools model.pdb keep="chain A" output.file_name="chain_A.pdb" phenix.pdbtools chain_A.pdb --show-adp-statistics If you have too many chain you cna compose a trivial script too loop over chain IDs and repeat the two above commands for each of them. As I replied before, I'll probably add something like this to PHENIX tools. Pavel. On 3/12/10 8:43 AM, Francis E Reyes wrote:
Is there anyway to get this quickly? Either by phenix util, web util, or whatever?
Thanks! FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
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participants (5)
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det102＠uoxray.uoregon.edu -
Francis E Reyes -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
vinothkumar