Hey Phenix team, I am trying to get real space correlation measurements for 1eao and ran into a problem. $ phenix.fetch_pdb --mtz 1eao $ phenix.real_space_correlation 1eao.pdb 1eao.mtz Multiple equally suitable arrays of observed xray data found. Possible choices: 1eao.mtz:FOBS,SIGFOBS 1eao.mtz:F(+),SIGF(+),F(-),SIGF(-) Please use .labels to specify an unambiguous substring of the target label. Looking in the options for phenix.real_space_correlation it is unclear how to specify the labels for the reflection file. Any assistance on this would greatly be appreciated. Thanks, Bradley -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry Please help me raise money for my ride to assist children with disabilities! http://www.ridewithoutlimits.org/site/TR?px=1166331&pg=personal&fr_id=1260&s_src=BF_emailbadge
Hi Bradley, it's a bug due to insufficient amount of tests exercising this tool. I'm working on the fix. The second bug here is that when you run phenix.fetch_pdb --mtz 1eao it outputs Model saved to /net/chevy/raid1/afonine/work/tmp/1eao.pdb Sequence saved to /net/chevy/raid1/afonine/work/tmp/1eao.fa Structure factors saved to /net/chevy/raid1/afonine/work/tmp/1eao-sf.cif while the actual output is 1eao.fa 1eao.mtz 1eao.pdb Meanwhile type phenix.model_vs_data 1eao.{pdb,mtz} comprehensive=true which will give you CC(2mFo-DFc, Fc) per atom or per residue (depending on resolution). Pavel On 8/20/12 11:42 AM, Bradley Hintze wrote:
Hey Phenix team,
I am trying to get real space correlation measurements for 1eao and ran into a problem.
$ phenix.fetch_pdb --mtz 1eao $ phenix.real_space_correlation 1eao.pdb 1eao.mtz
Multiple equally suitable arrays of observed xray data found.
Possible choices: 1eao.mtz:FOBS,SIGFOBS 1eao.mtz:F(+),SIGF(+),F(-),SIGF(-)
Please use .labels to specify an unambiguous substring of the target label.
Looking in the options for phenix.real_space_correlation it is unclear how to specify the labels for the reflection file. Any assistance on this would greatly be appreciated.
Thanks, Bradley
-- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry
Please help me raise money for my ride to assist children with disabilities! http://www.ridewithoutlimits.org/site/TR?px=1166331&pg=personal&fr_id=1260&s_src=BF_emailbadge
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Hi Pavel, When does it write CC per atom vs per residue? Can you please elaborate? Is there a way to tell the program to write CC one way or the other? Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 08/21/2012 09:18 AM, Pavel Afonine wrote:
phenix.model_vs_data 1eao.{pdb,mtz} comprehensive=true
which will give you CC(2mFo-DFc, Fc) per atom or per residue (depending on resolution).
Hi Abhinav,
When does it write CC per atom vs per residue? Can you please elaborate?
it's resolution dependent. Say you are looking at ARG (or something similar with long side chain), which has a few atoms sticking out of density, while the other atoms are well placed into density. Then if you compute CC for the whole residue it will still be high enough to mislead you thinking that everything is all right with this residue. However, if you compute CC per atom it will immediately red-flag these few atoms that are not in density. Computing CC per atom actually makes only sense if density shows you atoms, that is the data resolution is high enough. For example, you would not want to compute CC per atom at resolutions like 3A or so.
Is there a way to tell the program to write CC one way or the other?
phenix.real_space_correlation allows more fine tuning. In particular it allows you to specify whether to output CC per atom or per residue. Pavel
Thanks Pavel. Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 08/21/2012 09:48 AM, Pavel Afonine wrote:
Hi Abhinav,
When does it write CC per atom vs per residue? Can you please elaborate?
it's resolution dependent.
Say you are looking at ARG (or something similar with long side chain), which has a few atoms sticking out of density, while the other atoms are well placed into density. Then if you compute CC for the whole residue it will still be high enough to mislead you thinking that everything is all right with this residue. However, if you compute CC per atom it will immediately red-flag these few atoms that are not in density.
Computing CC per atom actually makes only sense if density shows you atoms, that is the data resolution is high enough. For example, you would not want to compute CC per atom at resolutions like 3A or so.
Is there a way to tell the program to write CC one way or the other?
phenix.real_space_correlation allows more fine tuning. In particular it allows you to specify whether to output CC per atom or per residue.
Pavel
Hi, the problem is fixed. You can get it now from svn or next nightly build will have it. Also, I changed (hopefully improved and simplified the interface). To illustrate, here are a few examples: - compute map CC and 2mFo-DFc and mFo-DFc density values: -- overall and per residue or per atom (programs makes the choice): phenix.real_space_correlation m.pdb d.mtz -- overall and per atom: phenix.real_space_correlation m.pdb d.mtz detail=atom -- overall and per residue: phenix.real_space_correlation m.pdb d.mtz detail=residue -- you can specify which data from input file to use: phenix.real_space_correlation m.pdb d.mtz data_labels=FOBS -- you can choose to use neutron scattering table: phenix.real_space_correlation m.pdb d.mtz scattering_table=neutron -- force program to show cc and map values for H atoms (decision is made automatically otherwise): phenix.real_space_correlation m.pdb d.mtz detail=atom use_hydrogens=true -- you can specify maps to use, for example: phenix.real_space_correlation m.pdb d.mtz map_1.type=Fc map_2.type="2mFo-DFc" phenix.real_space_correlation m.pdb d.mtz map_1.type="12Fo - 9.75Fcalc" map_2.type="2mFo-DFc" Pavel On 8/20/12 11:42 AM, Bradley Hintze wrote:
Hey Phenix team,
I am trying to get real space correlation measurements for 1eao and ran into a problem.
$ phenix.fetch_pdb --mtz 1eao $ phenix.real_space_correlation 1eao.pdb 1eao.mtz
Multiple equally suitable arrays of observed xray data found.
Possible choices: 1eao.mtz:FOBS,SIGFOBS 1eao.mtz:F(+),SIGF(+),F(-),SIGF(-)
Please use .labels to specify an unambiguous substring of the target label.
Looking in the options for phenix.real_space_correlation it is unclear how to specify the labels for the reflection file. Any assistance on this would greatly be appreciated.
Thanks, Bradley
participants (3)
-
Abhinav Kumar -
Bradley Hintze -
Pavel Afonine