phenix.model_vs_data or something else for 'most disagreeable reflections' ?
Hi phenixer's I'm looking for a utility that'll calculate Fc given a refined model and compare it to Fo not on a global scale, but on an individual reflection scale. ShelX does this a reflection list of 'most disagreeable reflections'. Is this possible in phenix? Or another utility (besides shelx)? 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
Hi Francis, do you want to compute R-factor for each reflection? There is no specific tool for this. In PHENIX you can compute Fcalc or Fmodel: Fmodel = scale_overall * exp(-h*U_overall*ht) * (Fcalc + k_sol * exp(-B_sol*s^2) * Fmask) Also, you can get a file with all Fmodel, Fcalc, Fobs, Fmask, ... etc. (see "export_final_f_model" option in phenix.refine), and write a simple script that will do it for you. Alternatively, if you send me the data and model file, I will write for you in 5 minutes and I will add it as an option for future use. Pavel. On 2/4/10 10:55 AM, Francis E Reyes wrote:
Hi phenixer's
I'm looking for a utility that'll calculate Fc given a refined model and compare it to Fo not on a global scale, but on an individual reflection scale. ShelX does this a reflection list of 'most disagreeable reflections'.
Is this possible in phenix? Or another utility (besides shelx)?
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
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Hi Pavel, I have a ligand (ADP or ATP) that partially lost the last phosphate group. Can I refine a group occupancy for the adenosine part of the ligand separately from the phosphate groups of this ligand. If I do atomic occupancies, they diminish for the terminal phosphate groups. I can imagine that I can refine them as two superposed ligands with different numbers of phosphates, but is it possible to do just different group occupancies for parts of the ligand? Maia
Hi Maia,
I had the same situation so I can answer a little bit. May be Pavel can help much better than me though.
You can do that while adding "refine.occupancies.constrained_grouop.selection=chain ATP(name of your ATP) and resseq 1 and (name PB or name O1B or name O2B or name O3B)" fyi. check your names on your ligand.
Hopefully, this will help.
Young-Jin
----- Original Message -----
From: "Maia Cherney"
Hi Maia, yes, Young-Jin is right, you can do it in phenix.refine. Use either "refine.occupancies.constrained_grouop.selection=" or edit altloc fields in the PDB file so phenix.refine sees them as two alternatives. Let me know if you need more help with this. Pavel. On 2/10/10 8:37 AM, Maia Cherney wrote:
Hi Pavel,
I have a ligand (ADP or ATP) that partially lost the last phosphate group. Can I refine a group occupancy for the adenosine part of the ligand separately from the phosphate groups of this ligand. If I do atomic occupancies, they diminish for the terminal phosphate groups. I can imagine that I can refine them as two superposed ligands with different numbers of phosphates, but is it possible to do just different group occupancies for parts of the ligand?
Maia
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Hi, Is it possible in PHENIX to convert a cv file into an mtz file? Raja
On Feb 10, 2010, at 2:52 PM, Raja Dey wrote:
Hi, Is it possible in PHENIX to convert a cv file into an mtz file?
Yes - from the command line, phenix.reflection_file_converter, or from the GUI, phenix.reflection_file_editor (or launch 'phenix' and click the button for "Reflection file editor"). You will need some external source of symmetry information (a PDB file will work in either case). http://www.phenix-online.org/documentation/reflection_file_tools.htm http://www.phenix-online.org/documentation/reflection_file_editor.htm -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
I am sorry. By mistake I attached a png file of ~416kb to show the PHENIX GUI error. Please disregard that mail.
Raja
----- Original Message -----
From: Nathaniel Echols
On Feb 10, 2010, at 2:52 PM, Raja Dey wrote:
Hi, Is it possible in PHENIX to convert a cv file into an mtz file?
Yes - from the command line, phenix.reflection_file_converter, or from the GUI, phenix.reflection_file_editor (or launch 'phenix' and click the button for "Reflection file editor"). You will need some external source of symmetry information (a PDB file will work in either case).
http://www.phenix-online.org/documentation/reflection_file_tools.htm http://www.phenix-online.org/documentation/reflection_file_editor.htm
-Nat
-------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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I am sorry. By mistake I attached a png file of ~416kb to show the PHENIX GUI error. Please disregard that mail.
A general reminder: messages sent to the list are capped at 40kB, and anything exceeding that is held for moderator approval. This is mainly due to very small disk quotas still in effect at some institutions - we occasionally see server errors when a subscriber's account has been deactivated because he/she is over quota. The side benefit is that it helps prevent accidentally sending private data such as reflection files to the list, which also happens occasionally. There are some situations where large attachments may be appropriate (screenshots of weird structure features, for instance), and I usually approve those postings, but please try to keep file size to a minimum. (And don't attach anything you wouldn't want one of your competitors to see.) (PS. A screenshot is rarely sufficient to tell me what's breaking in the GUI - in this particular case, most of the error message was cut off. I received the automatic bug report, however.) -Nat -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (6)
-
Francis E Reyes -
Maia Cherney -
Nathaniel Echols -
Pavel Afonine -
Raja Dey -
Young-Jin Cho