autosolve density modification question
Hi, a quick question: if when running autosolve on SAD data, if I set the parameter build = false, will that disable all model building, including any model building that would be a part of the density modification process? I'm especially curious about the case if build = false, but mask_type = histograms. I am currently assuming that the histogram matching does not use model building as part of it, and would like to know if this interpretation is correct. Thanks, Scott -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
Hi Scott,
"I am currently assuming that the histogram matching does not use model building as part of it, and would like to know if this interpretation is correct.?"
Yes, that is correct. The histogram matching part of resolve density modification does not require model-building. However if you use build=true then some density modification steps will indeed use the model-based information as part of the density modification target.
All the best,
Tom T
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From: [email protected]
Hi Scott, I'm sure Tom will address the rest in more details. Just one general comment:
I am currently assuming that the histogram matching does not use model building as part of it
This is a reasonable expectation since density modification and model building are two logically separate tasks that can benefit from each other in a number of ways but do not need to be executed all together. Density modification is a process of non-linear map transformation with the purpose to impose some prior knowledge on the map and thus improve its quality. Note: no model or model building is involved into the definition! PRISM approach may brake this logic, but you were specific enough with your question by mentioning "histogram matching", so this does not really apply then. Pavel
Hi, The translation vector is large, the NCS matrices determined by phenix.simple_ncs_from_pdb do not agree with rotation and translation matrices attained using other software -this does not happen when the translation vectors are small. Is this a bug, or is it from a difference in convention? If the latter, how can one go from the phenix convention to another convention? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
Hi Reza,
This could be a difference in whether space-group symmetry is being applied in the NCS operators or not. If you do not want it to be applied, use a very large (dummy) cell in your CRYST1 PDB record. (Very recent nightly builds also have the keyword use_space_group_symmetry=False to have the same effect.)
Let me know if that doesn't help!
All the best,
Tom T
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From: [email protected]
participants (4)
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Pavel Afonine -
Reza Khayat -
Scott Horowitz -
Terwilliger, Thomas Charles