autosol output to electron density figure in pymol
Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh
Hi Shivesh, this is what I usually do: manipulate the structure in Coot and make publishable pictures in Pymol. To do this, just take the output from Autosol and run phenix.refine - it will produce the Xplor formatted maps that you can use in Pymol: % phenix.refine overall_best.pdb data.mtz where data.mtz is you data file containing Fobs, freeR flags (please do not confuse it with map coefficients file overall_best_refine_map_coeffs.mtz). By default it will produce two files (with .map extensions) one containing 2mFo-DFc and another mFo-DFc. You can also ask phenix.refine to produce any number of maps with other coefficients, for example 3Fo-2Fc, 3.3Fo-2.2Fc, etc. (for this you will need the latest version of phenix.refine currently available from CCI Apps). Cheers, Pavel. shivesh kumar wrote:
Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh
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We have datasets measured on crystals of a 19 kD protein that are P212121, with cell constants of 66, 75, 136. Matthew's considerations say 3, 4, or 5 copies per au are probable. xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in height (origin=100) No self-rotation function peaks in xprep, that I can understand. Is this clearly translational symmetry that is making MR difficult? Hints as to how to go forward are welcome. thanks, Dave -- David N. Garboczi, PhD Phone: 301-496-4773 Investigator, Structural Biology Section (SBS) Laboratory of Immunogenetics (LIG) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax: 301-402-0284 Email: [email protected]
How certain are you regarding your space group ? The native peak at almost 0 -0.5 0 is suspicious. If you used HKL for indexing try something else with multiple images separated by e.g. 15 degrees and see if you can process your dataset in a different space group. Juergen David Garboczi wrote:
We have datasets measured on crystals of a 19 kD protein that are P212121, with cell constants of 66, 75, 136.
Matthew's considerations say 3, 4, or 5 copies per au are probable.
xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in height (origin=100)
No self-rotation function peaks in xprep, that I can understand.
Is this clearly translational symmetry that is making MR difficult?
Hints as to how to go forward are welcome.
thanks,
Dave
-- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
Data was integrated with XDS, indexed on all the frames. No other choice but primitive orthorhombic, I think. I was interpreting it as two mols along the y-axis were two fold related, which made a translation between them and the next au along y. Dave
How certain are you regarding your space group ? The native peak at almost 0 -0.5 0 is suspicious. If you used HKL for indexing try something else with multiple images separated by e.g. 15 degrees and see if you can process your dataset in a different space group.
Juergen
David Garboczi wrote:
We have datasets measured on crystals of a 19 kD protein that are P212121, with cell constants of 66, 75, 136.
Matthew's considerations say 3, 4, or 5 copies per au are probable.
xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in height (origin=100)
No self-rotation function peaks in xprep, that I can understand.
Is this clearly translational symmetry that is making MR difficult?
Hints as to how to go forward are welcome.
thanks,
Dave
-- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
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-- David N. Garboczi, PhD Phone: 301-496-4773 Investigator, Structural Biology Section (SBS) Laboratory of Immunogenetics (LIG) National Institute of Allergy and Infectious Diseases (NIAID) National Institutes of Health (NIH) Twinbrook 2/Room 110 12441 Parklawn Drive Rockville, Maryland 20852-1742 Fax: 301-402-0284 Email: [email protected] The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. The National Institute of Allergy and Infectious Diseases (NIAID) shall not accept liability for any statement made that are the sender's own and not expressly made on behalf of the NIAID by one of its representatives.
participants (4)
-
David Garboczi -
Juergen Bosch -
Pavel Afonine -
shivesh kumar