Hi Christian, Thanks for letting me know about this over-use of memory in phenix CombineFocusedMap that crashed your computer!. I found the problem and fixed it today, so starting with tomorrow's Phenix nightly build which will appear here when ready: https://phenix-online.org/download/phenix/nightly/?version=dev-5550 the CombineFocusedMap tool should work with large models and large maps, even if rigid-body refinement is done on each chain with the keyword rigid_body_refinement_single_unit=False (as is default). Let me know if this does not do it! All the best, Tom T On Tue, Dec 17, 2024 at 2:24 PM Christian Steinmetzger < [email protected]> wrote:
Hi Tom,
I trimmed the maps down from it's original size of 576 x 576 x 576 to 297 x 322 x 355 using "phenix.map_box model.cif map1.mrc "
and then submitted the resulting output model_box.cif, map1_box.ccp4 and map2_box.ccp4 to combine_focused_maps, but still got the same memory issue on the rigid-body refinement step. I monitored the job for a while and the python process had reached more than 90 GB memory use when I checked. My workstation has 128 GB RAM in total. I'm sending the full terminal output of the job below.
Nigel, I also encountered another issue with using elbow for restraint generation. For 4OC and UR3, the command phenix.elbow --chemical_component="$RES" --final_geometry="$RES" doesn't produce a cif file because it encounters an unusually long P-O bond in the phosphate group, ~150 or 182 Å respectively. A pdb file is still saved and there atom OP3 is clearly in a very odd position.
------------------------------------------------------------------------------------------------ Here is the terminal output from combine_focused_maps:
Starting job
=============================================================================== Validating inputs
************************************************************ PHENIX combine_focused_maps Tue Dec 17 18:27:58 2024 ************************************************************
Working directory: /home/csteinmetzger/workdir/maps_composite
PHENIX VERSION: dev-5533
Reading input data
Removed 1 residues with missing CA/P atoms Model with 10208 residues read from /home/csteinmetzger/workdir/model_box.cif
Map file read from /home/csteinmetzger/workdir/map1_box.ccp4 header_min: -0.215969517827 header_max: 0.890450239182 header_mean: 0.00580687774345 header_rms: 0.0463103465736
Information about FULL UNIT CELL: unit cell grid: (576, 576, 576) unit cell parameters: (436.32000732421875, 436.32000732421875, 436.32000732421875, 90.0, 90.0, 90.0) space group number: 1
Information about the PART OF MAP THAT IS PRESENT: map cell grid: (297, 322, 355) map cell parameters: (224.9775037765503, 243.91500409444174, 268.9125045140584, 90.0, 90.0, 90.0) map origin: (131, 125, 110) pixel size: (0.7575, 0.7575, 0.7575) Shift (grid units) to place origin at original position: (0, 0, 0) Wrapping (using unit_cell_translations to get map values) allowed: False
Map file read from /home/csteinmetzger/workdir/map2_box.ccp4 header_min: -0.172103002667 header_max: 0.68276655674 header_mean: 0.0004433694412 header_rms: 0.0258353501558
Information about FULL UNIT CELL: unit cell grid: (576, 576, 576) unit cell parameters: (436.32000732421875, 436.32000732421875, 436.32000732421875, 90.0, 90.0, 90.0) space group number: 1
Information about the PART OF MAP THAT IS PRESENT: map cell grid: (297, 322, 355) map cell parameters: (224.9775037765503, 243.91500409444174, 268.9125045140584, 90.0, 90.0, 90.0) map origin: (131, 125, 110) pixel size: (0.7575, 0.7575, 0.7575) Shift (grid units) to place origin at original position: (0, 0, 0) Wrapping (using unit_cell_translations to get map values) allowed: False
Input maps and matching models:
Map 1: /home/csteinmetzger/workdir/map1_box.ccp4 Model 1: /home/csteinmetzger/workdir/model_box.cif
Map 2: /home/csteinmetzger/workdir/map2_box.ccp4 Model 2: /home/csteinmetzger/workdir/model_box.cif
Normalizing maps (mean=0 sd=1) before use
Running rigid body refinement on each model and map Refining each chain of a molecule as a single unit Refining model 1 with rigid_body refinement Killed _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010