IMP-users January 2018

imp-users@salilab.org

3 participants
3 discussions

running imp with DNA sequence
by מירב בריטברד 05 Feb '18

05 Feb '18

Hi, Part of the structure that I am trying to find is a DNA sequence and not a protein. I have pdb with the DNA part, and I create a fasta file (both attached) but when I am running IMP, it's write this warning: "BuildSystem.add_state: -------- domain 0 of molecule DNA_1 represented by pdb file /cs/labs/dina/meravb/CENP_new_cross_links_and_PDB_renumbered/pdb_files/Nuc_numbering_fixed_in_map.pdb WARNING: Replacing sequence residue 1 "THR" with PDB type "DC" WARNING: Replacing sequence residue 2 "GLY" with PDB type "DT" WARNING: Replacing sequence residue 3 "CYS" with PDB type "DG" WARNING: Replacing sequence residue 4 "ALA" with PDB type "DC" WARNING: Replacing sequence residue 5 "GLY" with PDB type "DA" WARNING: Replacing sequence residue 6 "ALA" with PDB type "DG" WARNING: Replacing sequence residue 7 "THR" with PDB type "DA" WARNING: Replacing sequence residue 8 "THR" with PDB type "DT" WARNING: Replacing sequence residue 9 "CYS" with PDB type "DT"....." How can I run in imp in a way that will recognize the DNA? Thanks, Merav

2 1

IMP: moving a gaussian decorated flexible bead
by Fergal Duffy 31 Jan '18

31 Jan '18

Hi, I have noticed an odd thing when trying to shuffle flexible beads decorated with Gaussian particles. The code in IMP.pmi.tools.shuffle_configuration uses xyz=[fb.get_value(IMP.FloatKey(4)), fb.get_value(IMP.FloatKey(5)), fb.get_value(IMP.FloatKey(6))] to get the initial XYZ location of the Gaussian fb. However, this location does not return the same value as IMP.core.XYZ(fb) And it looks like IMP.core.XYZ is actually the correct location of the floppy body, leading to some odd results when shuffling based on the fb.get_value() based locations. What is the correct way to find the location of, and move, a Gaussian decorated flexible bead? Fergal Duffy Staff Scientist Center for Infectious Disease Research<http://www.cidresearch.org/> 307 Westlake Ave N, Suite 500 | Seattle, WA 98109 206.256.7435 | fergal.duffy(a)cidresearch.org<mailto:fergal.duffy@cidresearch.org>

2 1

a problem with the updated IMP
by מירב בריטברד 16 Jan '18

16 Jan '18

I install an updated IMP on my computer and try to run the modeling.py script. But when I try to open the rmf file from this run in chimera I got this message: [image: Inline image 2] What can I do in order to open the rmf file and work as usual? Thanks, Merav

2 1

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IMP-users January 2018