The problem hasn't been solved
Dear friends,
Can I ask how to eliminate "NUL"s when scoring PDBs? When I want to score PDB files, I have tried
1) -s /mnt/hgfs/test/name.pdb
2) -s /mnt/hgfs/test/*.pdb # for all the PDB files in the "test" folder
3) -l /mnt/hgfs/test/list.txt
Dear friends,
I am trying to use "loop_length_changing". The demonstrating file is straightforward.
rosettademos\public\AnchoredDesign\loop_length_changing
Can I ask
1) How to specify the loop file?
Hi,
Sorry for the newbie question, but I'm looking for some pdb's to practice packing methodologies on. This will be packing only to start with, not design, and I'm looking for a locked backbone, ( I've seen a function somewhere in the docs for this), and just perturbing the side chains exactly like in this video http://www.youtube.com/watch?feature=player_detailpage&v=_SDHZ-jxP4o....
Dear friends,
I am trying to use FloppyTail to determine a C-terminus tail structure of 6 consecutive His residues. However, several residues before the tail also experience conformation change though the majority is remained the same. Can I ask is there a way to only optimise the tail structure?
Dear friends,
I am trying to use the loopmodel ccd to build a loop region with missing residue positions in the original PDB file.
The whole sequence is of 228 amino acid and the missing region is 223-228.
Can I ask
1) As the loop to be built is at the end of the sequence (i.e. termini), how can I specify the loop file?
If I use "LOOP 222 228 0 0 0", I was told (ccd_1.log attached):
"core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch"
Dear friends,
I am trying to use "clustering.py" but I was told "OSError: [Errno 2] No such file or directory". Can I ask how to solve this?
I am sorry but it seems I have been asking technical questions all the time. Please tell me if there is something I can read to prepare my knowledge to debug. For example, how can I actually debug this python problem based on the error message?
Thank you very much.
Yours sincerely
Cheng
The following is the command line and prompt.
Dear all,
when I run the ab_initio Flexpepdock protocol, I got this error :src/core/fragment/ConstantLengthFragSet.cc line: 116
Can someone give me some comments?
this is my flag:
-s eq_1_0001.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-out:file:silent decoys.silent
-out:file:silent_struct_type binary
-pep_refine
-lowres_abinitio
-rep_ramp_cycles 10
-ex1
-ex2aro
-use_input_sc
-constant_seed
-jran 12456
-frag3 ../NullFragments0/output_files/frags.200.3mers
Hi Rosetta guys:)
Question about seemingly odd behaviour going from local rosetta run (rosetta_2014.16.56682_bundle) to mpi (2014.20.56383.mpi) and of course a slightly newer version of Rosetta3.5 though both are 3.5.
My normal docking scripts contains the flag
-residues:patch_selectors CENTROID_HA
this script runs smoothly.
When running on mpi I can do regular docking, but when introducing this flag (need it for SAXS runs), rosetta tells me that there is no such command on the top level.
I’m really happy with my PyRosetta prototype script, so it’s time for a production run!
But there is a problem. My nodes have 4GB of memory and 8 cores. But PyRosetta needs ~1.5GB of memory to run.