Dear Chimera-X users !

Just to UP this topic: Probably I found a bug during the loop refinement of thia PBD of the main protease (enclosed without any ligands or cofactors). Here the chain B consists of a small gap which I would like to restore using the modeller interphase. So in the loaded PDB I execute the following commands:

seq chain /B
ui tool show "Model Loops"
modeller refine 1/B:1:internal-missing numModels 1 fast false adjacentFlexible 1 protocol standard

and then got the following error:
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2987193 2917.181 2.849
openf___224_> Open ${MODINSTALL10v5}/modlib/omega.bin
openf___224_> Open ${MODINSTALL10v5}/modlib/omega.mdt
getdata_643_> Protein accepted: nir_apo.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 311
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 10521 10819
make_re_423_> Number of previous, current selected restraints: 10521 10508
make_re_417_> Restraint type to be calculated: chi1_dihedral

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 2987193 2917.181 2.849
openf___224_> Open ${MODINSTALL10v5}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v5}/modlib/chi1.mdt
getdata_643_> Protein accepted: nir_apo.pdb_1
getdata_289_> Proteins (all/accepted): 1 1

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3118265 3045.181 2.974
make_re_422_> Number of previous, current restraints : 10819 11075
make_re_423_> Number of previous, current selected restraints: 10508 10764
make_re_417_> Restraint type to be calculated: chi2_dihedral

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3118265 3045.181 2.974
openf___224_> Open ${MODINSTALL10v5}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v5}/modlib/chi2.mdt
getdata_643_> Protein accepted: nir_apo.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 11075 11254
make_re_423_> Number of previous, current selected restraints: 10764 10943
make_re_417_> Restraint type to be calculated: chi3_dihedral

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3118265 3045.181 2.974
openf___224_> Open ${MODINSTALL10v5}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v5}/modlib/chi3.mdt
getdata_643_> Protein accepted: nir_apo.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 11254 11319
make_re_423_> Number of previous, current selected restraints: 10943 11008
make_re_417_> Restraint type to be calculated: chi4_dihedral

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3118265 3045.181 2.974
openf___224_> Open ${MODINSTALL10v5}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v5}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: nir_apo.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 11319 11341
make_re_423_> Number of previous, current selected restraints: 11008 11030
make_re_417_> Restraint type to be calculated: DISTANCE

Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 3784373 3695.677 3.609

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4046517 3951.677 3.859
make_re_422_> Number of previous, current restraints : 11341 17568
make_re_423_> Number of previous, current selected restraints: 11030 17257
make_re_417_> Restraint type to be calculated: DISTANCE

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4570805 4463.677 4.359

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4832949 4719.677 4.609
make_re_422_> Number of previous, current restraints : 17568 23835
make_re_423_> Number of previous, current selected restraints: 17257 23524
make_re_417_> Restraint type to be calculated: DISTANCE

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5095093 4975.677 4.859
make_re_422_> Number of previous, current restraints : 23835 28835
make_re_423_> Number of previous, current selected restraints: 23524 28524
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 28835 31994
make_re_423_> Number of previous, current selected restraints: 28524 31683
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 31994 31994
make_re_423_> Number of previous, current selected restraints: 31683 31683
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 31994 31994
make_re_423_> Number of previous, current selected restraints: 31683 31683
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 31994 31994
make_re_423_> Number of previous, current selected restraints: 31683 31683
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 31994 31994
make_re_423_> Number of previous, current selected restraints: 31683 31683
0 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 31994 31994
make_re_423_> Number of previous, current selected restraints: 31683 31683
rmdupl__427_> 1782 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 31994 29901
openf___224_> Open chain_B.rsr
openf___224_> Open chain_B.rsr

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4773357 4661.481 4.552

Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5559789 5429.481 5.302
rdcsr2__307_> Number of restraints read : 29901
Number of excluded pairs read: 0
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 29901 29901
Explicitly excluded atom pairs in memory : 0
Pseudo atoms in memory : 0

No output models from Modeller; see log for Modeller text output.

Il giorno mar 27 ago 2024 alle ore 17:12 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Okay, thank you very much Elaine !

Yours sincerely

Enrico

Il giorno mar 27 ago 2024 alle ore 17:04 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Not a bug, that is the expected numbering in that situation.

If you want to renumber the residues before saving the PDB file, you can do it with the ChimeraX tool Renumber Residues or the command "renumber," see:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/renumber.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/renumber.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 27, 2024, at 7:47 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
>
> P.S. just one extra question:
>
> I noticed a small bug in the order of amino acids added by the modeller in the case where they are added in the N-terminal positions. For example, if 10 amino acids are added in the first position, they will be numbered in the sequence like -10,-9 ... 0, and than 1,2,3 (for residues that were in the original pdb).
> Do we need to use a special save command for the generated model something like:
> save test.pdb #2.1 + some specific options  ?
>
> Many thanks in advance
>
> Enrico
>