Hi Enrico,
You should report bugs to chimerax-bugs, not chimerax-users.  I will open a ticket for this.

—Eric

On Nov 16, 2024, at 2:19 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:

Hello Eric !

I still have some problems with the reconstructions of the loop fragments for the structures containing ligands. I've just tested the latest ChimeraX (1.9) and the problem is still there: where I fetch a PDB with the ligand and use it SEQRES to reconstruct the missed loop it produces the error indicating the sequence mismatch. When I remove all ligands, everything is OK. 

Example 1  - no problems with loop reconstructions
open 8OU9 ( the chain C contains 5 missed residues)
sequence chain #1/C
modeller refine 1/C:1:all-missing numModels 3 fast true adjacentFlexible 1 protocol standard

Everything works OK - in spite of the presence of the ligand and ZN in the chain C



Example 2 - the similar system with ligand and ZN, which has a problem in loop reconstruction with modeller

open 6BN7 (the chain B contains a gap of 9 residues)

Here is the example I've just tested with a new pdb where the chain B contains the 9 a.a missed fragments

open 6BN7
sequence chain #1/B
modeller refine 1/B:1:230-238 numModels 3 fast true adjacentFlexible 1 protocol standard

this produces the following error

modeller refine 1/B:1:230-238 numModels 1 fast true adjacentFlexible 1 protocol standard:

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1514284 1478.793 1.444
read_te_290E> Number of residues in the alignment and pdb files are different: 1305 1178
For alignment entry: 1 6bn7_1
x (mismatch at alignment position 1179)
Alignment DMSPQKFWGLTRSALLPTIP/SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFA
PDB DMSPQKFWGLTRSALLPTIP/
Match *********************

I've tried to assosiate the sequence with the structure and it did not find any mismatches:

Disassociated 6bn7 chain B from chain B
Associated 6bn7 chain B to chain B with 0 mismatches

One I removed all ligands- everything works OK:

delete ~protein
modeller refine 1/B:1:230-238 numModels 1 fast true adjacentFlexible 1 protocol standardWebservices job id: 602MBGXI5OKGYO2Z
Modeller job (ID 602MBGXI5OKGYO2Z) finished
Computing secondary structure



What is the difference between example 1 and example 2 and why do I have problems in the second case ?

Many thanks in advance

Enrico


Il giorno mar 24 set 2024 alle ore 18:40 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Similarly, this file lacks sequence information.

On Sep 24, 2024, at 8:28 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:

to update the issue: just tried to rebuild a missed loop on another pdb contained ligand (enclosed).

Now it submits job on server but rapidly produce the following error:

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 432277 422.146 0.412
read_te_290E> Number of residues in the alignment and pdb files are different: 141 142
For alignment entry: 1 xray_apo_proc2.pdb_1
x (mismatch at alignment position 142)
Alignment HLHTWIQDNGGWDAFVELYG/ -
PDB HLHTWIQDNGGWDAFVELYG/./
Match *********************

Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.

Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 xray_apo_proc2.pdb_1

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

Il giorno mar 24 set 2024 alle ore 12:11 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Hello Eric,

Actually, this was about the small loop (displayed as dashed lines in ChimeraX), between residues Cys44 and Asn51 of the chain B.

BTW I've just tired to run loop modeling for other protein and got this error:

2024-09-24 12:08:25,607 WARNING Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7cbdc5cc6090>: Failed to establish a new connection: [Errno 111] Connection refused')': /cxservices/api/v1/chimerax/services/modeller
Error launching job: ChimeraX Web Services unavailable. Please try again soon.


Il giorno mar 24 set 2024 alle ore 01:21 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico,
When I open the structure you sent, there are no missing-structure segments in chain B.  What “small gap” are you referring to?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Sep 23, 2024, at 8:12 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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
> 

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