Modelling of missed loop fragments in multi-chain structure
Dear Chimera-X users! I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit: open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard which very slowly produces 5 models of the chain A. The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ? Many thanks in advance Enrico
Hello, How to use the Modeller tools in ChimeraX for multichain complexes is explained in the help, see the second gray box: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html> To summarize, you need a separate sequence window for each chain, with the template for that chain associated with that sequence in that window. The command would be rather complicated, so I won't try to show it here. Instead you should try using the Model Loops GUI to do this (in menu under Tools... Structure Prediction). Using the GUI tool will show the corresponding command(s) in the Log. 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 26, 2024, at 2:17 PM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:
open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which very slowly produces 5 models of the chain A.
The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?
Many thanks in advance
Enrico
Thank you very much Elaine ! Actually I've tried to follow this but modeller did not work in that case. Briefly, to be clear I need to model only one chain (A) in my complex but considering the presence of other chains in order to omit any sterical clashes between newly built residues and other chains. So having all complex loaded in chimera-X window I loaded sequence for the chain A seq chain /A and then as it was mentioned associated it to the whole complex sequence associate #1 Then I run modeller from the GUI which indicated a problem in the alignment file 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 8hti_1 Il giorno lun 26 ago 2024 alle ore 23:42 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, How to use the Modeller tools in ChimeraX for multichain complexes is explained in the help, see the second gray box: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
To summarize, you need a separate sequence window for each chain, with the template for that chain associated with that sequence in that window.
The command would be rather complicated, so I won't try to show it here. Instead you should try using the Model Loops GUI to do this (in menu under Tools... Structure Prediction). Using the GUI tool will show the corresponding command(s) in the Log.
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 26, 2024, at 2:17 PM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:
open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which very slowly produces 5 models of the chain A.
The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?
Many thanks in advance
Enrico
So it seems that I could resolve the issue in the following manner. For the system contained 4 chains I opened all sequences sequence chain /R Alignment identifier is 1/R sequence chain /B Alignment identifier is 1/B sequence chain /A Alignment identifier is 1/A sequence chain /G Alignment identifier is 1/G and then run prediction of all missed fragments for ALL 4 chains, which produced at leas the model without steric clashes. ui tool show "Model Loops" modeller refine 1/A:1:all-missing 1/B:1:all-missing 1/G:1:all-missing 1/R:1:all-missing numModels 1 fast true adjacentFlexible 1 protocol standard Il giorno mar 27 ago 2024 alle ore 09:44 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
Thank you very much Elaine !
Actually I've tried to follow this but modeller did not work in that case.
Briefly, to be clear I need to model only one chain (A) in my complex but considering the presence of other chains in order to omit any sterical clashes between newly built residues and other chains. So having all complex loaded in chimera-X window I loaded sequence for the chain A seq chain /A and then as it was mentioned associated it to the whole complex sequence associate #1
Then I run modeller from the GUI which indicated a problem in the alignment file
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 8hti_1
Il giorno lun 26 ago 2024 alle ore 23:42 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, How to use the Modeller tools in ChimeraX for multichain complexes is explained in the help, see the second gray box: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
To summarize, you need a separate sequence window for each chain, with the template for that chain associated with that sequence in that window.
The command would be rather complicated, so I won't try to show it here. Instead you should try using the Model Loops GUI to do this (in menu under Tools... Structure Prediction). Using the GUI tool will show the corresponding command(s) in the Log.
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 26, 2024, at 2:17 PM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:
open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which very slowly produces 5 models of the chain A.
The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?
Many thanks in advance
Enrico
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 Il giorno mar 27 ago 2024 alle ore 12:15 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
So it seems that I could resolve the issue in the following manner. For the system contained 4 chains I opened all sequences
sequence chain /R Alignment identifier is 1/R sequence chain /B Alignment identifier is 1/B sequence chain /A Alignment identifier is 1/A sequence chain /G Alignment identifier is 1/G
and then run prediction of all missed fragments for ALL 4 chains, which produced at leas the model without steric clashes.
ui tool show "Model Loops" modeller refine 1/A:1:all-missing 1/B:1:all-missing 1/G:1:all-missing 1/R:1:all-missing numModels 1 fast true adjacentFlexible 1 protocol standard
Il giorno mar 27 ago 2024 alle ore 09:44 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
Thank you very much Elaine !
Actually I've tried to follow this but modeller did not work in that case.
Briefly, to be clear I need to model only one chain (A) in my complex but considering the presence of other chains in order to omit any sterical clashes between newly built residues and other chains. So having all complex loaded in chimera-X window I loaded sequence for the chain A seq chain /A and then as it was mentioned associated it to the whole complex sequence associate #1
Then I run modeller from the GUI which indicated a problem in the alignment file
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 8hti_1
Il giorno lun 26 ago 2024 alle ore 23:42 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, How to use the Modeller tools in ChimeraX for multichain complexes is explained in the help, see the second gray box: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>
To summarize, you need a separate sequence window for each chain, with the template for that chain associated with that sequence in that window.
The command would be rather complicated, so I won't try to show it here. Instead you should try using the Model Loops GUI to do this (in menu under Tools... Structure Prediction). Using the GUI tool will show the corresponding command(s) in the Log.
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 26, 2024, at 2:17 PM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera-X users!
I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit:
open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard
which very slowly produces 5 models of the chain A.
The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ?
Many thanks in advance
Enrico
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
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
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
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 <mailto: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 <mailto: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 <mailto: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
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 >
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
<xray_ven_proc2.pdb>
Thank you very much, Eric ! This was the source of the problem. And actually I had to remove the ligand (although it was defined as the chain C in my pdb) to predict loops and then paste it back to the PDB containing loops. 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
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
<xray_ven_proc2.pdb>
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
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
<xray_ven_proc2.pdb>
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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 >> > >> <nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
<xray_ven_proc2.pdb>
Hi Enrico, In order to use Modeller, you have to have the full sequence of the chain, otherwise Modeller has no idea what residues to insert into the gap. Your PDB file lacks SEQRES records which would provide that sequence information. So you either need to use a PDB file that has SEQRES records or you need to open a file containing the chain's sequence, in any of the formats that ChimeraX supports. Those formats are listed here: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#sequence --Eric
On Sep 24, 2024, at 3:11 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
<nir_apo.pdb>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Elaine Meng -
Enrico Martinez -
Eric Pettersen