Hi Jo,
You have two messages and I am not sure where you are. I mentioned earlier in my reply to replace the /...* with XXX* for the template and ...* for the model in your alignment file. It seems like you're still including the '/' character, which is unnecessary at the end of the sequence and may cause problems (shifts). The '/' is necessary to break the peptide sequence in the middle of the sequence, not at the end. IF you do a dimer for example you need it there between the monomers, but NOT at the end.
In option one,
> this gives this error: > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 517 516 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
the error is real and you should look for where the problem is in the pdb file vs the alignment file. As I understand it you should have the residues coordinates in the pdb file then two ligands AMP (515) and Mg (516), and then one water molecule, which should be marked as HETATM with the number 517. If this is the way it is and the second line of the template in alignment file is:
structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00
RKQLPEPDLTFXXX*
and the XXX* is aligned with the ...* AFTER the .ini is written (see below), then you should not get this error, unless you deleted something (a residue) by mistake.
In option 2:
You MUST check the alignment file for shifts after you exe or start the Modeler_Run AND the .ini file is written. Modeler 7 is known for introducing '-' into the sequence and things get messed up. This occurs near the '/' character.
In option 3:
Everyone else can correct me, if I am wrong, but I do not see the problem with water coming up as BLK. As long as it's in the proper position in the 3D structure, it's OK. Just replace BLK with HOH manually in the pdb file. If you do the XXX aligned with ... then all HETATM including water are treated as HETATM and renamed BLK.
In option 4:
I would leave water_IO = on out. Do not assume that all the commands work perfectly right. As I mentioned above Modeler 7 has this shift issues that was not present in Modeler 6.
Best regards,
Walid Mohsen
> From: modeller_usage-request@salilab.org > Reply-To: modeller_usage@salilab.org > Date: Fri, 6 Jan 2006 04:21:40 -0800 > To: modeller_usage@salilab.org > Subject: modeller_usage Digest, Vol 5, Issue 5 > > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. modelling with water again (jo hanna) > 2. Help needed (jo hanna) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Jan 2006 00:33:28 +0000 > From: jo hanna jfhanna@gmail.com > Subject: [modeller_usage] modelling with water again > To: modeller_usage@salilab.org > Message-ID: > 4b21263d0601031633p52f2b0dbid0d1190a1301f952@mail.gmail.com > Content-Type: text/plain; charset="iso-8859-1" > > Hello > > Many thanks for the advice Walid, I have done as you have suggested and have > made some progress but still am not seeing the behaviour that I am > expecting. > > I have been using the pap format for the alignment as this has being working > better and have tried the following varied options in the top and align > files, I should also mention that in my pdb i have the exact number of > ligands(2), and single water that i would want to include in my model > > Option 1: > remove water_io command from top file, > try X for water and not w therefore at end of alignment > structure = /..W > and seqeunce = /... > > this gives this error: > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 517 516 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Option 2: > water_io = on in top file, in alignment file, structure end aligmment = /..X > seqeunce end alignment = /... > gives this error > rdabrk__291E> Sequence difference between alignment and pdb : > > STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- > 1 517 24 UNK 28 TIP3 LTF..X > check_a_337E> Structure not read in: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Option 3: > water_io = on in top file, end of alignments, strcuture = /..w seqeunce = > /... > > This combination creates a model but there is no mention in the logfile of > the BLK residues or of whether the water is accepted and in the final model > the water O is written as a BLK residue. From previoud posts i was expecting > a message in the log file re the TIP3 water and also for the model to > contain a HOH or OH2 and not a BLK. > > Option 4: > water_io = on in top file and end os alignments strcuture = /..w seqeunce = > /..w > This once agaian produces the out of range error > delete__443_> Restraints marked for deletion were removed. > Total number of restraints before, now: 51247 47550 > nselat__596E> Atom index is out of range (iatm,natm): 4033 4032 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Any help would be greatly apprecaited. > > Thanks > Jo >
Sorry. when the .ini file is written it means Modeler accepted the alignment, right or wrong, and the run will not stop for the error mentioned in your option 1.
Best regards,
Walid Mohsen
------ Forwarded Message From: <Mohsen>, Al-Walid mohsaw@chp.edu Date: Fri, 06 Jan 2006 11:54:23 -0500 To: modeller_usage@salilab.org Conversation: Ligand clues and water blues Subject: Re: Ligand clues and water blues
Hi Jo,
You have two messages and I am not sure where you are. I mentioned earlier in my reply to replace the /...* with XXX* for the template and ...* for the model in your alignment file. It seems like you're still including the '/' character, which is unnecessary at the end of the sequence and may cause problems (shifts). The '/' is necessary to break the peptide sequence in the middle of the sequence, not at the end. IF you do a dimer for example you need it there between the monomers, but NOT at the end.
In option one,
> this gives this error: > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 517 516 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
the error is real and you should look for where the problem is in the pdb file vs the alignment file. As I understand it you should have the residues coordinates in the pdb file then two ligands AMP (515) and Mg (516), and then one water molecule, which should be marked as HETATM with the number 517. If this is the way it is and the second line of the template in alignment file is:
structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00
RKQLPEPDLTFXXX*
and the XXX* is aligned with the ...* AFTER the .ini is written (see below), then you should not get this error, unless you deleted something (a residue) by mistake.
In option 2:
You MUST check the alignment file for shifts after you exe or start the Modeler_Run AND the .ini file is written. Modeler 7 is known for introducing '-' into the sequence and things get messed up. This occurs near the '/' character.
In option 3:
Everyone else can correct me, if I am wrong, but I do not see the problem with water coming up as BLK. As long as it's in the proper position in the 3D structure, it's OK. Just replace BLK with HOH manually in the pdb file. If you do the XXX aligned with ... then all HETATM including water are treated as HETATM and renamed BLK.
In option 4:
I would leave water_IO = on out. Do not assume that all the commands work perfectly right. As I mentioned above Modeler 7 has this shift issues that was not present in Modeler 6.
Best regards,
Walid Mohsen
> From: modeller_usage-request@salilab.org > Reply-To: modeller_usage@salilab.org > Date: Fri, 6 Jan 2006 04:21:40 -0800 > To: modeller_usage@salilab.org > Subject: modeller_usage Digest, Vol 5, Issue 5 > > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. modelling with water again (jo hanna) > 2. Help needed (jo hanna) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 4 Jan 2006 00:33:28 +0000 > From: jo hanna jfhanna@gmail.com > Subject: [modeller_usage] modelling with water again > To: modeller_usage@salilab.org > Message-ID: > 4b21263d0601031633p52f2b0dbid0d1190a1301f952@mail.gmail.com > Content-Type: text/plain; charset="iso-8859-1" > > Hello > > Many thanks for the advice Walid, I have done as you have suggested and have > made some progress but still am not seeing the behaviour that I am > expecting. > > I have been using the pap format for the alignment as this has being working > better and have tried the following varied options in the top and align > files, I should also mention that in my pdb i have the exact number of > ligands(2), and single water that i would want to include in my model > > Option 1: > remove water_io command from top file, > try X for water and not w therefore at end of alignment > structure = /..W > and seqeunce = /... > > this gives this error: > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 517 516 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Option 2: > water_io = on in top file, in alignment file, structure end aligmment = /..X > seqeunce end alignment = /... > gives this error > rdabrk__291E> Sequence difference between alignment and pdb : > > STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- > 1 517 24 UNK 28 TIP3 LTF..X > check_a_337E> Structure not read in: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Option 3: > water_io = on in top file, end of alignments, strcuture = /..w seqeunce = > /... > > This combination creates a model but there is no mention in the logfile of > the BLK residues or of whether the water is accepted and in the final model > the water O is written as a BLK residue. From previoud posts i was expecting > a message in the log file re the TIP3 water and also for the model to > contain a HOH or OH2 and not a BLK. > > Option 4: > water_io = on in top file and end os alignments strcuture = /..w seqeunce = > /..w > This once agaian produces the out of range error > delete__443_> Restraints marked for deletion were removed. > Total number of restraints before, now: 51247 47550 > nselat__596E> Atom index is out of range (iatm,natm): 4033 4032 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Any help would be greatly apprecaited. > > Thanks > Jo >
Mohsen, Al-Walid wrote: > You have two messages and I am not sure where you are. I mentioned earlier > in my reply to replace the /...* with XXX* for the template and ...* for the > model in your alignment file.
'X', strictly speaking, is the UNK PDB residue type, which is probably not what you want here.
> model in your alignment file. It seems like you're still including the '/' > character, which is unnecessary at the end of the sequence and may cause > problems (shifts). The '/' is necessary to break the peptide sequence in the > middle of the sequence, not at the end. IF you do a dimer for example you > need it there between the monomers, but NOT at the end.
The '/' is a chain break character, so should be used if your ligand (or water) is in a different chain to your protein (i.e. the PDB file has a TER record between them). This also instructs the Modeller optimizer not to complain if the distance between adjacent residues is too large (since if they are in different chains, they can be far apart).
> You MUST check the alignment file for shifts after you exe or start the > Modeler_Run AND the .ini file is written. Modeler 7 is known for introducing > '-' into the sequence and things get messed up. This occurs near the '/' > character.
This is not correct. Modeller has to introduce gaps into the sequence to correspond with chain breaks in aligned sequences, since the '/' character is not a real residue type, and so cannot align with anything other than a gap. Modeller 7 does indeed put the - characters in the wrong place when writing out the alignment files, but the internal representation used for modeling is correct. (Modeller 6 did not have this problem, because it did not handle multi-chain sequences properly anyway. But you shouldn't be using Modeller 7 - use Modeller 8 instead, which will read your scripts just fine, and which has this minor output bug fixed.) Neither Modeller 7 nor 8 will overwrite your original alignment file, in any case.
> Everyone else can correct me, if I am wrong, but I do not see the problem > with water coming up as BLK. As long as it's in the proper position in the > 3D structure, it's OK. Just replace BLK with HOH manually in the pdb file. > If you do the XXX aligned with ... then all HETATM including water are > treated as HETATM and renamed BLK.
The difference is a minor one; BLK residues are treated as rigid bodies, and are not modeled by the energy function (although simple harmonic distance restraints are used to keep them near approximately the same set of residues as in the template). Water residues are treated in the same way as ordinary amino acids, although by default Modeller does not model hydrogen atoms, so each water will be represented simply by the O atom.
> I would leave water_IO = on out. Do not assume that all the commands work > perfectly right. As I mentioned above Modeler 7 has this shift issues that > was not present in Modeler 6.
I am not aware of any release of Modeller which does something incorrect with water_io. It simply instructs the code to read any residue from the PDB which matches the water types defined in modlib/restyp.lib (i.e. HOH, H2O, OH2, MOH, and WAT).
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Mohsen, Al-Walid