I would like to ask a question re the check.py and prosa2003 analysis of my model
In the model I am building the check.py script identifies a region int
he modeller produced alignment where the distance is greater than 8
angstroms
This region corresponds to an insertion in the sequence to be modelled which aligns with a helix region in the template.
Using prosa to assess the quality of a model built with this alignment
shows that the energy for this region is lower than that of the
template (there is a peak in the template at this region of beta sheet
of 0.7).
adjusting the alignment to remove this insertion against the region of
secondary structure, and to move it to a region of no secondary
strcuture, provides a clean check.py result but a combined energy peak
in prosa at the postion this previous insertion was which is 0.8 and
matches the template.
As I have mentioned in the template there is a helix located at this
position, In the secondary strcuture for the sequence, thetre is no
predicted helix in the corresponding region.
Could anyone please give me any thoughts on this behaviour?!
Message: 1 Date: Fri, 06 Jan 2006 11:59:36 -0500 From: "Mohsen, Al-Walid" <">> Subject: [modeller_usage] FW: Ligand clues and water blues
(correction) To: <">> Message-ID: <BFE40C28.2154%">BFE40C28.2154%> Content-Type: text/plain; charset="US-ASCII"
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 <">> Date: Fri, 06 Jan 2006 11:54:23 -0500 To: <">
> 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:
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: <">> > Reply-To: <
">> > Date: Fri, 6 Jan 2006 04:21:40 -0800 > To: <">>
> Subject: modeller_usage Digest, Vol 5, Issue 5 > > Send modeller_usage mailing list submissions to > "> > > To subscribe or unsubscribe via the World Wide Web, visit
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> 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 <">
> > Subject: [modeller_usage] modelling with water again > To: "> > Message-ID: > <">
> > 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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: >
http://salilab.org/archives/modeller_usage/attachments/20060103/993953d7/attac > hment.html > > ------------------------------ > > Message: 2 > Date: Fri, 6 Jan 2006 12:04:05 +0000
> From: jo hanna <">> > Subject: [modeller_usage] Help needed > To: ">
> Message-ID: > <">> > Content-Type: text/plain; charset="iso-8859-1"
> > Hello > > I have been trying for some time now to model with 2 ligands and 1 water > molecule and I feel that I have tried everything from the list, faq and > tutorials and not got very far.
> I have posted a number of questions to the list but can still not get this > to work, properly! > I have managed to include the ligands and the water O into my output pdb by > using the script and alignment below, however there is not recognition that
> this oxygen is a water and in the output model it is listed as BLK along > with the other ligands. From reading posts in the user list I was expecting > this water oxygen to be recognised as such, since i have used the w
> character to represent it and also HOH in the pdb file (the file has been > edited to include only the protain, ligand and water that I am wishing to > model around). I cannot type w at the end of the sequence alignment however
> as this causes modeller to fail with an out of range error. > I would really appreciate some help as I have completelty exhaused all of my > options now. > > Thanks > Jo > > top
> INCLUDE > SET ALNFILE = 'CcHh1-Bamu.pap', ALIGNMENT_FORMAT = 'PAP' > SET KNOWNS = 'Bamu' > SET SEQUENCE = 'CcHh1' > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 1 > SET HETATM_IO = on, WATER_IO = on
> CALL ROUTINE = 'model' > > end of alignment (pap format) alignment > _aln.pos 480
490
500
510 520 > Bamu RKQLPEPDLTF/..w > CcHh1 RNALPEPVIPA/... > > produce model with water included as: > >
HETATM 4032 O BLK
525 37.988 89.184 33.629 1.00
25.09 > 2SG4034 > END > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: >
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> "> > http://salilab.org/mailman/listinfo/modeller_usage > >
> End of modeller_usage Digest, Vol 5, Issue 5 > ********************************************
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