On 1/6/06, modeller_usage-request@salilab.org < modeller_usage-request@salilab.org> wrote:

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Today's Topics:

   1. FW: Ligand clues and water blues (correction) (Mohsen, Al-Walid)

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Message: 1
Date: Fri, 06 Jan 2006 11:59:36 -0500
From: "Mohsen, Al-Walid" <mohsaw@chp.edu>
Subject: [modeller_usage] FW: Ligand clues and water blues
        (correction)
To: <modeller_usage@salilab.org>
Message-ID: <BFE40C28.2154%mohsaw@chp.edu>
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 <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
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> ------------------------------
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> Message: 2
> Date: Fri, 6 Jan 2006 12:04:05 +0000
> From: jo hanna <jfhanna@gmail.com>
> Subject: [modeller_usage] Help needed
> To: modeller_usage@salilab.org
> Message-ID:
> <4b21263d0601060404m203dce19lae5257b5b29d1054@mail.gmail.com>
> 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
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