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Mehdi Talebzadeh Farooji | 1 Mar 2012 05:16
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Re: Xeasy to xplor format

Hi Charles,

I applied the modification you mentioned in  last email, I also converted the XEASY shift list (.prot file)  to pipp by dataconverter on BMRB site, however when I run the script "initMatch TCL" there is error message:

"Missing required flag -fromHeavyatomColumnName
Neither -pot nor -shiftAssignments defined in call to recordUnfoldedPositions"

Do you have any idea what the problem would be?

Thank you very much

Mehdi

From: Charles Schwieters <charles <at> schwieters.org>
To: Mehdi Talebzadeh Farooji <mahditzf <at> yahoo.com>
Cc: "xplor-nih <at> nmr.cit.nih.gov" <xplor-nih <at> nmr.cit.nih.gov>
Sent: Tuesday, February 28, 2012 5:30:04 PM
Subject: Re: [Xplor-nih] Xeasy to xplor format


Hello Mehdi--

>
> Thank you for your reply; Actually one of output options of  SPARKY is XEASY
> format, how can I convert the xeasy format (chemical shift list and peak
> list) to the readable format by XPLOR or PASD?MARVIN facility?
>

xeasy should be directly readble by PASD. In your initMatch TCL
script, place a

package require xeasy

at the top

and then use process3dXeasyPeakTable

Shift tables must be in nmrstar or pipp format. If there is an xeasy
shift format I will gladly add that.

best regards--
Charles


--
Charles Schwieters    email:  Charles <at> Schwieters.org
                      www:    http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt



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Charles Schwieters | 1 Mar 2012 15:37

Re: Xeasy to xplor format


Hello Mehdi--

>
> I applied the modification you mentioned in  last email, I also converted the
> XEASY shift list (.prot file)  to pipp by dataconverter on BMRB site, however
> when I run the script "initMatch TCL" there is error message:
>
> "Missing required flag -fromHeavyatomColumnName
> Neither -pot nor -shiftAssignments defined in call to
> recordUnfoldedPositions"
>

These messages indicate that arguments to the function calls are
missing. If you send me your script, I think I can fix things up.

best regards--
Charles


--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt


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S.P. Skinner | 2 Mar 2012 14:08
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file generation for PRE docking with more than 6 spin labels

Dear All,

At present I have generated pdb, psf and par for PRE docking using spin 
labels in 6 positions with four orientations for each.  I have recently 
attempted to utilise the same script for generation of the above files 
for 9 spin labels.  However, when I do so I am presented with a 
parameter error, such that it cannot find a specific atom of 7th spin 
label and therefore xplor terminates.  I have not encountered this error 
before using 6 positions and all I have done is to increase the total 
number of spin labels and included the relevant mutation sites for xplor 
to read.  Is it possible that xplor cannot handle too many i.e. > 24 
spin labelled positions due to the number of coordinates being read in 
and created at one time?  I have further tried using 7 spin labels and I 
am presented with the same error. 

Many Thanks and Kind Regards

Simon Skinner

--

-- 
Simon P Skinner
Protein Chemistry Group
Leiden Institute of Chemistry, Universiteit Leiden
Phone: +31 71 527 6089 / Fax: +31 71 527 4349
E-mail : skinnersp <at> chem.leidenuniv.nl
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Charles Schwieters | 2 Mar 2012 15:53

Re: file generation for PRE docking with more than 6 spin labels


Hello Simon--
>
> At present I have generated pdb, psf and par for PRE docking using spin
> labels in 6 positions with four orientations for each.  I have recently
> attempted to utilise the same script for generation of the above files
> for 9 spin labels.  However, when I do so I am presented with a
> parameter error, such that it cannot find a specific atom of 7th spin
> label and therefore xplor terminates.  I have not encountered this error
> before using 6 positions and all I have done is to increase the total
> number of spin labels and included the relevant mutation sites for xplor
> to read.  Is it possible that xplor cannot handle too many i.e. > 24
> spin labelled positions due to the number of coordinates being read in
> and created at one time?  I have further tried using 7 spin labels and I
> am presented with the same error.
>

Please send the error output, and we should get to the bottom of this
issue quickly. I modified eginput/pre/refine/generate.py in the
Xplor-NIH distribution to generate 9 tags, and that worked just fine.

best regards--
Charles

--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt


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Mehdi Talebzadeh Farooji | 2 Mar 2012 23:11
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Re: Xeasy to xplor format

Dear Charles,

Thank you very much for your help; the initMatch3dC.tcl for the conversion of 13C peaks worked very fine, I applied the same modifications on initMatch3dN.tcl however when I tried with 15N peaks there was another error message:
"Missing required flag -namePrefix
Neither -pot or -peakList defined in call to correctUpBoundsForMethyls"

I checked the log file in the beginning it reads the peaks but it stops and gives error message:
"Neither -pot or -peakList defined in call to correctUpBoundsForMethyls
    while executing
"error "Neither -pot or -peakList defined in call to correctUpBoundsForMethyls""
    (procedure "correctUpBoundsForMethyls" line 13)
    invoked from within
"correctUpBoundsForMethyls -peakList [$pot peaks]"
    (procedure "standard3dInitMatch" line 119)
    invoked from within
"standard3dInitMatch -pot $noe \
    -fromProtonSpectralRangePPM  [list 7 10] \
    -fromHeavyatomSpectralRangePPM [list 103 132] \
    -toProtonSpectr..."

I was wondering if you have idea or if I miss something.

Thank you very much,

Mehdi
From: Charles Schwieters <charles <at> schwieters.org>
To: Mehdi Talebzadeh Farooji <mahditzf <at> yahoo.com>
Sent: Thursday, March 1, 2012 3:46:42 PM
Subject: Re: [Xplor-nih] Xeasy to xplor format


Hello Mehdi--

>
> Thank you very much for your help. I have attached files, the tcl script,
> shift list in XEASY format, shift list in pipp format and peak list in xeasy
> format.
>

It turns out there were a couple of problems in the .tcl file, and an
inconsistency in the .str file. I'm attaching revised versions of
both. I may have confused the IDs of the from/to proton ID. Please
check this. In any event, no assignments are made at this
point. Please see the output .peaks.stage1 file. Hopefully, some
simple fixes can move things along...

best regards--
Charles


--
Charles Schwieters    email:  Charles <at> Schwieters.org
                      www:    http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt



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Charles Schwieters | 2 Mar 2012 23:17

Re: Xeasy to xplor format


Hello At Fri, 2 Mar 2012 22:11:02 +0000,
Mehdi Talebzadeh Farooji wrote:
>
> Dear Charles,
>
> Thank you very much for your help; the initMatch3dC.tcl for the conversion of
> 13C peaks worked very fine, I applied the same modifications on
> initMatch3dN.tcl however when I tried with 15N peaks there was another error
> message:
> "Missing required flag -namePrefix
> Neither -pot or -peakList defined in call to correctUpBoundsForMethyls"
>
> I checked the log file in the beginning it reads the peaks but it stops and
> gives error message:
> "Neither -pot or -peakList defined in call to correctUpBoundsForMethyls
>     while executing

Did you add the
  -namePrefix 3dn
option to the call to process3dXeasyPeakTable?

Charles

--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt


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Mehdi Talebzadeh Farooji | 2 Mar 2012 23:35
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Re: Xeasy to xplor format

Thank you, I had forgot to add one of -namePrefix

All the best,

Mehdi

From: Charles Schwieters <charles <at> schwieters.org>
To: Mehdi Talebzadeh Farooji <mahditzf <at> yahoo.com>
Cc: xplor-nih <at> nmr.cit.nih.gov
Sent: Friday, March 2, 2012 5:17:55 PM
Subject: Re: [Xplor-nih] Xeasy to xplor format


Hello At Fri, 2 Mar 2012 22:11:02 +0000,
Mehdi Talebzadeh Farooji wrote:
>
> Dear Charles,
>
> Thank you very much for your help; the initMatch3dC.tcl for the conversion of
> 13C peaks worked very fine, I applied the same modifications on
> initMatch3dN.tcl however when I tried with 15N peaks there was another error
> message:
> "Missing required flag -namePrefix
> Neither -pot or -peakList defined in call to correctUpBoundsForMethyls"
>
> I checked the log file in the beginning it reads the peaks but it stops and
> gives error message:
> "Neither -pot or -peakList defined in call to correctUpBoundsForMethyls
>    while executing

Did you add the
  -namePrefix 3dn
option to the call to process3dXeasyPeakTable?

Charles

--
Charles Schwieters    email:  Charles <at> Schwieters.org
                      www:    http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt



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Mehdi Talebzadeh Farooji | 3 Mar 2012 00:11
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Re: Xeasy to xplor format

Dear Charles,

I apologize for so many emails, I was wondering if there is any tcl script for conversion of 2D spectrum.

All the best,

Mehdi

From: Charles Schwieters <charles <at> schwieters.org>
To: Mehdi Talebzadeh Farooji <mahditzf <at> yahoo.com>
Cc: xplor-nih <at> nmr.cit.nih.gov
Sent: Friday, March 2, 2012 5:17:55 PM
Subject: Re: [Xplor-nih] Xeasy to xplor format


Hello At Fri, 2 Mar 2012 22:11:02 +0000,
Mehdi Talebzadeh Farooji wrote:
>
> Dear Charles,
>
> Thank you very much for your help; the initMatch3dC.tcl for the conversion of
> 13C peaks worked very fine, I applied the same modifications on
> initMatch3dN.tcl however when I tried with 15N peaks there was another error
> message:
> "Missing required flag -namePrefix
> Neither -pot or -peakList defined in call to correctUpBoundsForMethyls"
>
> I checked the log file in the beginning it reads the peaks but it stops and
> gives error message:
> "Neither -pot or -peakList defined in call to correctUpBoundsForMethyls
>    while executing

Did you add the
  -namePrefix 3dn
option to the call to process3dXeasyPeakTable?

Charles

--
Charles Schwieters    email:  Charles <at> Schwieters.org
                      www:    http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt



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Vitaly Vostrikov | 3 Mar 2012 00:11
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"AND" logic in distance restraints

Dear Charles,

I am assembling a structure of a homopentamer using XPLOR-NIH. There are several ambiguous distance
restraints that I would like to implement, but I am not sure if it is possible to group the restraints using
"and" and "or" logic. As an example, suppose there is a residue "B" in one monomer that has an NOE contact
with either residue "A" or residue "C" of an adjacent monomer. I would like a statement something among the
lines of:

assign [((MON1 B) (MON2 A)) AND ((MON2 B) (MON3 A)) AND ... ] OR [((MON1 B) (MON2 C)) AND ((MON2 B) (MON3 C)) AND
... ]

Is this something that can be done? Or do I have to specify this for only one protomer and the symmetry
restraints will take care of the rest?

Thank you,
Vitaly
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Charles Schwieters | 3 Mar 2012 16:39

Re: "AND" logic in distance restraints


Hello Vitaly--

>
> I am assembling a structure of a homopentamer using XPLOR-NIH. There
> are several ambiguous distance restraints that I would like to
> implement, but I am not sure if it is possible to group the
> restraints using "and" and "or" logic. As an example, suppose there
> is a residue "B" in one monomer that has an NOE contact with either
> residue "A" or residue "C" of an adjacent monomer. I would like a
> statement something among the lines of:
>
> assign [((MON1 B) (MON2 A)) AND ((MON2 B) (MON3 A)) AND ... ] OR
> [((MON1 B) (MON2 C)) AND ((MON2 B) (MON3 C)) AND ... ]
>
> Is this something that can be done? Or do I have to specify this for
> only one protomer and the symmetry restraints will take care of the
> rest?

You could write a separate table for each subunit, or you can use a
single segid-less table and specify the nMono parameter using the
pot.setNMono(5)
accessor.

Of course symmetry restraints should be used as well. In your case
these are ``ncs'' and distance symmetry. These should look something
like:

from selectTools import getSegsResidues
segsResidues=getSegsResidues("name CA")
segids=sorted(segidsResidues.keys())
resids=segidsResidues[segids[0]]

from posDiffPotTools import create_PosDiffPot
ncs = PotList('ncs')
for (i,a) in enumerate(AtomSel("(not segid A) and resid %d" % resids[0])):
    segid=a.segmentName()
    ncs.append( create_PosDiffPot('ncs%d'%i,
                                  "segid A",
                                  "segid %s" % segid) )
    pass
ncs.setScale(50)
potList.append(ncs)

from distSymmTools import create_DistSymmPot, genPolyRestraints
dSymm = create_DistSymmPot('dSymm)
for (i,a) in enumerate(segids):
    j= (i+1) % len(segids)
    K= (i+2) % len(segids)
    dSymm.addRestraints(
      genPolyRestraints(resids=range(resids[0],resids[:-1]+1,5),
                        segids=(segids[i],segids[j],segids[k])))
    pass
dSymm.setScale(50)
potList.append(dSymm)

best regards--
Charles


--
Charles Schwieters     email:   Charles <at> Schwieters.org
                       www:     http://schwieters.org/cds
phone: (301) 402-4914  PGP key: http://schwieters.org/cds/pgp.txt


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