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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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Xplor-nih <at> nmr.cit.nih.gov
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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



_______________________________________________
Xplor-nih mailing list
Xplor-nih <at> nmr.cit.nih.gov
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
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Charles Schwieters | 3 Mar 2012 21:46

Re: Xeasy to xplor format


Hello Mehdi--

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

Please try process2dXeasyPeakTable, and do let me know if you have
problems.

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 | 5 Mar 2012 05:33
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Re: Xeasy to xplor format

Dear Charles,

Thank you very much. I got it to work.

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" <xplor-nih <at> nmr.cit.nih.gov>
Sent: Saturday, March 3, 2012 3:46:24 PM
Subject: Re: [Xplor-nih] Xeasy to xplor format


Hello Mehdi--

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

Please try process2dXeasyPeakTable, and do let me know if you have
problems.

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



_______________________________________________
Xplor-nih mailing list
Xplor-nih <at> nmr.cit.nih.gov
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Mehdi Talebzadeh Farooji | 19 Mar 2012 19:41
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Reading PDB file

Dear Charles,
Thanks a lot for your help regarding converting inputs from XEASY to xplor.

I ran a structure calculation with PASD/MARVIN module, at the end of pass2 , when I executed the summarize_pass2.tcl script,  I faced some errors:
On the terminal there is error message:
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/local/xplor-nih-2.30/python/selectTools.py", line 699, in correctSymmetricSidechains
    d =  dihedral.Dihedral(sel0, sel1, sel2, sel3)
  File "/usr/local/xplor-nih-2.30/python/wrappers/dihedral.py", line 76, in __init__
    this = _dihedral.new_Dihedral(*args, **kwargs)
IndexError: argument 1: bad number: string segid "   A" and resid 36 and name cd must contain a single atom
PyInterp::command: error executing: >correctSymmetricSidechains()<

I also checked the summarize_pass2.tcl.out and there is error for all atoms in pdb file.
PDBTool:read: atom not found in structure: 

The script seems to working and it generates the input files for pass3, however I was wondering if you have any idea about these errors.

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" <xplor-nih <at> nmr.cit.nih.gov>
Sent: Saturday, March 3, 2012 3:46:24 PM
Subject: Re: [Xplor-nih] Xeasy to xplor format


Hello Mehdi--

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

Please try process2dXeasyPeakTable, and do let me know if you have
problems.

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



_______________________________________________
Xplor-nih mailing list
Xplor-nih <at> nmr.cit.nih.gov
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Charles Schwieters | 19 Mar 2012 22:20

Re: Reading PDB file


Hello Mehdi--

>
> I ran a structure calculation with PASD/MARVIN module, at the end of pass2 ,
> when I executed the summarize_pass2.tcl script,  I faced some errors:
> On the terminal there is error message:
> Traceback (most recent call last):
>   File "<string>", line 1, in <module>
>   File "/usr/local/xplor-nih-2.30/python/selectTools.py", line 699, in
> correctSymmetricSidechains
>     d =  dihedral.Dihedral(sel0, sel1, sel2, sel3)
>   File "/usr/local/xplor-nih-2.30/python/wrappers/dihedral.py", line 76, in
> __init__
>     this = _dihedral.new_Dihedral(*args, **kwargs)
> IndexError: argument 1: bad number: string segid "   A" and resid 36 and name
> cd must contain a single atom

I wonder if resid 36 in segid A is somehow missing some atoms? What residue
type is this?

thanks--
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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