Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

2017-06-21 Thread Robert Campbell 
Hi Leila,

You need the "CRYST1" line from the template pdb file.  That is where PyMOL 
gets the symmetry information from.

Cheers,
Rob

On Wed, 2017-06-21 09:29  +0200,  leila karami  wrote:

> Dear PYMOL users,
> 
> I have done a homology modelling using swiss model. Template pdb file
> contain 3 chains (A, B, C). I used only chain A for homology
> modelling as template.
> 
> There is a symmetry operator in template pdb file (temp.pdb). I want
> to use symexp to obtain dimeric structure for modeled pdb file
> (model.pdb).
> 
> I manually added following records (from temp.pdb) at the first of the
> modeled pdb file:
> ===
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
> REMARK 290
> REMARK 290  SYMOP   SYMMETRY
> REMARK 290 NNNMMM   OPERATOR
> REMARK 290   1555   X,Y,Z
> REMARK 290   2555   -X,Y,-Z
> REMARK 290   3555   X+1/2,Y+1/2,Z
> REMARK 290   4555   -X+1/2,Y+1/2,-Z
> REMARK 290
> REMARK 290 WHERE NNN -> OPERATOR NUMBER
> REMARK 290   MMM -> TRANSLATION VECTOR
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED MOLECULES.
> REMARK 290   SMTRY1   1  1.00  0.00  0.000.0
> REMARK 290   SMTRY2   1  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   1  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   2 -1.00  0.00  0.000.0
> REMARK 290   SMTRY2   2  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   2  0.00  0.00 -1.000.0
> REMARK 290   SMTRY1   3  1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   3  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   3  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   4 -1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   4  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   4  0.00  0.00 -1.000.0
> REMARK 290
> CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1  12
> ORIGX1  1.00  0.00  0.000.0
> ORIGX2  0.00  1.00  0.000.0
> ORIGX3  0.00  0.00  1.000.0
> SCALE1  0.005619  0.00  0.0028110.0
> SCALE2  0.00  0.017671  0.000.0
> SCALE3  0.00  0.00  0.0134360.0
> 
> ===
> 
> After using symexp sym,model,(model),1 in command line, I encountered
> with:
> 
> ExecutivesSymexp-Error: No Symmetry loaded!
> 
> temp.pdb and model.pdb files are in following links:
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D=0
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D=0
> 
> Any help will be highly appreciated.
> 
> Best,
> Leila




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

--
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Re: [PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

2017-06-21 Thread Robert Campbell 
Hi Leila,

I responded too quickly without reading carefully!  Adding those lines should 
have worked (but only the CRYST1 line is needed).  Your model.pdb file that you 
linked to on Dropbox does not have the CRYST1 line.  Adding that line works for 
me.

Cheers,
Rob

On Wed, 2017-06-21 09:29  +0200,  leila karami  wrote:

> Dear PYMOL users,
> 
> I have done a homology modelling using swiss model. Template pdb file
> contain 3 chains (A, B, C). I used only chain A for homology
> modelling as template.
> 
> There is a symmetry operator in template pdb file (temp.pdb). I want
> to use symexp to obtain dimeric structure for modeled pdb file
> (model.pdb).
> 
> I manually added following records (from temp.pdb) at the first of the
> modeled pdb file:
> ===
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
> REMARK 290
> REMARK 290  SYMOP   SYMMETRY
> REMARK 290 NNNMMM   OPERATOR
> REMARK 290   1555   X,Y,Z
> REMARK 290   2555   -X,Y,-Z
> REMARK 290   3555   X+1/2,Y+1/2,Z
> REMARK 290   4555   -X+1/2,Y+1/2,-Z
> REMARK 290
> REMARK 290 WHERE NNN -> OPERATOR NUMBER
> REMARK 290   MMM -> TRANSLATION VECTOR
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED MOLECULES.
> REMARK 290   SMTRY1   1  1.00  0.00  0.000.0
> REMARK 290   SMTRY2   1  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   1  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   2 -1.00  0.00  0.000.0
> REMARK 290   SMTRY2   2  0.00  1.00  0.000.0
> REMARK 290   SMTRY3   2  0.00  0.00 -1.000.0
> REMARK 290   SMTRY1   3  1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   3  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   3  0.00  0.00  1.000.0
> REMARK 290   SMTRY1   4 -1.00  0.00  0.00   88.99000
> REMARK 290   SMTRY2   4  0.00  1.00  0.00   28.29500
> REMARK 290   SMTRY3   4  0.00  0.00 -1.000.0
> REMARK 290
> CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1  12
> ORIGX1  1.00  0.00  0.000.0
> ORIGX2  0.00  1.00  0.000.0
> ORIGX3  0.00  0.00  1.000.0
> SCALE1  0.005619  0.00  0.0028110.0
> SCALE2  0.00  0.017671  0.000.0
> SCALE3  0.00  0.00  0.0134360.0
> 
> ===
> 
> After using symexp sym,model,(model),1 in command line, I encountered
> with:
> 
> ExecutivesSymexp-Error: No Symmetry loaded!
> 
> temp.pdb and model.pdb files are in following links:
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D=0
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D=0
> 
> Any help will be highly appreciated.
> 
> Best,
> Leila




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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[PyMOL] ExecutivesSymexp-Error: No Symmetry loaded!

2017-06-21 Thread leila karami 
Dear PYMOL users,

I have done a homology modelling using swiss model. Template pdb file
contain 3 chains (A, B, C). I used only chain A for homology modelling as
template.

There is a symmetry operator in template pdb file (temp.pdb). I want to use
symexp to obtain dimeric structure for modeled pdb file (model.pdb).

I manually added following records (from temp.pdb) at the first of the
modeled pdb file:
===
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290  SYMOP   SYMMETRY
REMARK 290 NNNMMM   OPERATOR
REMARK 290   1555   X,Y,Z
REMARK 290   2555   -X,Y,-Z
REMARK 290   3555   X+1/2,Y+1/2,Z
REMARK 290   4555   -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290   MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.00  0.00  0.000.0
REMARK 290   SMTRY2   1  0.00  1.00  0.000.0
REMARK 290   SMTRY3   1  0.00  0.00  1.000.0
REMARK 290   SMTRY1   2 -1.00  0.00  0.000.0
REMARK 290   SMTRY2   2  0.00  1.00  0.000.0
REMARK 290   SMTRY3   2  0.00  0.00 -1.000.0
REMARK 290   SMTRY1   3  1.00  0.00  0.00   88.99000
REMARK 290   SMTRY2   3  0.00  1.00  0.00   28.29500
REMARK 290   SMTRY3   3  0.00  0.00  1.000.0
REMARK 290   SMTRY1   4 -1.00  0.00  0.00   88.99000
REMARK 290   SMTRY2   4  0.00  1.00  0.00   28.29500
REMARK 290   SMTRY3   4  0.00  0.00 -1.000.0
REMARK 290
CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1  12
ORIGX1  1.00  0.00  0.000.0
ORIGX2  0.00  1.00  0.000.0
ORIGX3  0.00  0.00  1.000.0
SCALE1  0.005619  0.00  0.0028110.0
SCALE2  0.00  0.017671  0.000.0
SCALE3  0.00  0.00  0.0134360.0

===

After using symexp sym,model,(model),1 in command line, I encountered with:

ExecutivesSymexp-Error: No Symmetry loaded!

temp.pdb and model.pdb files are in following links:

https://www.dropbox.com/s/t8m1nrkx2s69wi9/model.pdb?dl=0

https://www.dropbox.com/s/mt7toc0wtenr779/temp.pdb?dl=0

Any help will be highly appreciated.

Best,
Leila
--
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