phenix refine

sbiswas2＠ncsu.edu

11 Jun 2009 11 Jun '09

3:56 p.m.

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42 Does anyone know how to resolve this thanks, Shya

Show replies by date

Pavel Afonine

11 Jun 11 Jun

4:06 p.m.

Hi Shya, - use phenix.ready_set: phenix.ready_set model.pdb The above command will produce a CIF file that you can use when running phenix.refine: phenix.refine model.pdb data.mtz file_name.cif - it is a good idea to make sure that your PDB file contains element type in column 77 (or 78 - I forgot exactly, check it). Pavel. On 6/11/09 8:56 AM, [email protected] wrote:

...

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Folmer Fredslund

4:06 p.m.

Dear Shya 2009/6/11 :

...

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "

First of all, glycerol should be called GOL not GLC. Do you mean glucose ?

...

... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya

You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/) Best regards, Folmer Fredslund

...

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

sbiswas2＠ncsu.edu

9:35 p.m.

Hi Folmer and Pavel, Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb file so I ran elbow which gave me the cif file as the output and this runs and refines fine now (just to let everyone know). Folmer, the molecule was glycerol and not glucose anyway the problem was the cif file which I could easily generate in elbow. Thanks Shya

...

Dear Shya

2009/6/11 :

...
Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "

First of all, glycerol should be called GOL not GLC. Do you mean glucose ?

...
... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya

You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/)

Best regards,

Folmer Fredslund

...
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Folmer Fredslund

12 Jun 12 Jun

6:42 a.m.

Dear Shya, So did you rename your glycerol? You have to do that. See http://xray.bmc.uu.se/hicup/GOL/ and http://xray.bmc.uu.se/hicup/GLC/ Best regards, Folmer Fredslund 2009/6/11 :

...

Hi Folmer and Pavel, Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb file so I ran elbow which gave me the cif file as the output and this runs and refines fine now (just to let everyone know). Folmer, the molecule was glycerol and not glucose anyway the problem was the cif file which I could easily generate in elbow. Thanks Shya

...
Dear Shya

2009/6/11 :

...
Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "

First of all, glycerol should be called GOL not GLC. Do you mean glucose ?

...
... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya

You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/)

Best regards,

Folmer Fredslund

...
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

sbiswas2＠ncsu.edu

12:55 p.m.

Hi, This was not necessary it just ran fine with the cif file. thanks, shya

...

Dear Shya,

So did you rename your glycerol? You have to do that. See http://xray.bmc.uu.se/hicup/GOL/ and http://xray.bmc.uu.se/hicup/GLC/

Best regards, Folmer Fredslund

2009/6/11 :

...
Hi Folmer and Pavel, Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb file so I ran elbow which gave me the cif file as the output and this runs and refines fine now (just to let everyone know). Folmer, the molecule was glycerol and not glucose anyway the problem was the cif file which I could easily generate in elbow. Thanks Shya

...
Dear Shya

2009/6/11 :

...
Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "

First of all, glycerol should be called GOL not GLC. Do you mean glucose ?

...
... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya

You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/)

Best regards,

Folmer Fredslund

...
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Bjørn Panyella Pedersen

1:27 p.m.

Dear Shya I think what Folmer means is that before you publish your pdb-file, you should rename the gycerol atoms to GOL, as that is the correct name (just as you wouldn't publish a pdb-file where you have named all ALA atoms as MET for instance ;)). Best of luck -Bjørn [email protected] wrote:

...

Hi, This was not necessary it just ran fine with the cif file. thanks, shya

...
Dear Shya,

So did you rename your glycerol? You have to do that. See http://xray.bmc.uu.se/hicup/GOL/ and http://xray.bmc.uu.se/hicup/GLC/

Best regards, Folmer Fredslund

-- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: [email protected] http://www.bioxray.au.dk

Engin Ozkan

2:47 p.m.

But you still have to rename your glycerol. Otherwise, we may not be able to interpret your pdb correctly when you finally publish it. Please always check from HICUP or CCP4 monomer library for the naming (and you can get cif files from there, too). Engin On 6/12/09 5:55 AM, [email protected] wrote:

...

Hi, This was not necessary it just ran fine with the cif file. thanks, shya

...
Dear Shya,

So did you rename your glycerol? You have to do that. See http://xray.bmc.uu.se/hicup/GOL/ and http://xray.bmc.uu.se/hicup/GLC/

Best regards, Folmer Fredslund

2009/6/11:

...
Hi Folmer and Pavel, Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb file so I ran elbow which gave me the cif file as the output and this runs and refines fine now (just to let everyone know). Folmer, the molecule was glycerol and not glucose anyway the problem was the cif file which I could easily generate in elbow. Thanks Shya

...
Dear Shya

2009/6/11:

...
Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "

First of all, glycerol should be called GOL not GLC. Do you mean glucose ?

...
... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya

You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/)

Best regards,

Folmer Fredslund

...
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Pavel Afonine

3:57 p.m.

I absolutely agree with those suggesting to rename it. Glycerol is a standard item from the monomer library, therefore if it is named correctly in PDB file then there is no need to run elbow and create a CIF file - phenix.refine will recognize it just fine. If phenix.refine chocks on it then it means there is something wrong with the names and it is the best to fix it right from the beginning, rather than keep masking it. Pavel. On 6/12/09 7:47 AM, Engin Ozkan wrote:

...

But you still have to rename your glycerol. Otherwise, we may not be able to interpret your pdb correctly when you finally publish it. Please always check from HICUP or CCP4 monomer library for the naming (and you can get cif files from there, too).

Engin

On 6/12/09 5:55 AM, [email protected] wrote:

...
Hi, This was not necessary it just ran fine with the cif file. thanks, shya

...
Dear Shya,

So did you rename your glycerol? You have to do that. See http://xray.bmc.uu.se/hicup/GOL/ and http://xray.bmc.uu.se/hicup/GLC/

Best regards, Folmer Fredslund

2009/6/11 :

...
Hi Folmer and Pavel, Thanks for your suggestions. Phenix readyset gave me only .eff and .pdb file so I ran elbow which gave me the cif file as the output and this runs and refines fine now (just to let everyone know). Folmer, the molecule was glycerol and not glucose anyway the problem was the cif file which I could easily generate in elbow. Thanks Shya

...
Dear Shya

2009/6/11 :

...
Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J "

First of all, glycerol should be called GOL not GLC. Do you mean glucose ?

...
... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this thanks, Shya

You need a cif file for the extra molecule. Can be found at eg. the HICup server (http://xray.bmc.uu.se/hicup/)

Best regards,

Folmer Fredslund

...
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

------------------------------------------------------------------------

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

5513

Age (days ago)

5514

Last active (days ago)

List overview

Download

8 comments

5 participants

participants (5)

Bjørn Panyella Pedersen
Engin Ozkan
Folmer Fredslund
Pavel Afonine
sbiswas2＠ncsu.edu

phenix refine

sbiswas2＠ncsu.edu

Pavel Afonine

Folmer Fredslund

sbiswas2＠ncsu.edu

Folmer Fredslund

sbiswas2＠ncsu.edu

Bjørn Panyella Pedersen

Engin Ozkan

Pavel Afonine

tags

participants (5)