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  <[email protected]>:
    
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  <[email protected]>:
        
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