Messages

1

General discussions (Q&As) /

« on: November 06, 2006, 02:34:31 pm »

Hi, Xiang-Jun
Here is my understanding of this issue. The original PDb format did not require the specification of CONECT record for the standard amino acids and nucleic acids. The CONECT was mainly required for the non-standard residues and HETATMS.
PDBML does not have any CONECT records. Instead it would be using a Chemical Component Dictionary which records all the non standard residues (and small molecules) available in the PDB.  This dictionary contains the connect information. Description of this dictionary is available at
http://deposit.pdb.org/cc_dict_tut.html
So as I understand, based on the residue name in the PDBML file (or mmCIF), the reader would cross reference the Chemical Component Dictionary to obtain the connectivity information available in this dictionary. So the CONECT record will not be present in the pdb file in either the xml  or mmCIF format.
Thanks.
Surjit

2

General discussions (Q&As) / pdbml

« on: October 23, 2006, 10:14:14 am »

Hi, Xiang-Jun
That is great. I have checked the files with jV and they are read without any problem.
Thank you so much.
Surjit

3

General discussions (Q&As) /

« on: October 09, 2006, 10:44:28 am »

Xiang-Jun,
That would be very valuable. Thanks a lot.
Surjit

4

General discussions (Q&As) /

« on: October 06, 2006, 01:25:05 pm »

Hi Xiang-Jun
Using the pseudo-PDb format sounds like one simple option. May be you could just use %15.3f for the floats, not sure if that extra precision in %15.5f would help. But the general problem with this format would be that nost of the structure viewing programs are not going to read it.

The central portion of the PDBML format that you would be interested in is like the following for each atom.
   
      <PDBx:atom_site id="1">
         <PDBx:group_PDB>ATOM</PDBx:group_PDB>
         <PDBx:type_symbol>N</PDBx:type_symbol>
         <PDBx:label_atom_id>N</PDBx:label_atom_id>
         <PDBx:label_alt_id xsi:nil="true" />
         <PDBx:label_comp_id>GLY</PDBx:label_comp_id>
         <PDBx:label_asym_id>A</PDBx:label_asym_id>
         <PDBx:label_entity_id>1</PDBx:label_entity_id>
         <PDBx:label_seq_id>1</PDBx:label_seq_id>
         <PDBx:Cartn_x>13.603</PDBx:Cartn_x>
         <PDBx:Cartn_y>47.057</PDBx:Cartn_y>
         <PDBx:Cartn_z>32.218</PDBx:Cartn_z>
         <PDBx:occupancy>1.00</PDBx:occupancy>
         <PDBx:B_iso_or_equiv>24.40</PDBx:B_iso_or_equiv>
         <PDBx:auth_seq_id>1</PDBx:auth_seq_id>
         <PDBx:auth_comp_id>GLY</PDBx:auth_comp_id>
         <PDBx:auth_asym_id>A</PDBx:auth_asym_id>
         <PDBx:auth_atom_id>N</PDBx:auth_atom_id>
         <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
      </PDBx:atom_site>

Essentially it is the familiar PDB line with each atom property between those tags. Each atom is an atom_site and all the atoms are present between
<PDBx:atom_siteCategory> and </PDBx:atom_siteCategory>
There is a lot of header details in the XML schema that you would not be addressing.
As you see there would be not format restrictions for the coordinate values.
The complete schema is available at
http://pdbml.rcsb.org/schema/pdbx.xsd
You can download any pdb file from RCSB in XML (PDBML) format  for more examples. I am sure with time all the graphics programs would start reading this format. At present there is atleast one visualization program that I am aware of (jV released by PDB Japan) that is reading these PDBML files.
Thanks.
Surjit

5

General discussions (Q&As) / PDBML output in 3DNA

« on: October 04, 2006, 09:59:12 am »

Hello, Xiang-Jun,
As you are aware, I use your 3DNA program to construct DNA models based on MD data at my website
        http://humphry.chem.wesleyan.edu:8080/M ... Pages.html
       
When I construct some interesting but very long DNA structure (~15 KB), although 3DNA gives me a pdb format or alchemy format output file there is usually a coordinate overflow. This happens because of the pdb format lmitation of F8.3 (or F9.4? in alchemy) on the coordinate values in these files.
       
One alternative that might overcome this problem is if we can output the file in PDBML format instead of PDB.
       
Is there anyway we could work this out ? I will be glad to   incorporate this extension in 3DNA.
       
Thanks.
Surjit