[Jmol-developers] [ jmol-Feature Requests-1907294 ] Improve the "write" command

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Feature Requests item #1907294, was opened at 2008-03-04 14:26
Message generated for change (Settings changed) made by hansonr
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Category: None
Group: None
>Status: Closed
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Improve the "write" command

Initial Comment:
The outputed .pdb files should be correct and complete PDB format, which means that the identifiers such as "TER", "MODEL", "ENDMDL", etc., should be included in the output files, so that these files can be further used. 
In fact, presently (Jmol 11.4RC6), the PDB files outputed by Jmol itself cannot be correctly loaded by Jmol itself! This seems vary strange thing.
Hopefully, this can be corrected.

bgMa%at%sdut.edu.cn

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Comment By: Nobody/Anonymous (nobody)
Date: 2008-03-05 17:33

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Great! Thanks.

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Comment By: Nobody/Anonymous (nobody)
Date: 2008-03-05 12:54

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MODEL, ENDMDL are added; TER is much trickier, and I have not implemented
it. 

Bob

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Comment By: Nobody/Anonymous (nobody)
Date: 2008-03-05 10:38

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Bob, 

Thank you for your comments.
It's really a problem if no such identifiers, especially for NMR
structures.
For example, if without the "MODEL" and "ENDMDL" identifiers, the
structure loaded into
Jmol is just interpreted as one model. This is of course not right for a
multi-model structure.
I have tried to output an NMR structure with 20 models by the "write"
cammand of Jmol.
When I reloaded the outputed PDB file into Jmol, I found that all the 20
models were treated as just one model
because of the lack of model identifiers. So everything messed up.
You may try an NMR structure in this way, and see what's out.
To reproduce the structure correctly, these identifiers seem to be
necessary. 

Since it's pretty basic and easy to be done, I hope this can be improved
in a future version of Jmol. 
And eventually, I hope that Jmol can be used as a Convertor of molecular
structure files as well, in addition to 
its strong function as a molecular operator and visualizer, provided that
all its output are correct and complete.

Bin-Guang


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Comment By: Nobody/Anonymous (nobody)
Date: 2008-03-04 14:46

Message:
Logged In: NO 

bgMa,

Right, there is no intent to write full PDB format files -- including TER,
MODEL, and ENDMDL. It's pretty basic. Jmol and RasMol read the coordinates
and bonding correctly. 

So this writing is really just the ATOM, HETATM, and CONECT blocks
necessary to reproduce the set of atoms selected. 

How much more would you need -- just TER, MODEL, and ENDMDL -- to get the
sort of output you could use?
Might be able to add that....

Bob Hanson
 





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