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misc problems and feature requests
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Zsolt

Joined: 27 Mar 2006
Posts: 32

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Link to postPosted: Mon Jun 18, 2007 7:26 pmPost subject: misc problems and feature requests Reply with quote

Hello, we have some problems and requests for Marvinspace, they are listed below in our priority order.

Thanks,
Zsolt

1. Cannot open every pdb file (saved and modified files, files created by Modeller9v2), I have attached some problematic ones. They work in another programs.
2. Label- export image: many unnecessary labels appear
3. Select amino acid residues in command line
4. Zoom to packet-amino acid residues within 4 A should be highlighted(shows much more) and should be available to select in command line.
5. Color by atomtype- more sets are needed (so the ligand and amino acid residues look different; Color-by element-many sets appearing in Pymol)
6. Label- font color cannot be set (only if background color is chosen as well)
7. Sequence display missing, select amino acid residues in sequence (display sequence command in pymol)
8. Rendering function missing
9. Cannot save a session file or a pdb file with changed coordinates
10. Component cannot be closed



 Filename: 1A2seq.B99990001.pdb    Filesize: 308.98 KB    Downloaded: 436 Time(s)
 Description:  

 Filename: 1OG5.pdb    Filesize: 353.08 KB    Downloaded: 468 Time(s)
 Description:  
Miklos
ChemAxon personnel
Joined: 21 May 2004
Posts: 1194

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Link to postPosted: Wed Jun 20, 2007 3:19 pmPost subject: Reply with quote

Hi Zsolt,

we will discuss these issues internally then get back to you with details.

Regards,
Miklos
Miklos
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Joined: 21 May 2004
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Link to postPosted: Tue Jun 26, 2007 2:47 pmPost subject: Reply with quote

O.K., so here's a more detailed response to your inquires.
Quote:
1. Cannot open every pdb file (saved and modified files, files created by Modeller9v2), I have attached some problematic ones. They work in another programs.
Indeed, 3rd party PDB-s cause lot's of headache. MSpace's PDB reader support standard PDB files, this was a design decision made earlier. However, it turned out to be a bad idea. A new reader is on the way that ignores the PDB standard (as all other programs) and tries to use data provided with no respect to its internal inconsistencies.
Quote:
2. Label- export image: many unnecessary labels appear
Indeed, and some other features disappear (e.g. the smooth background, anti-aliasing). It's not rocket science but needs substantial work to sort out these problems. We'll surely do this work.
Quote:
3. Select amino acid residues in command line
It'd make the commandline far too complicated. We'd rather think that a scripting language should support sch complex selection. Would that be sufficient?
Quote:
4. Zoom to packet-amino acid residues within 4 A should be highlighted(shows much more) and should be available to select in command line.
By saying 4A you mean that you'd like to able to specify the cavity size in an explicit manner? And do you think that 4 should be a reasonable default value?
Regarding cmdline see comments above.
Quote:
5. Color by atomtype- more sets are needed (so the ligand and amino acid residues look different; Color-by element-many sets appearing in Pymol)
O.k. agreed. pyMol coloring is really flexible (though the gui is less intuitive).
We'll support this later.
Quote:
6. Label- font color cannot be set (only if background color is chosen as well)
Hm... it works for us really well. Please tell us more about this problem.
Quote:
7. Sequence display missing, select amino acid residues in sequence (display sequence command in pymol)
Yes, this is needed. Should also come later.
Quote:
8. Rendering function missing
We aren't quite sure what you mean here. Do you refer to achieving the highest possible quality that the graphic card allows?
Quote:
9. Cannot save a session file or a pdb file with changed coordinates
Both very true.... We see it's importance.
Quote:
10. Component cannot be closed
Which component you mean? Do you refer to components that appear in the right hand side selection panel? Or you are talking about the mspace/msketch inter-operation?

Thanks for the good suggestions and the many feature request, all are relevant. Their development is question of available developer resources. Thus, giving us your priority could help a lot to meet your primary requirements.

Thanks and regards,
Judit, Miklos
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