Rendering of DNA and Water

Rendering of Water


When Mspace shows water molecules on the java applet, why arent the hydrogens bonded to the water molecules? It looks like hydrogens exists individually close to the water molecule without any bonds





Rendering of DNA


If you are using a secondary sturcture, It seems like the DNA line is passing thru the center of the bases. It would be much better if it goes through P or P and C4'. Is that possible? It also look better if dna looks thicker. The optimal thickness should be half of a beta sheet.

Thank you for your thoroughness.


Yes, they are already in the pipeline, though with lower priority. It's not too much work so we can fix them soon.


Judit

Hi,





in the test applet http://www.chemaxon.com/marvinspace/1_3_2 the water molecules are displayed with bonds if hydrogens are described in the pdb file.





This will be released along with the other changes.





Judit

In the latest release Marvin 4.1.2 with MarvinSpace 1.3.2 there is a new secondary structure representation of nucleic acids.


Could you please check it, and give us a feedback?





Thanks,


Judit

We love the new DNA rendering. Its awesome!





As for the water, It still shows up as a plus sign when i open the original PDB file. The water in charmm pdb is very nice. It would be great if you can add a parameter for us to set the width of the water bonds in the charmm pdb file. We set it for now, by clicking on


Dislpay>Options and changing the line width of water to 0.5, can we have a parameter like this?


("water(or ligand, protein or ion)" , "line width" ,"0.5")


?





or is there a parameter already? right now, we only need to reduce the size of the water in order to see the protein inside the water box more clearly.

We're glad that you like it. Your cooperation helped us a lot in developing. We're grateful for it!





Reducing the size of water depends:


1/ if hydrogens are also displayed, you cannot change the bond length, though it could be done - do you need this?


2/ in case when hydrogen atoms are not displayed (because it is not described in the PDB file or they are just switched off), the water size can be changed with


("Water.BallRadius", "0.5"). This will affect all display modes of water except the spacefill.





The available parameters can be found in the Parameters and Events. Would it be hard to use, please tell us and we will try to make it better.





Judit