From: David J. <DJa...@ar...> - 2004-11-26 11:50:41
|
Is it possible to view 2 superimposed molecules?=20 I wish to show, using the applet, a ligand in a protein's active site; I = have the protein pdb and an sdf (with coordinates already adjusted to tho= se of the pdb) for the ligand.=20 If not, is this something which could fit easily in the JMol applet's mod= el? David Confidentiality Notice:=0AThe contents of this email from Arrow Therapeut= ics are confidential to the ordinary user of the email address to whom it= was addressed. No-one else may copy or forward all or any of it in any f= orm. If you receive this email in error please reply to the sender so tha= t we can arrange for proper delivery and then please delete the message f= rom your inbox. Thank You.=0A=0A |
From: Egon W. <e.w...@sc...> - 2004-11-26 12:51:41
|
On Friday 26 November 2004 12:50, David Jackson wrote: > Is it possible to view 2 superimposed molecules? If in the same file, yes. > I wish to show, using the applet, a ligand in a protein's active site; I > have the protein pdb and an sdf (with coordinates already adjusted to those > of the pdb) for the ligand. This would only require the ability to load a new file into a new model, without first deleting the old content... Say, the PDB has 1 model, the ligand molecule should be loaded into the second model... I don't think such is possible at this moment. Rene/Miguel, would such be difficult to implement? > If not, is this something which could fit easily in the JMol applet's > model? Egon -- e.w...@sc... PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 |
From: Miguel <mi...@jm...> - 2004-11-27 01:55:55
|
> On Friday 26 November 2004 12:50, David Jackson wrote: >> Is it possible to view 2 superimposed molecules? > > If in the same file, yes. Correct. If you put them in the same file then you can have multiple 'models' that= can be displayed at the same time. But, they cannot be manipulated independently. >> I wish to show, using the applet, a ligand in a protein's active site;= I >> have the protein pdb and an sdf (with coordinates already adjusted to >> those >> of the pdb) for the ligand. > > This would only require the ability to load a new file into a new model= , > without first deleting the old content... > > Say, the PDB has 1 model, the ligand molecule should be loaded into the= > second model... > > I don't think such is possible at this moment. > > Rene/Miguel, would such be difficult to implement? > >> If not, is this something which could fit easily in the JMol applet's >> model? It is something that we will add in the future. Note that it may be more complicated than it may seem. Two (or more) models probably need to be somewhat independent. - they need to rotate independently - they need to translate independently - we will need to change the translation mechanism so that translations actually take place in 3D - defining the 'center of rotation' will be more complicated - zoom levels presumably need to be locked together The UI will need to support independently moving the different models, then locking them together. This will not be easy. Miguel |