From: Anders P. <and...@sb...> - 2005-06-24 00:56:48
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To display docking results with a protein PDB-file and a SD-file with = poses, you dont need independent rotation and translation. The centering = should be the same for both molecules. I.e. if (10,20,30) is the center = of mass for the first molecule, then (10,20,30) should be deducted from = the coordinates of both molecules. Anders. -----Original Message----- From: jmo...@li... [mailto:jmo...@li...]On Behalf Of Miguel Sent: Thursday, June 23, 2005 11:10 PM To: jmo...@li... Subject: Re: [Jmol-users] implementing simultaneous molecules >>> Q: What scaling factor would you expect to be applied? >>> >>the same 1A =3D 1A >> > I agree with Jan. Certainly 1A is always 1A. The question is ... how many pixels per angstrom? Q: If I load a large molecule followed by a small one, does the small = one just 'fit in' without changing the scaling of the large one? Q: If I load a small molecule followed by a large one, what happens? > >>> Regarding centering ... >>> >>> The first model gets centered on the screen. >>> >>> Q: I assume that you do not want the second model centered on the >>> screen ... please confirm. >>> >>the same operation, which had been automatically applied to the first >>molecule should be repeated to the second > > I don't understand this, but I think I we are saying the same thing: = how > does Jmol determine placement of a single molecule? it should do the = same > for each molecule IMO. If it does the same thing for each molecule then every molecule will get centered. I fear that I may not have adequately explained the issue. Let us assume that we load up a molecule. We take the mean of the coordinates of the atoms. (Some call it 'unweighted center of gravity', but that is simply the mean.) Let's say that the mean is 10,20,30. Then all points have 10,20,30 subtracted from their coordinates so that everything is translated to a 0,0,0 center. Now you want to load another molecule. Let's say that mean of the points in that file is 200,200,200. Q: What do you want to do? >>> If not, and if it is necessary to manipulate each model >>> independently, then it is a *lot* of work. >>> >>independent manipulation (rotation, translation) like in RasMol2.7.2 >>would be nice >> > I would go so far as to say independent rotation and translation are > necessary. OTOH I don't think zoom or slab need to be independent. I think that zoom needs to be wired together, otherwise the scaling will be different for different molecules and things will get messed up. If we need independent rotation and translation then we can probably terminate the discussion ... it is a *lot* of work and will not happen = in 2005. Miguel ------------------------------------------------------- SF.Net email is sponsored by: Discover Easy Linux Migration Strategies from IBM. Find simple to follow Roadmaps, straightforward articles, informative Webcasts and more! Get everything you need to get up to speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dick _______________________________________________ Jmol-users mailing list Jmo...@li... https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Bob H. <ha...@st...> - 2005-06-24 14:07:58
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what's an "SD file with poses"? Anders Poulsen wrote: > To display docking results with a protein PDB-file and a SD-file with p= oses, you dont need independent rotation and translation. The centering s= hould be the same for both molecules. I.e. if (10,20,30) is the center of= mass for the first molecule, then (10,20,30) should be deducted from the= coordinates of both molecules. >=20 > Anders. >=20 > -----Original Message----- > From: jmo...@li... > [mailto:jmo...@li...]On Behalf Of Miguel > Sent: Thursday, June 23, 2005 11:10 PM > To: jmo...@li... > Subject: Re: [Jmol-users] implementing simultaneous molecules >=20 >=20 >=20 >>>>Q: What scaling factor would you expect to be applied? >>>> >>> >>>the same 1A =3D 1A >>> >> >>I agree with Jan. >=20 >=20 > Certainly 1A is always 1A. >=20 > The question is ... how many pixels per angstrom? >=20 > Q: If I load a large molecule followed by a small one, does the small o= ne > just 'fit in' without changing the scaling of the large one? >=20 > Q: If I load a small molecule followed by a large one, what happens? >=20 >=20 >>>>Regarding centering ... >>>> >>>>The first model gets centered on the screen. >>>> >>>>Q: I assume that you do not want the second model centered on the >>>>screen ... please confirm. >>>> >>> >>>the same operation, which had been automatically applied to the first >>>molecule should be repeated to the second >> >>I don't understand this, but I think I we are saying the same thing: h= ow >>does Jmol determine placement of a single molecule? it should do the s= ame >>for each molecule IMO. >=20 >=20 > If it does the same thing for each molecule then every molecule will ge= t > centered. >=20 > I fear that I may not have adequately explained the issue. >=20 > Let us assume that we load up a molecule. We take the mean of the > coordinates of the atoms. (Some call it 'unweighted center of gravity', > but that is simply the mean.) Let's say that the mean is 10,20,30. Then > all points have 10,20,30 subtracted from their coordinates so that > everything is translated to a 0,0,0 center. >=20 > Now you want to load another molecule. Let's say that mean of the point= s > in that file is 200,200,200. >=20 > Q: What do you want to do? >=20 >=20 >>>>If not, and if it is necessary to manipulate each model >>>>independently, then it is a *lot* of work. >>>> >>> >>>independent manipulation (rotation, translation) like in RasMol2.7.2 >>>would be nice >>> >> >>I would go so far as to say independent rotation and translation are >>necessary. OTOH I don't think zoom or slab need to be independent. >=20 >=20 > I think that zoom needs to be wired together, otherwise the scaling wil= l > be different for different molecules and things will get messed up. >=20 > If we need independent rotation and translation then we can probably > terminate the discussion ... it is a *lot* of work and will not happen = in > 2005. >=20 >=20 > Miguel >=20 >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=3Dick > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users >=20 >=20 > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_idt77&alloc_id=16492&op=CCk > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users --=20 Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, = MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr |