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Re: [PyMOL] save icosohedral virus structure with all subunits present?
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From: Dr. D. J. W. P. <da...@ch...> - 2004-04-02 15:30:55
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Ok, biological unit, thats great! but now, how do I save this virus capsid as a a pdb or mol file where each of the many subunits have a different chain identifier. When I save the virus caspid structure with all subunits visible, the=20 pdb file still only has on subunit in it, not all of them... I want to open it in Bodil (or Pymol or whatever) and only view the=20 chains I want to see. I just want to see the subunits around one of the 5 fold symmetry axes, ie with the 5 fold axis in the middle surrounded by the 5=20 trimers/triangles that surround the 5 fold axis. cheers Dan On 2 Apr 2004, at 17:57, Todd Geders wrote: > I've found the easiest way to do this under PyMOL is to download the > "Biological Unit" version of the PDB file. They've already = regenerated > the virus particle for you. It will only show one of the particles at=20= > a > time unless you check Movie->Show All States. > > ~Todd Geders > > On Fri, 2004-04-02 at 07:14, Dr. Daniel James White PhD wrote: >> Hi, >> >> I have a virus envelope protein structure pdb entry, >> and I want to rebuild the whole virus protein shell >> using the symmetry transformations given in the 180 (60 trimers) >> >> REMARK 350 BIOMT1 1 1.00000 0.00000 0.00000 >> REMARK 350 BIOMT2 1 0.00000 1.00000 0.00000 >> REMARK 350 BIOMT3 1 0.00000 0.00000 1.00000 >> REMARK 350 BIOMT1 2 0.80900 0.30900 0.50000 >> REMARK 350 BIOMT2 2 etc... >> REMARK 350 BIOMT3 2 etc... >> etc...... >> >> lines of the pdb file. These lines give the transformations to give=20= >> the >> complete protein spherical capsid structure. >> >> can I use pymol >> symexp command to do this? >> >> I tried loading the file then doing >> symexp sym=3D1ch8h,(1ch8h),20 >> >> but nothing seemed to happen? >> I'm doing it wrong i'm sure..... >> >> >> I did manage to do this in SwissPDBViewer, but I cant save the=20 >> complete >> capsid structure as a file that Bodil reads properly. Pymol of course >> reads the file ok....... So suppose it is a bodil problem... >> >> anyway, can i use symexp to do this automatically. you have to do it=20= >> by >> hand 1 by 1 in SwissPDBviewer (and the linux version is a bit=20 >> funny...i >> did it on a mac) >> >> cheers >> >> Dan >> >> Dr. Daniel James White BSc. (Hons.) PhD >> Cell Biology >> Department of biological and environmental science >> PO Box 35 >> University of Jyv=E4skyl=E4 >> Jyv=E4skyl=E4 FIN 40014 >> Finland >> +358 (0)14 260 4183 (work) >> +358 (0)414740463 (mob) >> >> http://www.chalkie.org.uk >> da...@ch... >> wh...@cc... >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: IBM Linux Tutorials >> Free Linux tutorial presented by Daniel Robbins, President and CEO of >> GenToo technologies. Learn everything from fundamentals to system >> administration.http://ads.osdn.com/?ad_id=1470&alloc_id638&op=CCk >> _______________________________________________ >> PyMOL-users mailing list >> PyM...@li... >> https://lists.sourceforge.net/lists/listinfo/pymol-users >> > > Dr. Daniel James White BSc. (Hons.) PhD Cell Biology Department of biological and environmental science PO Box 35 University of Jyv=E4skyl=E4 Jyv=E4skyl=E4 FIN 40014 Finland +358 (0)14 260 4183 (work) +358 (0)414740463 (mob) http://www.chalkie.org.uk da...@ch... wh...@cc... |
