
Hi all, I was working with Chimera for some time, beeing convinced I don't need no help, until I'd got to this. Is there a possibility of conjoining several (let's say four, nine or sixteen) unit cells? I use the el. density map (converted to cpp4, so it could be loaded by Chimera) for structural alignment and such an operation would be very usefull. Thanks in advance, Bartek ____________________________________________________________________________ Czy już jesteś w Yahoo!? Masz dosyć spamu? Poczta Yahoo! dysponuje najlepszą ochroną przed spamem http://pl.mail.yahoo.com

Hi Bartek, Although the Unit Cell tool generates only a single unit cell, the Multiscale Models tool can generate a 3x3x3 block of unit cells. It is under Tools... Higher-Order Structure. Choose the Multimer option "3x3x3 crystal unit cells" and then click "Make models". See the man page for more details on Multiscale Models: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/ framemulti.html A possibly tricky thing is that for computational expediency, Multiscale Models first generates only low-resolution surfaces for all the additional copies. If you need atomic coordinates for some or all of those copies, select those copies in Multiscale Models and then choose a different Style of display. All the styles other than Surface force loading of the atomic coordinates (Ribbon, Wire, Stick, Ball&Stick, Sphere). Loading coordinates for the copies creates additional molecule models in Chimera. Their coordinates can be saved to file(s) with File... Save PDB in the main Chimera menu. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jun 19, 2007, at 7:22 AM, Bartosz Siemiński wrote:
Hi all, I was working with Chimera for some time, beeing convinced I don't need no help, until I'd got to this. Is there a possibility of conjoining several (let's say four, nine or sixteen) unit cells? I use the el. density map (converted to cpp4, so it could be loaded by Chimera) for structural alignment and such an operation would be very usefull. Thanks in advance, Bartek

Hi Bartek, Do you mean that you want to show several copies of the unit cell density map? Or several copies of the unit cell PDB models? There is no currently capability to show multiple copies of the density map with the proper crystal unit cell translations. You could open the map multiple times and change their origin, but the Chimera volume viewer will shift all copies by the same amount if you use its Origin and Scale entry fields. So you would have to make copies of the map file with different names -- quite tedious. An alternative would be to open multiple copies and leave the origin the same but use the Chimera "move" command to shift individual copies of the map. Tom
participants (3)
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Bartosz Siemiński
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Elaine Meng
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Tom Goddard