I have installed chimera-1.2470 on Debian Linux i386. Thank you. I want to insert a protein into a lipid membrane in a precise opientation, then save the protein pdb in this configuration. I used VMD in the last few days to this redard. I wonder whether I can stick to Chimera for this purpose too. I tried by selecting "protein", though it was difficult to proceed. Thanks francesco pietra ____________________________________________________________________________________ Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how. http://overview.mail.yahoo.com/
Dear Francesco, Chimera does not have any option to create a lipid bilayer. If you have a bilayer structure already, open as a different model, you can move the protein and bilayer individually by activating/deactivating them for motion. Then you would have to delete lipid molecules that overlap the protein manually before saving to a file. In other words, there is no automatic embedding of a structure in a membrane or a solvent box. about activating/deactivating for motion: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef about writing a PDB file: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb Note even if you save to a single file, the models will still be treated as separate models. You would still have to manually edit the file to get everything into one model, avoiding use of duplicate atom numbers, etc. Best 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 Nov 18, 2007, at 8:26 AM, Francesco Pietra wrote:
I have installed chimera-1.2470 on Debian Linux i386. Thank you. I want to insert a protein into a lipid membrane in a precise opientation, then save the protein pdb in this configuration. I used VMD in the last few days to this redard. I wonder whether I can stick to Chimera for this purpose too. I tried by selecting "protein", though it was difficult to proceed. Thanks francesco pietra
--- Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Francesco, Chimera does not have any option to create a lipid bilayer.
That I can make for POPC with VMD If you
have a bilayer structure already, open as a different model, you can move the protein and bilayer individually by activating/deactivating them for motion. Then you would have to delete lipid molecules that overlap the protein manually before saving to a file.
Manually graphically? Neither the POPC molecules nor the water molecules embedded in have a number, only detectable on file through their xyz values. I understand that there is no trick to delete around the protein, by say 1A distance.
In other words, there is no automatic embedding of a structure in a membrane or a solvent box.
about activating/deactivating for motion: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef
about writing a PDB file: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb
Note even if you save to a single file, the models will still be treated as separate models. You would still have to manually edit the file to get everything into one model, avoiding use of duplicate atom numbers, etc.
Combining can be easily done with xleap in Amber. Already tried successfully, getting top/crd for the whole as a single unit. As that of the bilayer is a step after docking to run MD with Amber, that is OK. Thanks francesco
Best 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 Nov 18, 2007, at 8:26 AM, Francesco Pietra wrote:
I have installed chimera-1.2470 on Debian Linux i386. Thank you. I want to insert a protein into a lipid membrane in a precise opientation, then save the protein pdb in this configuration. I used VMD in the last few days to this redard. I wonder whether I can stick to Chimera for this purpose too. I tried by selecting "protein", though it was difficult to proceed. Thanks francesco pietra
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On Nov 18, 2007, at 10:16 AM, Francesco Pietra wrote:
Manually graphically? Neither the POPC molecules nor the water molecules embedded in have a number, only detectable on file through their xyz values. I understand that there is no trick to delete around the protein, by say 1A distance.
Hi Francesco, I am not sure I understand your question, but in Chimera/graphically you can of course make a selection of the lipid molecules within some zone of the structure and then delete the selection. I just meant there is no function that combines the steps for you. For example, if you had the membrane as model 0 in Chimera and the protein as model 1, these commands would select and remove lipid residues within 1.5 A of the protein: select #0 & #1 z<1.5 delete sel Best 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
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Elaine Meng -
Francesco Pietra