Dear Sir/Madam I am trying to reconstruct an ion channel molecule (1p7b). The molecule was submitted to pdb in the alternate form (1/2 molecule). Can I recreate the complete molecule in Chimera. If not do you know a program that I can use to import the reconstructed molecule into chimera. Secondly, can I tag a series of residues one at a time but not in a sequence? So far I am really enjoying your program. Manning Correia Manning J. Correia, Ph. D. Jehu M. Robison Distinguished Professor of Otolaryngology and Physiology & Biophysics and Anatomy & Neurosciences Telephone: 409-772-(2708), 5883, 9802 Fax: 409-772-2694 e-mail: mjcorrei@utmb.edu ---------------------------------------------------------------------- "Are you still wasting your time with spam?... There is a solution!" Protected by GIANT Company's Spam Inspector The most powerful anti-spam software available. http://www.giantcompany.com <http://www.giantcompany.com/>
Hi Manning, We have a feature in our development version of Chimera that will make the second half of th 1p7b ion channel. But it is not released yet. Here is a way to do it with the currently distributed Chimera 1700. It is not pretty. First I looked at the PDB file in an editor to see what matrix gives the position second copy. Here it is. REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 92.84000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 105.62000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 This means rotate about the z axis by 180 degrees and then translate by (92.84, 105.62, 0). Here are the steps. 1. Open 1p7b twice in the same Chimera. 2. Use Favorites/Model Panel and click off the "active" switch by model 0. This will make the following move commands only act on model 1. 3. Use Tools/Viewing Parameters/Rotation and set center of rotation method to fixed and set the rotation center to 0, 0, 0. This is needed because the rotation done in the next step has to be about the origin of the coordinate system. 4. Use Favorites/Command line and type the command "turn z 180". 5. Type command "move x 92.84" 6. Type command "move y 105.62". If all went well you should now see the full ion channel. 7. Switch back on the active switch for model 0 in the Model Panel. 8. Switch the center of rotation method back to "center of models". Of course you don't want to do this again next time you need to look at the ion channel. You can use File/Save Session As... to save the full ion configuration. If you want a single PDB file with the full channel use the Chimera command "pdbrun cat > filename.pdb". There is a "Write PDB" button in Model Panel that can write both copies to a single file in our development Chimera, but the ability to write multiple copies to one file is not in the current release. I don't completely understand your question about "tagging residues". You can select residues using Model Panel. First click on the model in the model panel list of models, then press "Sequence...", then select residues in the sequence. To select non-contiguous residues use Select/Selection Mode/Append and then select them from the sequence panel. You can put labels on selected residues with Actions/Label. Tom
participants (2)
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Correia, Manning -
Thomas Goddard