Hi Jerry, If you wanted the mathematically exact axis, you _should_ be able to just make two pseudoatoms, position them at the proper position at the end of your axis and then use the orient command:
pseudoatom axisMin, pos=[x1, y1, z1] pseudoatom axisMax, pos=[x2, y2, z2] orient axis* But, there is a bug with 'orient' on pseudoatoms: it's orienting the pseudoatoms along their 2nd principal axis, not the first. So, after you type those three command, follow up with: turn z, 90 and that should do it. Hope this helps, -- Jason On Tue, Sep 7, 2010 at 1:37 PM, Sampson, Jared <[email protected]> wrote: > Hi Jerry, > > If your protein has an NCS symmetry axis parallel to a cell edge, you can try > using the “orient” command. > > http://www.pymolwiki.org/index.php/Orient > > Best, > Jared > > > On 9/3/10 7:31 PM, "James Stroud" <[email protected]> wrote: > > On Sep 3, 2010, at 4:03 PM, Jerry McCully wrote: > It is a Pymol question. How can I set up the view through one axis of the > unit cell? > > By eye. Use orthoscopic view to help. Show the unit cell as a guide: > > http://www.pymolwiki.org/index.php/Cell > > James > > > > > -- > Jared Sampson > Xiangpeng Kong Lab > NYU Langone Medical Center > New York, NY 10016 > (212) 263-7898 > > ------------------------------------------------------------ > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check this > email and any attachments for the presence of viruses. The organization > accepts no liability for any damage caused by any virus transmitted by this > email. > ================================= > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120
