Drawing with BILD commands directly from Chimera command line
Hello all, Is there an option to type in BILD commands directly into the Chimera command line? (I know you can create a file with BILD commands and open it with Chimera but it would be helpful just to open the command line and type them in) Thank you, Dany
Hi Dany, Not exactly, other than using "open" to open the BILD file. However, you might be interested in using the "shape" command instead. The result is a little different (makes a surface model) but if it has all the shapes you need, it might be even better because you can make later modifications to the surface model. For example, you could later change the color of the shape by selecting it and using the Actions… Color menu. "shape" documentation, including examples: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> There is also a "define" command that creates discs to show planes and cylinders to show axes, where the planes and axes are calculated from specified atoms: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 1, 2013, at 2:29 AM, Dan Cohen <bojemoi@gmail.com> wrote:
Hello all, Is there an option to type in BILD commands directly into the Chimera command line? (I know you can create a file with BILD commands and open it with Chimera but it would be helpful just to open the command line and type them in) Thank you, Dany
I'm trying to use the "vop cover" command to extend an electron density map (read in in ccp4 format) to cover an atomic model. The following command: vop cover #0 atomBox #1:1-20 pad 2.0 useSymmetry true results in the error: Keyword 'useSymmetry' doesn't match any known keywords. Can you see what I am doing wrong? Background: I know that the manual says that "true" is the default value for useSymmetry, but the bold font in the usage statement suggests that "false" might actually be the default. If I leave out the "useSymmetry" keyword, the results look like only unit cell periodicity is being used (i.e. looks like useSymmetry is set to "false"). This is why I am trying the above command. ...thanks!....dave case
Hi Dave, The useSymmetry option is default true. Sorry about the inconsistent bolding, I'll fix it ASAP. As to why you get a message that the keyword isn't found, could it be that you are using an older version of Chimera? I believe this option was new in Chimera 1.7 (Jan 2013). The latest release is 1.8 (Jun 2013). That would also explain why the behavior is as if the option were set to false. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 3, 2013, at 5:28 AM, David A Case wrote:
I'm trying to use the "vop cover" command to extend an electron density map (read in in ccp4 format) to cover an atomic model. The following command:
vop cover #0 atomBox #1:1-20 pad 2.0 useSymmetry true
results in the error:
Keyword 'useSymmetry' doesn't match any known keywords. Can you see what I am doing wrong?
Background: I know that the manual says that "true" is the default value for useSymmetry, but the bold font in the usage statement suggests that "false" might actually be the default. If I leave out the "useSymmetry" keyword, the results look like only unit cell periodicity is being used (i.e. looks like useSymmetry is set to "false"). This is why I am trying the above command.
...thanks!....dave case
On Wed, Jul 03, 2013, Elaine Meng wrote:
As to why you get a message that the keyword isn't found, could it be that you are using an older version of Chimera?
Indeed: I was still at verion 1.6. Version 1.8 works fine. Thanks for your quick help! ...dave
participants (3)
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Dan Cohen -
David A Case -
Elaine Meng