Re: [PyMOL] visualization of vector data

Anatoliy, I haven't yet tried a vector field. Can you share the raw data file? Cheers, -- Jason On Wed, Apr 18, 2012 at 10:33 AM, Anatoliy Volkov wrote: > Dear Jason, > > Thank you very much for your prompt reply. > > My program can already write out CCP4 maps > but only for scalar properties.

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Hi Rolf, That's pretty strange. Any chance you can share the file? It looks like PyMOL's somehow missing the last number in the result. I've easily loaded millions of atoms before and got the correct atom count. Cheers, -- Jason On Wed, Apr 18, 2012 at 8:54 PM, Rolf S. Arvidson wrote: > I am u

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Hi Jason, Thanks for the speedy reply. I've posted the ASCII .xyz data file, compressed equivalent, and screen caps at http://www.ruf.rice.edu/~rsa4046/_private/pymol/ I have had some recent problems with pymol apparently hanging on this machine (possibly due to an opengl + nouveau-nvidia driver

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Hi Jason, I've also posted a screen cap of VMD with the same file loaded http://www.ruf.rice.edu/~rsa4046/_private/pymol/cap4.png in which the correct atom count is reported. In addition, I tried this with my licensed copy of PyMOL on my laptop (win7), also with same (truncated) result as Linux

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Hi Rolf, the count_atoms command is fine. PyMOL truncates the first line of the xyz file to 6 characters, so it actually stopped reading the file after 139814 atoms. The fix is easy: --- layer2/ObjectMolecule.c (revision 3996) +++ layer2/ObjectMolecule.c (working copy) @@ -3481,7 +3481,

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Rolf, Thanks for posting the file. I will look at it later tonight and get back to you. Cheers , Sent from my Android. On Apr 19, 2012 5:58 AM, "Rolf S. Arvidson" wrote: > Hi Jason, > > Thanks for the speedy reply. I've posted the ASCII .xyz data file, > compressed equivalent, and screen caps

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Hi Thomas, Thanks very much for this patch, I will apply and post back results. Cheers! // Rolf On Thu, Apr 19, 2012 at 11:46 AM, Thomas Holder wrote: > Hi Rolf, > > the count_atoms command is fine. PyMOL truncates the first line of the > xyz file to 6 characters, so it actually stopped reading t

[PyMOL] Rigimol error

Hi, I'm trying to use rigimol for the first time. After creating an object with the 2 states, I run these commands from epymol import rigimol rigimol.morph("morph_in","morph_out",refinement=5,async=1) It runs for a few seconds, and then, error: Write-Interpolation>end Morph-Error: no rigi

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Hi Thomas, Your patch got the file loaded in its entirety, thanks! $ pymol $SIM -c -d "@./png.pml" ExecutiveLoad: "output/flicker-1811000.xyz" loaded as "flicker-1811000", through state 1. PyMOL>@./png.pml Selector: selection "cube" defined with 1398146 atoms.

Re: [PyMOL] order-of-magnitude apparent pymol error in report of total number of atoms loaded (139814 versus 1398146 actual)

Thomas, Thanks--we'll add the fix ASAP. Cheers, -- J On Thu, Apr 19, 2012 at 9:46 AM, Thomas Holder wrote: > Hi Rolf, > > the count_atoms command is fine. PyMOL truncates the first line of the > xyz file to 6 characters, so it actually stopped reading the file after > 139814 atoms. The fix is