[PyMOL] help

Hello everyone: I need help because I have a pdb of a monomer but I know that it is a dimer by crystallographic symmetry, how can I make a new molecule of it? because I could make it by generate/symmetry mate...but I could not save it...any help will be great! Thanks in advance! --

Re: [PyMOL] Atoms appears on cartoon at high resolution

Hi Lucile, Thanks for the pse (off-list). Please hide the "nonbonded" representation: PyMOL> hide nonbonded Nonbonded rep is shown by default. In ray tracing, those are rendered as cylinders, with a radius that depends on the zoom level, that's why you may not see them when zooming in. Cheers

Re: [PyMOL] help

Hi Clarisa, If I understand correctly you generate the dimer, but you are not able to save it. Wich error did you get? Did you select all the object when saving the file? By the way, may be you will find this wiki page useful. Cheers, Osvaldo. On Wed, Oct

Re: [PyMOL] help

Clarisa, Depending on what you want to do with the file, you may not need to save a new PDB at all. You could for example, * Issue the command symexp ,,(all),4.0 to generate nearby symmetry mates, then remove the objects you don't need to form the proper dimer. ( is your PD

[PyMOL] APBS problem

Hello: I am trying to calculate the protein surface electstatic properities by APBS plugin in pymol. But it always failed with messages: Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist? Does a

[PyMOL] how to setup environment for APBS?

Hello: I noticed that each time when I try to use APBS plugin, pymol always ask to specify the location of: apbs psize.py pdb2pqr.py I am just wondering can we somehow write the location of those program into .pymolrc file so that each time Pymol APBS plugin can find it automatically? thanks

Re: [PyMOL] APBS problem

Hi Albert, I apologize that I take your email for a grumpy old man's rant, but I feel this mailing list is getting washed out with poorly formulated questions. What happened to specifying what OS you use, what version of PyMOL, what version of the apbs plugin. Also, to give answers, it would hel

Re: [PyMOL] APBS problem

thanks a lot for reply. Problem solved after I specify the maloc library path explicitly in my tcsh environment. setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib On 10/08/2015 05:02 PM, Andreas Forster wrote: Hi Albert, I apologize that I take your email for a grumpy old

Re: [PyMOL] how to setup environment for APBS?

Hi Albert, As far as I know you can set the environmental variables APBS_BINARY_DIR, APBS_PSIZE_DIR and APBS_PDB2PQR_DIR or just set the values for this variable inside the plugin. Anyone knows any other method? Cheers, Osvaldo On Thu, Oct 8, 2015 at 4:54 PM, Albert wrote: > Hello: > > I no