[PyMOL] spectrum colouring for dashes?

Dear Pymol Users, I'm creating dashes between atoms via the distance command. So far I have always indicated the size of the distance simply by the label that pops up automatically with the distance command. I was wondering however whether it is actually possible to also colour dashes

Re: [PyMOL] Secondary structure motifs

Hi James, The 2D representation of secondary structures you show, is not possible with PyMOL. You would need to extract the secondary and code up the solution yourself. I bet there are servers out there that will do this for you, Cheers, -- Jason On Sun, Nov 20, 2011 at 11:20 AM, James

[PyMOL] Pymol on Intel HD Graphics 3000

The problem disappears upon upgrading from Opensuse 11.4 (running kernel 2.6) to OpenSuse 12.1 (running kernel 3.1). -- All the data continuously generated in your IT infrastructure contains a definitive record of

Re: [PyMOL] Work with pdb's enssemble

Jason, but as I've understood super did alignment only for two structures, Is there any way to do the same operation for ensemble ? (for CE as I understood this could be done by alignto command but it lack for seq alignment iin this case) James 2011/11/21 Jason Vertrees

Re: [PyMOL] query

here it is: http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts vitali On Mon, Nov 21, 2011 at 8:50 AM, rjayashree13-scie...@yahoo.co.in rjayashree13-scie...@yahoo.co.in wrote: Thank you. It works, but it does not bring out the type of

[PyMOL] how to manually dock protein with DNA

Hi all, I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to translate and shift-left-click-and-drag to rotate. I opened both PDBs, and when I pressed shift, and click on the

Re: [PyMOL] how to manually dock protein with DNA

By the way, I am using mac pymol... On Mon, Nov 21, 2011 at 5:07 PM, Wei Shi wei.shi...@gmail.com wrote: Hi all, I want to manually dock a protein with a piece of DNA. I found in a previous post that it could be done by opening two PDB and shift-middle click-and-drag on the molecule to

Re: [PyMOL] how to manually dock protein with DNA

Hey Wei, have you set your mouse to Editing mode? Do this first via the application menu Mouse-3 Button Editing and then repeat the steps you described. Cheers, Abdullah On 21 Nov 2011, at 23:07, Wei Shi wrote: Hi all, I want to manually dock a protein with a piece of DNA. I found in a

Re: [PyMOL] PyMOL 1.5 release

On 15:47 Thu 10 Nov , Jason Vertrees wrote: As has always been the case, some new features added to Incentive PyMOL v1.5.0 will not be immediately added to the open-source project, as Incentive subscribers pay to have priority access to these new features. I always wonder, are there