[PyMOL] writing selection to a external file

Hi All, I'm using pymol to select (by residue) all the atoms around 10 angstroms from a certain atom. Now I would like to write the residue id's of my selection to an external file, so that I can integrated in the ndx file from Gromacs. Do you have any idea how I could do that? Thanks, Marius

Re: [PyMOL] writing selection to a external file

Hi, This should've gone to the list... (isn't there an option send replies to list rather than to poster to the mailing list?) Tsjerk On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Marius, You want iterate. You do have to make sure though that the numbering of

Re: [PyMOL] writing selection to a external file

Tsjerk Wassenaar schrieb: Hi, This should've gone to the list... (isn't there an option send replies to list rather than to poster to the mailing list?) Tsjerk Depends on the list, but there is a nifty addon for thunderbird

Re: [PyMOL] writing selection to a external file

Hi, It seems that I run into a little problem. When I try to write a large selection I get only a partial list of ID. If for example I print ID after the iterate command, all the list is printed into pymol window. Do you have any idea why? I run Pymol 1.1pre5 under Fedora 8. On Fri, Jun 27, 2008

Re: [PyMOL] How to display two or multiple eleectrostatic maps simultaneously with PyMol?

Hi, The current version of the APBS Plugin (http://www.umich.edu/~mlerner/PyMOL) has two visualization panes. You can use them to control two separate molecule/map combinations. Please let me know if you need more assistance, -Michael On Thu, Jun 26, 2008 at 10:28 PM, Youzhong Guo

[PyMOL] How to view electron densities from the PDB

Hi, This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL doesn't seem to read the CIF file (?), so I downloaded and installed the PDB's

Re: [PyMOL] How to view electron densities from the PDB

Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com wrote: This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif.

Re: [PyMOL] How to view electron densities from the PDB

Robert Campbell wrote: Hi, On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com wrote: This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download

Re: [PyMOL] How to display two or multiple eleectrostatic mapssimultaneously with PyMol?

Youzhong, If you're still having trouble getting what you want with Michael's APBS Plugin, here's how I might display two such maps using PyMOL commands directly: load pdbset1.pqr load pdbset_1.dx load pdbset3.pqr load pdbset_3.dx ramp_new ramp1, pdbset_1, [ -3, 0, 3] ramp_new ramp3, pdbset_3,

Re: [PyMOL] writing selection to a external file

Marius, Hmm...are you perhaps looking at the output before the file is closed and/or flushed? You should issue ndx.flush() or ndx.close() before attempting to use the output file. Cheres, Warren _ From: pymol-users-boun...@lists.sourceforge.net