[PyMOL] Deleting and Loading multiple SDF files

p { margin-bottom: 0.08in; } Dear Pymol users I have to do TWO jobs simultaneously in PYMOL. JOB 1: Load multiple *sdf files I have set of ligand files in *.sdf format as follows: /home/user/Model_1/cluster_1.sdf /home/user/Model_1/cluster_2.sdf /h

Re: [PyMOL] Deleting and Loading multiple SDF files

Hi Renuka, If I understand correctly, this is what you want to do: 1. Load up all of the cluster*.sdf files in Model_1. 2. Analyze them 3. Delete them 4. Load up all of the cluster*.sdf files in Model_2. 5. Analyze them 6. Delete them etc. If that's right, I think the easiest thing is just to ch

Re: [PyMOL] Deleting and Loading multiple SDF files

Hi Renuka, Check out the loadDir PyMOL script ( http://www.pymolwiki.org/index.php/LoadDir). You can do stuff like, # load all PDBs in the directory ../ loadDir ../, *.pdb # load all SDFs in ../../mySDFs loadDir ../../mySDFs/state*.sdf Cheers, -- Jason On Wed, Sep 22, 2010 at 9:12 AM, Renuka

[PyMOL] Access viewport size

The output of the get_view command does not save the size of the viewport. Thus if you want to recreate an image for ray tracing so it will have the same size and scale, one also needs to save the viewport dimensions. Is there some way to access this information? The viewport command only set

[PyMOL] Fwd: emovie scripting

Still no ideas? Guys, how then you do movie without gui mode??? -- Forwarded message -- From: Sergey Ivanov Date: 2010/9/21 Subject: emovie scripting To: pymol-users@lists.sourceforge.net Hello, help me please create script that loads frames (say, 30) from pdb files and rotate e

Re: [PyMOL] zoom w/o ray-trace

Sergey, After looking over your data (in another email), PyMOL was not zooming correctly because none of your "atoms" were connected. (PyMOL got the extents right, but was still confused.) To get around this, you can just create a simple connected object, like a methane (8 atoms) and position ea

Re: [PyMOL] Fwd: emovie scripting

Hi Sergey, I either use the GUI or when not in the UI I utilize the moviemaking commands: mdo mview mset Also, import movie and check out what it has to offer: import movie print dir(movie) Here are some moviemaking references: http://pymol.sourceforge.net/newman/user/S0300movies.htm

[PyMOL] Super Bug Report

In preparing my test for the odd request that I just sent, I came across what seems to be a bug in super. It has to do with this weird nucleic acid thing I was talking about. Here's the script this time: from pymol import cmd cmd.fetch('1acb', async=0) cmd.fetch('1acb', '1acb_2', async=0) cmd.fe

[PyMOL] Request: Change in behavior of super on nucleic acids?

I realize this is an edge case, where behavior is not always well defined in programs, but I have a request for a behavior (and the behavior actually seemed to change between 1.2 and 1.3) My example script: from pymol import cmd cmd.fetch('1acb', async=0) cmd.fetch('1acb', '1acb_2', async=0) cmd.

Re: [PyMOL] Access viewport size

Hi Mark, We used to be able to call this to get the viewport size. But, somewhere along the line Warren removed this. I'll see if I can add it back in, or find out why he removed it. Cheers, -- Jason On Wed, Sep 22, 2010 at 2:06 PM, Mark A Saper wrote: > The output of the get_view command do