[PyMOL] why is PyMOL renaming my residues?

says You clicked NAP: /test1///164/OA23 (i.e. it gives me the original name). thanks, -michael -- michael lerner

[PyMOL] Re: why is PyMOL renaming my residues?

and LMN respectively. also, i noticed that PyMOL is changing the atom ID (OA22 was 1313 in the first file, but 1 in the second). that's not actually causing me any trouble, but i'm curious: is there a way to make PyMOL leave the IDs alone? thanks, -michael michael lerner wrote: Hi, If I

Re: [PyMOL] why is PyMOL renaming my residues?

are the real problems) on the same systems, and anything that makes this less painful is great! I'll probably set retain_order and pdb_retain_ids in my .pymolrc.py and upgrade to the CVS version within the next couple of days. Thanks! -michael -- michael lerner

[PyMOL] Can PyMOL read amber8 trajectory files?

I have some stuff from an amber8 (sander) MD run that I'd like to visualize in PyMOL. When I load it up, PyMOL says something like assuming amber6 format and dies. I'm using fink/pymol-py24 on an intel macbook pro. I always forget how to load amber files anyway, so I could easily be screwing

[PyMOL] How do I show multiple conformations in a single crystal structure?

I have a crystal structure that contains two conformations for a flexible loop. They're both in the crystal structure, but have occupancies less than one. When I look at the structure in PyMOL, I see only one conformation. Is there a command similar to split_states that will allow me to view

Re: [PyMOL] How do I show multiple conformations in a single crystal structure?

Oh, if it helps, the residues are all named things like ACYS and BCYS for the different conformations. On 7/25/06, Michael Lerner mgler...@gmail.com wrote: I have a crystal structure that contains two conformations for a flexible loop. They're both in the crystal structure, but have

Re: [PyMOL] rejected atoms during alignment

This is not a great answer, but do you know about the object parameter for the align command? I often type something like align struct1, struct2, object=alignment and then just look at which things were included/excluded. -michael On 8/3/06, Marc Bruning brun...@mpghdb.desy.de wrote: hello,

Re: [PyMOL] Paths to loaded objects

I think he means for you to have a Load button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). On 8/19/06, Ron Jacak r...@email.unc.edu wrote: Peter, I'm working on a plugin that reads information appended to the end of PDB

[PyMOL] Showing the surface

, -Michael Lerner -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net

Re: [PyMOL] New plugin and Doubt with APBS Tools

Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera butil_li...@yahoo.com wrote: Dear all, Two things. First, I just

Re: [PyMOL] New plugin and Doubt with APBS Tools

this question, -michael On 1/9/07, Michael Lerner mgler...@gmail.com wrote: Raúl, I don't have time to look at this in detail right now, but .. what exactly do you mean that the potentials change between frames? What happens if you draw isosurfaces? Do they change? -michael On 1/7/07, Raúl Mera

Re: [PyMOL] Side by side views

parts of a dynamics run, etc. In your case, you might need to align all of the structures to one reference structure first, so that the views are similar. Hope this helps, -Michael Lerner On 25 Jan 2007 16:32:21 +, David F Burke df...@cam.ac.uk wrote: Pymol users, I wish to compare several

Re: [PyMOL] Visualizing Molecular Orbitals in PyMol

correctly, my problems with bricks were mostly that I wasn't using them correctly, but I didn't figure out how to use them correctly until after I'd already converted everything to DX. -Michael Lerner On 2/19/07, BuzB bmb...@gmail.com wrote: Hi All, Thanks to everyone and for the responses

Re: [PyMOL] reload modified wizard

Actually, I did this when I was developing the APBS Plugin. I put all of the interesting code in a module called _apbs_tools. apbs_tools was just a little wrapper where the init function would import and reload _apbs_tools and then call through to it. -Michael On 2/24/07, DeLano Scientific

Re: [PyMOL] reload modified wizard

SomethingOrOtherTools.SomethingOrOtherTools(thing) Let me know if you have any more questions. -michael On 2/24/07, Michael Lerner mgler...@gmail.com wrote: Actually, I did this when I was developing the APBS Plugin. I put all of the interesting code in a module called _apbs_tools. apbs_tools was just a little

Re: [PyMOL] Electrostatic surface visualization

On 3/3/07, se...@uniroma2.it se...@uniroma2.it wrote: Dear all, I'm new to this list and to the software. I used PyMOL and APBS to calculate an electrostatic surface for a small protein (I'm using the WindowsXP version) and everything seems fine. Now I would like to visualize this surface AND

Re: [PyMOL] APBS surface

PyMOL doesn't know where the electrostatic potential map comes from. If you load up a map and a structure, it will show the potential from that map on that structure. On 4/2/07, Gianluigi Caltabiano chimic...@yahoo.it wrote: YesI have already done as wrote My question iswhat if I

Re: [PyMOL] Single transparent sphere

The pseudoatom business looks very cool. I'll have to try it out. In the meantime, I wanted to mention that you certainly can make transparent CGOs. Here's some code that I wrote to visualize dock output in our lab. The files it reads in have lines that look like junk x y z r junk temp junk

Re: [PyMOL] APBS

Hi, Can you try installing the most recent version of my plugin from http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use the normal Install Plugin menu option .. there's no need to do things by hand anymore)? It fixes some problems and gives better error messages on others.

[PyMOL] Command-line arguments when using PyMOL to launch a script

Hi, I have a script that uses PyMOL to aid with a lot of calculations. So, I run the script like this: pymol -c script.py The script has grown so that it has a lot of options. Right now, I edit the script every time I want to change them. If it were a normal Python script, I'd run it like

[PyMOL] Are there any feature requests for the PyMOL-APBS plugin?

it might be to implement (that's not a promise that I'll implement it .. just that I'll consider it :) ). Thanks, -Michael Lerner -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner

[PyMOL] Why can't I get to sys.argv on Linux?

Hi, I'm using PyMOL as a front end to a few scripts. So, I need to get my hands on sys.argv to process the command-line arguments. On OS X, everything works just like I'd expect. However, on Linux, I can't get sys.argv. Here's a very simple Python script: #!/usr/bin/env python import sys print

Re: [PyMOL] electron density map representation as dot

You can do this with the isodot command. Are you using the PyMOL-APBS plugin to generate or view electron density maps? If so, would you like me to add dot representations to the plugin in the next release? Thanks, -michael -- Biophysics Graduate Student Carlson Lab, University of Michigan

Re: [PyMOL] APBS-electrostatics

It looks like quite a few people are actually still using the electrostatics wizard, so I updated the code on my website (http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use the visualization pane of the APBS plugin these days, but I understand if the wizard is a little cleaner

[PyMOL] Trouble making pictures in a script

Hi, I have a Python script that sets a system up and then calls cmd.png() to render an image. I use it to process several files at a time, and there's no need to look at it while it's working, so I use pymol -qcr myscript.py to launch it. It works fine when I ray trace things, but if I just set

Re: [PyMOL] apbs plugin for macpymol

I would like to use apbs from within PyMOL. I have downloaded and installed the latest version of apbs, and apbs_tools.py exists in $PYMOL_PATH/modules/pmg_tk/startup/. However, I find no plugins entry in any of the PyMOL menus. I think that you need to rename the application bundle to

Re: [PyMOL] Distance labels

An object whose name begins with an underscore will not appear in the menu. On Feb 11, 2008 3:13 PM, Toni Pizà servo...@gmail.com wrote: Hi! When I create a distance in a pymol session, an object called dist n is created, and a label with there name is shown at the right of the screen, with

Re: [PyMOL] Command-line arguments when using PyMOL to launch a script

Hi, First, the initial error you were seeing was a syntax error: from sys import argv my_argv =3D argv[argv.index(--):] print my_argv[1], my_argv[2] is failing because of the word 3D Second, that used to fail on Linux systems anyway (it worked on some other systems). I tend to use optparse,

Re: [PyMOL] Will Pymol participate in Google Summer of Code 2008?

On Fri, Mar 7, 2008 at 5:04 PM, DeLano Scientific del...@delsci.info wrote: So from where I sit, the obvious open-source candidates are: APBS (electrostatics -- improve the current plugin) Please let me know if anyone decides to do this. I have an (unreleased) improved version, and several

Re: [PyMOL] interior protein-surfaces

@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 http://www.umich.edu/~mlerner

Re: [PyMOL] how to get version?

/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909 Rockville, MD 20852 http

Re: [PyMOL] drawing axes

or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA

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

for just about anything Open Source. http://sourceforge.net/services/buy/index.php ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral

[PyMOL] How to view electron densities from the PDB

, PyMOL gives me errors when I try to load the resulting .xplor file. This may not be directly related to PyMOL, but I'm hoping it's a common enough task that someone can point me in the right direction. Thanks, -michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory

Re: [PyMOL] select by absolute coordinate

://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS)

Re: [PyMOL] Missing external GUI and search for the APBS plug-in for PyMOL

-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda

Re: [PyMOL] pymol question

? -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory

Re: [PyMOL] is this how i would write a coding sequence?

-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909

Re: [PyMOL] problems with apbs/pqr

list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers

Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory

Re: [PyMOL] segmentation fault!

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow

Re: [PyMOL] APBS plugin woes

@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD

Re: [PyMOL] APBS plugin woes

mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635

Re: [PyMOL] Pymol access denied at the NIH

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology

Re: [PyMOL] Pymol access denied at the NIH

Access to pymol.org has been restored. On Fri, Dec 4, 2009 at 8:25 PM, Michael Lerner mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote: I have no idea why it's been blocked. I filed a ticket with the help desk (by clicking on the link in the middle of the Access Denied

Re: [PyMOL] dynamic bonding

/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314

Re: [PyMOL] unable to initialize plugin

-- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- This SF.Net email

Re: [PyMOL] select atoms near electron density

@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA

[PyMOL] Rendering plugin

window when you click Ray. That doesn't seem to be necessary anymore, at least on my MacBook Pro. [image: ?ui=2view=attth=12651b51d47cc010attid=0.1disp=attdrealattid=ii_12651b51d47cc010zw] Cheers, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

) #cmd.png(self.filename.getvalue(), dpi=int(self.dpi.getvalue())) cmd.extend('rayy',rayy) On Thu, Jan 21, 2010 at 11:52 AM, Michael Lerner mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote: The ray command bugs me, so I'll take a stab at improving it this afternoon. Can someone

Re: [PyMOL] Feature Requests/Ideas (Sean Law)

=height,**kwargs) cmd.extend('rayy',rayy) On Thu, Jan 21, 2010 at 2:39 PM, Michael Lerner mglerner+sourcefo...@gmail.com mglerner%2bsourcefo...@gmail.com wrote: I think this works. It handles different units (in and cm). If you leave out width or height, it gets scaled correctly. If you leave

Re: [PyMOL] Rendering plugin

/index.php/User:Mglerner ). If you add it to your .pymolrc, you will be able to type rayy 3 in, 2 in, dpi=300 from the PyMOL command line 4. Followed Luca Jovine's suggestion to change the order of rayy's arguments. Cheers, -Michael On Thu, Jan 21, 2010 at 11:29 AM, Michael Lerner mgler

[PyMOL] Pre-release version of the PyMOL-APBS plugin

* Gives better diagnostic information so that PyMOL/APBS developers can find bugs more easily * Lots of internal code cleanup You can find this same information on the PyMOL wiki: http://pymolwiki.org/index.php/User:Mglerner Thanks, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow

Re: [PyMOL] color by element

://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx

[PyMOL] Showing electric field lines

this series of commands from the PyMOL prompt: gradient my_grad, pymol-generated ramp_new my_grad_ramp, pymol-generated color my_grad_ramp, my_grad I'm considering building this into the next version of the plugin. Cheers, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory

Re: [PyMOL] New Feature Ideas

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow

Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 5

://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

[PyMOL] Some plugin development questions

: print prog_out return (retcode,prog_out) -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] Pymol and APBS

://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD

Re: [PyMOL] Pymol and APBS

mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635

Re: [PyMOL] Start PyMOL from command line

/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] Wizard Measurement

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow

Re: [PyMOL] Deleting and Loading multiple SDF files

. --- On *Wed, 22/9/10, Michael Lerner mglerner+sourcefo...@gmail.commglerner%2bsourcefo...@gmail.com * wrote: From: Michael Lerner mglerner+sourcefo...@gmail.commglerner%2bsourcefo...@gmail.com Subject: Re: [PyMOL] Deleting and Loading multiple SDF files To: Renuka Robert renukarob

Re: [PyMOL] OpenDX files from opendx.org

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory

Re: [PyMOL] Wiki down?

/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314

Re: [PyMOL] Visualizing two surfaces using APB2tools2.1

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] APBS surface data export

://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx

Re: [PyMOL] Color scale changed in APBS?

Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS

Re: [PyMOL] R: Re: plugin dependencies

://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality

Re: [PyMOL] movie with morph and electrostatics

://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] Adding Hydrogens

://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx

Re: [PyMOL] How to get pymol 1.4

-- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Enable your software

Re: [PyMOL] How to save APBS-generated maps

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Create

Re: [PyMOL] Convert pml script to Pymol Python script

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] Get Protein Dimension

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH

Re: [PyMOL] Hiding individual dash/distance objects within a merged-dash object

off the ones not connected to a residue of interest. Even better (if possible) would be to only show dashes connected to a residue of choice. I hope that makes sense. Thank you for your help, Harry On 26 Apr 2011, at 13:59, Michael Lerner wrote: Hi Harry, If they've been combined using

[PyMOL] Fetching scripts

this as a userland script first. If issues relating to security and validation can be resolved, we'll see if the official builds want to include it. Cheers, -Michael -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314

Re: [PyMOL] Fetching scripts

be possible if it there's a strong push for it. -Michael Pete Michael Lerner wrote: Hi all, I'm considering building in a mechanism for automatically fetching scripts from the PyMOL Wiki. The goal is to allow users to say fetch findSurfaceResidues, type=script findSurfaceResidues doShow

Re: [PyMOL] APBS Plugin: protein out of grid

-sd ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA

Re: [PyMOL] How to construct a view showing only a single contiguous cavity

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- What

Re: [PyMOL] ContactsNCONT script error

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS

Re: [PyMOL] RMSD calculation sans alignment

@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) as of August 15th: Department of Physics and Astronomy Earlham College 801

Re: [PyMOL] How to manage plugin dependencies

@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314

Re: [PyMOL] loading gro files

@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095

Re: [PyMOL] Get pymol 1.4.1 source to windows. Easy.

mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635

Re: [PyMOL] Electrostatic calculations with ligand bound

://p.sf.net/sfu/splunk-novd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael

[PyMOL] writing out the surface

Hi all, If I have a surface representation, is there currently a way to write it out as points (perhaps with a desired spacing) to a file? I know that the answer used to be no, but I thought I'd check just in case there was a new function that I didn't know about. Cheers, -Michael -- Michael

Re: [PyMOL] writing out the surface

/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Michael

[PyMOL] 3D printing question

to use as intermediates between the two is proving to be troublesome. Cheers, -Michael -- Michael Lerner Department of Physics and Astronomy Earlham College - Drawer 111 801 National Road West Richmond, IN 47374-4095

Re: [PyMOL] writing out the surface

, -Michael On Mon, Jun 11, 2012 at 10:47 PM, Michael Lerner mgler...@gmail.com wrote: Hi all, Tsjerk- Thanks. I'm not sure how I missed that, given that it's even mentioned on the wiki on the surface page under the clear heading Exporting Surface/Mesh Coordinates to File :-|. ( http