Re: [PyMOL] isomesh for electrostatic potential

On Tue, 18 Apr 2006, Chun Tang wrote: Dear PyMoler, In the pymol apbs tool, there is an option to show the negative/positive isosurface (not the molecular surface) upon loading an electrostatic map. My question is if there is a way to show the electrostatic potential surface as mesh instead of

RE: [PyMOL] Producing publication quality images

It's not pretty, and this is easy enough to do by hand, but I've had enough people ask me about this that I hacked up a little rendering plugin just now. Can someone grab it from http://www-personal.umich.edu/~mlerner/PyMOL/rendering.py put it in $PYMOL_PATH/modules/pmg_tk/startup/ (or whatev

RE: [PyMOL] Multiple origins possible?

I was going to suggest the same thing. FWIW, I have a version that you can run from your .pymolrc on my webpage here: http://www-personal.umich.edu/~mlerner/PyMOL/mg_pymol_utils.py -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII

Re: [PyMOL] ball-and-sticks, controlling bond color

set stick_color, grey the image looks a little more like set stick_color, grey90 but I can't quite tell. -michael -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML emai

RE: [PyMOL] Can I use the mouse to control multiple windows?

yster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: Warren DeLano Sent: Friday, January 06, 2006 2:54 PM To: 'Michael George Lerner&#x

[PyMOL] Can I use the mouse to control multiple windows?

Longshot, but .. I'm looking at a structure under two different sets of conditions, so I have two PyMOL windows open. I'm constantly get_view and set_view[*] to synchronize the two windows. Is there some way to set things up so that I can drag things around in one window and have the scene i

Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

| mler...@umich On Tue, 20 Dec 2005, Michael George Lerner wrote: There's a new version on my website (http://www.umich.edu/~mlerner/PyMOL/). Please feel free to try it out and let me know if it works. I've tested it on a few systems that I work with, and it seems fine. One pe

Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

There's a new version on my website (http://www.umich.edu/~mlerner/PyMOL/). Please feel free to try it out and let me know if it works. I've tested it on a few systems that I work with, and it seems fine. One person has reported some difficulties, but these may not be related to my plugin.

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #1085 - 5 msgs

It's broken at the moment. I'm working on a new version. It should be out asap. -- www.umich.edu/~mlerner |_ |Michael Lerner This isn't a democracy;| ASCII ribbon campaign ( ) | Michigan it's a cheer-ocracy. | - against HTML email X | Biophysics -Torrence, Bri

[PyMOL] How can I get the color ramp to show up in raytraced images?

Hi, When I use the APBS plugin to look at electrostatic potentials, I get a color ramp at the bottom of the window (e.g. red and -1 on the left, blue and +1 on the right) that shows the color scale that I'm using. When I raytrace, that ramp goes away. How can I make it show up in the raytrac

Question about commandline -d option (was RE: [PyMOL] displaying protein with propeptide)

This is awesome. It looks like this has been a valid setting for a *long* time, but I've never seen it. I look at a lot of MCSS-type structures, and I have some really painful scripts that get the bonds right once the structure is loaded in PyMOL. Now, I can just stamp the CONECT records at

Re: [PyMOL] PyMOL featured on Apple Store site?

On Wed, 19 Oct 2005, Sabuj Pattanayek wrote: nm, I found the url: http://store.apple.com/1-800-MY-APPLE/WebObjects/AppleStore.woa/72303/wo/iG1ZdpmENibK2kKdLwyNuAAR9NW/0.SLID?nclm=PowerMac&mco=586014F6 That URL complains that the session has expired. - go to www.apple.com - click on the Sto

Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #996 - 2 msgs

On Tue, 13 Sep 2005, surendra negi wrote: check this link! http://www.csb.yale.edu/userguides/graphics/pymol/electro.html That page is actually quite out of date. I emailed them about it a few months ago, but didn't get a response. You don't need to go through any of that hassle to use t

Re: [PyMOL] Displaying an electrostatic potential on msms

On Mon, 12 Sep 2005, Anna Feldman-Salit wrote: Dear All, I have a 0.98 PyMol version with APBS and Iso_Sliders plugins. However, my aim is not just visualize isosurfaces of electrostatic potential at certain values, but to display/map it on molecular surface. Hi, The APBS plugin will show y

Re: [PyMOL] Setting transparency for CGOs

Quoting tanri...@stud.uni-frankfurt.de: # Hi everybody, # # i've just created many CGOs, which show up solid surfaces like spheres and # ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5 # and leave the others solid? # I've checked out the reference and the manual, an

Re: [PyMOL] Mix pml script and PDB file

On Mon, 18 Jul 2005, Sebastien Moretti wrote: Hello, Is there a way to get one file with pymol commands (pml script) and with the structure (PDB file) ? I can get this with Rasmol and the ras script file. Can I get the same kind of file with PyMOL ? You can use the read_pdbstr command, li

Re: [PyMOL] Setting grid boundaries in APBS

On Tue, 12 Jul 2005, Miguel Alejandro Pabon Sanclemente wrote: APBS-users in PyMOL: The APBS plugin is not setting the grid boundaries correctly. Segments of the proteins I have been working on are not included in the calculations because they are outside of the grid boundaries. Even if I try

Re: [PyMOL] list residues in a selection

I asked a similar question a while ago, and Kristan Rother archived the answer at . Here it is: Using PyMOL commands: list=[] iterate (name ca),list.append((resi,resn)) print list [('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HI

Re: [PyMOL] Pymol/ABPS

On Sun, 12 Jun 2005, Dyda wrote: I'd like to know what charges Pymol uses when generates a pqr file from a pdb. The follow-up would be is whether there was a way to change this, say if one wanted to use charmm charges rather than amber. PyMOL uses amber99 charges and radii. This is taken car

Re: [PyMOL] saving commands created by cmd.extend() in session files

On Mon, 11 Apr 2005, Michael George Lerner wrote: hi, i have some scripts that load a bunch of files and do various smart things to make it easy to work with my data. in particular, they define functions and use cmd.extend() to register those functions. the setup takes a long time, and is th

[PyMOL] saving commands created by cmd.extend() in session files

hi, i have some scripts that load a bunch of files and do various smart things to make it easy to work with my data. in particular, they define functions and use cmd.extend() to register those functions. the setup takes a long time, and is therefore inconvenient. i'd like to go through it o

Re: [PyMOL] combine distance objects

On Tue, 8 Mar 2005, Robert Campbell wrote: Hi, Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote: I want to create a lot of distance objects (in the hundreds) between particular atomic pairs. Obviously I can make a script like the following, inserting the exact atomic selections that I

Re: [PyMOL] Getting Closer to Wiki Time!

On Tue, 15 Feb 2005, Douglas Kojetin wrote: While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? if you compile python from source (it's pretty easy on most linux systems (i had

Re: [PyMOL] Getting Closer to Wiki Time!

On Tue, 15 Feb 2005, Douglas Kojetin wrote: While we're throwing out all these ideas and possibilities: Is it ... possible? ... relatively painless? ... difficult? ... to use BioPython modules in PyMOL scripts? if you compile python from source (it's pretty easy on most linux systems (i had

Re: [PyMOL] Getting Closer to Wiki Time!

Please revise, extend, and embellish. plugins - a list of existing plugins - a tutorial on writing plugins -michael Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-09

Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

that help? Question: do people want the APBS plugin to support multiple molecules? I can probably put something in, but it would take a bit of work (and I'll have to think about how to keep the interface small enough for "normal" screen sizes). -michael Thank you very much,

Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

Hi, I've been meaning to update APBS tools so that some of the warnings are larger and better explained. WARNING: 53 atoms did not have properties assigned means that PyMOL couldn't automatically assign properties for 53 atoms in yoru molecule. This is usually because you have non-standar

Re: [PyMOL] Multiple ATOM selection

select thingy, id 688+689+690+1247+1259+1961+1862 - for some reason, 688-690... doesn't seem to work for me - i've had problems with id in the past .. PyMOL used to re-number things, but i don't think it re-numbers them these days (i could easily be wrong about this) - be careful in scri

[PyMOL] combining models in a biounit

hi, i want to combine the models in a biounit file. for example, ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/ky/1kyw.pdb2.gz has two models. so, i - load it - split_states on it - save everything into a pdb file but .. the pdb file ends up empty (it's just an END line).

[PyMOL] Re: APBS plugin - warnings generating pqr files (and a question for Warren)

Peter - I can't remember if you sent this to the whole list or not (I only have one sent to me, but if you send it to both places, I get two coppies, and I often delete one of those), so I appologize in advance if you only sent it to me. On Mon, 22 Nov 2004, Peter Haebel wrote: On Monday

[PyMOL] Re: APBS plugin - warnings generating pqr files

Hi, I've heard this from a few people, and the answer seems to be that the new version of APBS doesn't like chain information in the PyMOL-generated PQR files. I'll release a new version of the plugin that fixes this soon, but in the meantime, the easy solution is to remove the chain informa

RE: [PyMOL] RE: wire mesh spheres?

South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael George Lerner Sent

Re: [PyMOL] RE: wire mesh spheres?

I think you're talking about the same thing I noticed .. if so, I asked Warren about it and he said that it's on purpose; PyMOL only shows the first transparent surface in order to make transparent protein surfaces look less confusing/cluttered/distracting. If that's what you're seeing, try

[PyMOL] wire-mesh spheres?

Hi, I want to draw a bunch of spheres of various sizes and colors. I'm currently using cgos for this. No problem. Now, I also want to draw wire-mesh spheres. Does anyone have a script for making these? While I'm at it, is there a way to make cgos transparent? Thanks, -Michael -- This

Re: [PyMOL] still abou surfaces

Hi, Did you get an answer to this already? I've been swamped recently, so I haven't answered many PyMOL/APBS questions. Anyway .. I don't know anything about MSMS data and plotting surfaces, but I know a bit about PyMOL + APBS. APBS calculations (like a lot of other electrostatics calculations

RE: [PyMOL] long loading times as the number of existing objects increases

On Tue, 7 Sep 2004, Warren DeLano wrote: > In relation to this, I just noticed something very important: > > If you "set auto_zoom, off" before loading a series of structures, you'll > boost PyMOL's loading performance dramatically: by 10X at least...perhaps > much more. Just zoom once manually

Re: [PyMOL] (almost) using APBS within PyMOL

> 1) maloc and apbs have been successfully compiled from source and > installed in /usr/local > > 2) M. Lerner's APBS Tools plugin 'About' tab says to load a structure; > the 'Visualization' tab says to load a "molecule and a map" So, I just > loaded a pdb file like I usually do, and displayed as

Re: [PyMOL] help compiling/ running APBS plugin on macG5

> I also notice that the same place that has APBS has this site that > computes electrostatics from a PDB file and returns a PQR file. This > would be lovely for people like me to use for the calculations. Now > how can I use the PQR file to create an electrostatic surface with > pymol? A PQR fi

Re: [PyMOL] running APBS plugin on macG5

Hi, I don't have a Mac, so I can't really help you here .. I know there are quite a few people on the PyMOL list who've gotten APBS to work on Macs, though, so maybe one of them will chime in. If you don't get help here, you can probably get some more advice on the APBS mailing list. In case you

[PyMOL] Capturing a selection with a plugin

Hi, With the old wizard interface, I could capture selection actions with the do_select method. Is there a similary way with the Plugins? (I'm willing to write more code, I just don't know quite where to start.) Thanks, -michael -- This isn't a democracy;|_ |Michael L

Re: [PyMOL] controlling pymol externally (pipes?)

PyMOL comes with an XML-RPC server .. I don't know anything about it, but I found this post on the MMTK list: http://starship.python.net/pipermail/mmtk/2002/000435.html -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign (

Re: [PyMOL] rms commands

Hi, I could be wrong about this, but there are a couple of very picky alignment/fitting commands in PyMOL, and I think this is one of them. If it's one of the picky ones, it'll only work if everything about the two selections looks the same. In this case, your residue ids don't match up. Can you

Re: [PyMOL] A faster way of unbonding things?

y slow when dealing with so many objects (it was faster to do the cmd.do('unbond...')). any other ideas? thanks, -michael > On Tuesday 17 August 2004 17:02, Michael George Lerner wrote: > > to the protein, but not to eachother. So, lots of the ligands overlap. > > When

[PyMOL] A faster way of unbonding things?

Hi, I have a file which contains a protein and a bunch of ligands. The ligands come from a Monte Carlo simulation where they were allowed to talk to the protein, but not to eachother. So, lots of the ligands overlap. When PyMOL sees this, it draws bonds between the ligands. Every time I load up

Re: [PyMOL] displaying electrostatic maps

Hi, > I'm am a very new PYMOL user. I'm trying to calculate and display and > electrostatic map, similar to what I used to get in GRASP. I haven't used GRASP, but I wrote the PyMOL APBS plugin, soI'll see if I can help :). > I displayed my molecule. From the 'Plugin' drop down I selected 'APBS

Re: [PyMOL] Re: PyMOL-APBS os x

Hi, That sounds like APBS's psize.py is having trouble with your input data .. you could try going to the "APBS Location" tab and deleting the path to psize.py .. then it'll use my code instead. For some reason, it's reading "1.00103.81" where it expects a floating point number .. it's possible t

[PyMOL] A couple of quick PyMOL + APBS notes

Hi all, I've been getting two questions about APBS from a few people, so I thought I'd send the answers here: 1) Does APBS take a lot of memory? APBS can certainly take a lot of memory. In addition, my plugin sets up a grid that's a little finer than the APBS default (more grid points == better

[PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations

Hi all, APBS (http://agave.wustl.edu/apbs/) is a package that allows you to perform very fast, accurate electrostatics calculations. I've written a PyMOL plugin that allows you to run APBS and visualize the results very easily from within PyMOL (version 0.96 or higher). The plugin lets you confi

Re: [PyMOL] Plug-in Menu

Hi, There's some example code in pymol/modules/pmg_tk/startup/__init__.py. You can see how it works by copying it (uncommented) into a new file and placing that file in pymol/modules/pmg_tk/startup. You'll see the new plugins the next time you start PyMOL. I have a larger plugin that I've writte

Re: [PyMOL] Electronic density maps

On Tue, 22 Jun 2004, Konrad Hinsen wrote: > Bad news. My map has a grid spacing of 2 angstrom, I need better > resolution than that for placing it. > > So now I am trying chempy.brick. If you're using the CVS version of PyMOL, you might try DX multigrid formatted files. You can find some brief d

Re: [PyMOL] scripts with inline PDB

> Does anyone know of a way to embed coordinates within a pymol script? Have you seen cmd.read_pdbstr() and its companion cmd.get_pdbstr()? -michael > I'd like to be able to programmatically generate a self-contained pymol > script which loads the embedded coords, defines selections, and > highl

Re: [PyMOL] Breaking down PDB files

I think that PyMOL can only align different objects, not different selections. There may be a more elegant way, but .. If your chains are A,B,C..H, try this from the PyMOL prompt to create different objects: for c in 'A B C D E F G H'.split():cmd.create(c+'_chain','chain '+c) and this to align

Re: [PyMOL] problem with dist

I think the current way is to use the pk1 and pk2 selections. Assuming you're not using the distance wizard, Ctrl-right-click selects something as pk1 and gets rid of the other pkX selections. Double-right-click selects something as the next pkX selection. So .. Ctrl-right click to select the fir

Re: [PyMOL] loading electrostatic maps generated with apbs

Hi Cameron, > hi Michael, > > I finally got the APBS plugin to work > (http://mccammon.ucsd.edu/~cmura/PYMOL_examples/apbs_plugin.html). Great! (and nice pictures :)) > The only catch was that I had to make the following changes near line > 500 of your layer4/Cmd.c in order to build the CVS vers

Re: [PyMOL] loading electrostatic maps generated with apbs

Hi, > (1) fresh, clean install of the pymol-0.95-1.rh90.py22 RPM, downloading > the various electrostatics.py, dx.py, etc. modules from your website and > then using the load_dx() function with DX maps already calculated in a > standalone APBS run... This won't work. For now, PyMOL needs to be r

Re: [PyMOL] loading electrostatic maps generated with apbs

Hi, My code should work again. The parsing errors were probably caused by the fact that my code was out of date with respect to the current CVS version of PyMOL. Please let me know if it doesn't work! Thanks, -michael > Has anyone had luck with loading DX format electrostatic potential maps >

[PyMOL] trouble with Pmw?

Hi, I don't know much abotu Pmw, but when I compile the CVS version of PyMOL and the included version of PMW (1.1) with python 2.3, things break a bit. When I run pymol, the main window shows up but the gui doesn't. I get a traceback that ends with File "/home/mlerner/pymol/modules/Pmw/Pmw_1_

Re: [PyMOL] loading electrostatic maps generated with apbs

Hi, This is my fault. The scripts are a bit out of date and my Linux box is broken at the moment, so I haven't been able to bring my code up to date with the most recent PyMOL build. I'll put a warning on my webpage. My electrostatics wizard should still work, but the APBS tools (which are requ

Re: [PyMOL] Selections

> For example, I found a PDB online called 'pope.pdb' (a cool lipid > bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to > select all the hydrophobic tails and hydrophilic heads so that I may > apply different attributes to each. If I need to select the tails, > which in the PD

Re: [PyMOL] embeding pymol in a web page

On Mon, 29 Mar 2004, Nat Echols wrote: > > The downloaded script is then executed by Pymol, which can uses Python's > > socket abilities to download PDB files and run Pymol commands on them. > > H, I like this idea. Can PyMOL open files directly over the web? It > would be nice to simply typ

[PyMOL] How do I get PyMOL to keep TER cards?

Hi, I have a file called test.pdb that looks like this: ATOM 13268 O00 U00 1945 -18.065 -4.226 1.590 ATOM 13269 H03 U00 1945 -17.394 -4.877 1.447 ATOM 13270 C04 U00 1945 -19.175 -4.837 2.212 ATOM 13271 H05 U00 1945 -19.963 -4.104 2.383 ATOM 13272 H06 U00

Re: [PyMOL] how to search PyMOL-users archive?

hi, i posted one answer to this before, but i guess you'd need to know how to search for it before you could find it :) anyway, here's what i wrote before: Sourceforge has one here: http://sourceforge.net/mailarchive/forum.php?forum_id=60 (there's a search box in the top left corner) but it d

[PyMOL] Surface coloring with ChemPy bricks?

Does surface coloring work with ChemPy bricks? I took the script in examples/devel/brick01.py and changed it to make a ChemPy brick that goes from [0,0,0]-->[5,5,5] like so ... ... brik.setup_from_min_max( [0.0,0.0,0.0], [5.0,5.0,5.0], [0.5,0.5,0.5]) ... ... and then loaded up a pdb f

Re: [PyMOL] Help for user-defined functions

Hi, I haven't seen this documented anywhere, so I have no idea if it's the Right Way to do things, but I think all you need to do is add cmd.help_sc.append('some_func') after the cmd.extend('some_func',some_func) call. should this be built in to cmd.extend()? -michael -- This isn't a democrac

Re: [PyMOL] controlling atom sphere radii

to make all spheres smaller, try something like this: set sphere_scale, 0.3 play around with the 0.3 bit to get the size you want. last time i checked, you could only have one sphere_scale per object, so if you want different sized spheres in the same picture (i don't think you do), you may need

[PyMOL] Plugging APBS into PyMOL for electrostatics

Howdy, So, I got PyMOL+APBS working over the holidays. It's not quite ready for prime time, though, as you have to recompile PyMOL first. I also made a wizard that guides you through the electrostatics calculations and makes it easy to visualize the results. If you want to see it now, check out

Re: [PyMOL] searchable archive?

Sourceforge has one here: http://sourceforge.net/mailarchive/forum.php?forum_id=60 (there's a search box in the top left corner) but it doesn't always seem to work for me. There's another archive here: http://chips.csb.ki.se/pymol/ where the searches seem to actually work. I have no idea who

Re: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)

> > What's the problem? Both PyMOL and APBS are licensed under the GPL so I > > see no problems there. > > Well, pymol isn't obviously. Note to self: Don't post about licensing > stuff after an evening of mulled wine. I've had an evening of nice port .. we'll see how a port-influenced evening comp

RE: [PyMOL] Trying to plug APBS into PyMOL for electrostatics (almost working)

Hi again, I've gotten the code much closer to working. Also, I think it's factored well enough that most of it should be non-GPL-contaminated. After I actually get it working completely, I'll email the APBS folks to see if they care about licensing issues. Right now, I can generate isomeshes an

[PyMOL] Trying to plug APBS into PyMOL for electrostatics (not working yet)

NOTE: this doesn't actually work yet, so most people can probably ignore this message completely .. but i'd love some help! :) Hi, I've been doing all of my electrostatics calculations in MOE, but I'd like to switch to PyMOL. I looked/asked around a bit and found APBS

[PyMOL] Problems with PyMOL on IRIX 6.5.20m?

Hi, I'm having some trouble with PyMOL on my SGI's. When we upgraded from (I think) 6.5.11 to 6.5.20m, things stopped working for me. Here's what we have right now: mlerner: uname -aR IRIX64 oregano 6.5 6.5.20m 04091957 IP30 We also upgraded the compilers, and we're now using this: mlerner:

Re: [PyMOL] double bonds

On Mon, 9 Dec 2002, John Duperon wrote: > Hello everyone, > > hopefully this is a question which is not answered in some FAQ that I > missed...is it possible to have PyMol show double bonds in a simple > manner not unlike what would be found in a high school text book? Just > a black and white st

[PyMOL] A little script for massaging pdb files

The electron densities of Carbon, Nitrogen and Oxygen look basically the same to crystallographers. So, sometimes they get them confused in pdb files. In particular, one often has to flip the orientation of the side chains in Asn or Gln. Also, this means that the Nitrogens may be placed incorrec

[PyMOL] editing question

Hi, I'm trying to cycle through the various protonation states of a Histidine residue (HIE,HIP,HID). I have resn and the residue number stored as 'curr_state' and 'i' respectively. My first shot at a function looked basically like this (the real function has a a doc string and some gunk to set u

[PyMOL] Question about crystallographic symmetry

Hi, I'm looking at a PDB file which, due to symmetry, only provides me with part of the unit cell (in this case I'm looking at 1HHP, which is a dimer but only gives coordinates for the monomer, but I've run across the problem before). I'd like to see the full unit cell. I understand that I can u

[PyMOL] Installing from source on a linux box

Hi, I have PyMol up and running on my windows partition .. the installation was super easy. Now, I want to set it up on my Linux partition. I have Mandrake 8.1 installed, which means that my default python version is 2.1. It also means that many things (Numeric, zlib, etc..) are pre-installed fo