[PyMOL] Display vectors of some atoms by arrow?

2009-09-09 Thread S4C6Ar Chung 
Dear all,

  Is it possible to show normal model/vectors of the "selected atoms" by
arrow in Pymol? Thank you for any suggestion and help.

Best Wishes,

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

2009-09-09 Thread Warren DeLano 
Michael,
 
Assuming you have a PyMOL 1.2 build with the Tcl/Tk user interface
displayed:
 
Load a small-molecule or peptide structure or simply type "fab "
then
 
(1) activate the builder by clicking on the "Builder" button on the
upper window
 
(2) click the "Bumps" checkbox
 
(3) click the Sculpt button
 
Now CTRL-click-and-drag atoms around in the 3D viewer.  You'll see the
little disks appear when the van der Waals radii overlap.  When done,
click the Clean button to minimize the structure into a nearby local
energy minimum.
 
Cheers,
Warren



From: Michael Lerner [mailto:mglerner+sourcefo...@gmail.com] 
Sent: Friday, September 04, 2009 6:15 AM
To: a...@artforscience.com
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Creating a single PDB from two PDB - ala
docking by hand


I definitely remember some mode where PyMOL would show good/bad
contacts with red/green dots, but I can't seem to figure it out now. It
was in Warren's talk as he was manually docking in a ligand. I searched,
but couldn't figure it out myself. Does anyone know how to put PyMOL
into that mode?

Cheers,

-Michael


On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg
 wrote:


Bring up both pdb files in one session,
orient the ligand by going to editing mode and using the
shift key with
the left mouse button (3 button mouse mode) to move just
the ligand.
Once you have it in the position you want,
type select all in the command line and then hit enter,
In the A menu for the (sele) you just created pick copy
to object.
PyMOL will create a new pdb with all of the coordinates
of the two pdb
files as they are positioned on screen.
Rename it if you'd like, and save the new pdb out from
the File
menu/save molecule.



Mark Benson wrote:
> Dear All,
>
> I am trying to build a single PDB file from two
different PDB
> files.  One PDB has a small organic ligand, and the
second PDB
> contains amino acid side chains from an active site.
>
> I load both PDB files, but I want to "freeze" the
orientation of
> the amino acid side chains PDB ( not move it), and
then place and
> orient the ligand PDB in a certain pose with respect
to the amino
> acid side chains.
>
> Ideally, I would then like to save the coordinates for
both the
> amino side chains and the ligand coordinates to a
single PDB
> file.
>
> In the long run, I want to run a simple minimization
on an
> possible active site cluster and I want to get a feel
for the
> energetics of the ligand in the active site.  I don't
like working
> with MOLDEN or some of the other suites out there and
I wanted to
> try this with PyMOL.  I've gone through the manual,
the web,
> pymolwiki, the "masking" and "protecting" options, and
I've tried
> examining the use of frames and split_states, but I
haven't come
> up with anything.
>
> I've heard about a demo that Warren DeLano put on for
the ACS
> where, as part of the demo, he showed off some toy
example where
> he docked a ligand in by hand, complete with having
PyMOL show
> red/green dots for steric clashes/matches.
>
> Any ideas?
>
> -Mark
>
>
>

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

2009-09-09 Thread Warren DeLano 
Mark,

Assuming you have one of our PyMOL 1.2r1 builds (on Mac, launch as
PyMOLX11Hybrid, not MacPyMOL), try the following command sequence:

load $TUT/1hpv.pdb

remove not (polymer or organic)

remove not byres (organic expand 4)

h_add

flag fix, not organic

show sticks, organic

orient organic

Now you can use the Builder to manipulate the ligand in the presence of
fixed protein atoms as per my previous post (see modified excerpt
below).

Everyone please keep in mind that PyMOL is just a "toy" modeler only
useful for setting up 3D poses that will be used as input for other
software.  If you want to do "real" modeling, please get Maestro,
M.O.E., Sybyl, etc.

Cheers,
Warren

Builder use:

(1) activate the builder by clicking on the "Builder" button on the
upper window
 
(2) click the "Bumps" checkbox
 
(3) click the "Sculpt" button
 
Now CTRL-click-and-drag (ligand) atoms (only) around in the 3D viewer.
(be careful not to click protein atoms).  You'll see the little disks
appear when the van der Waals radii overlap.  When done, click the
"Clean" button to minimize the structure into a nearby local minimum.   

NOTE: Ctrl-Z will actually undo conformational changes (ignore the Undo
button for now).
 
> -Original Message-
> From: Mark Benson [mailto:m...@ufl.edu] 
> Sent: Thursday, September 03, 2009 8:57 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Creating a single PDB from two PDB - ala 
> docking by hand
> 
> Dear All,
> 
> I am trying to build a single PDB file from two different PDB 
> files.  One PDB has a small organic ligand, and the second 
> PDB contains amino acid side chains from an active site.
> 
> I load both PDB files, but I want to "freeze" the orientation 
> of the amino acid side chains PDB ( not move it), and then 
> place and orient the ligand PDB in a certain pose with 
> respect to the amino acid side chains.
> 
> Ideally, I would then like to save the coordinates for both 
> the amino side chains and the ligand coordinates to a single PDB file.
> 
> In the long run, I want to run a simple minimization on an 
> possible active site cluster and I want to get a feel for the 
> energetics of the ligand in the active site.  I don't like 
> working with MOLDEN or some of the other suites out there and 
> I wanted to try this with PyMOL.  I've gone through the 
> manual, the web, pymolwiki, the "masking" and "protecting" 
> options, and I've tried examining the use of frames and 
> split_states, but I haven't come up with anything.
> 
> I've heard about a demo that Warren DeLano put on for the ACS 
> where, as part of the demo, he showed off some toy example 
> where he docked a ligand in by hand, complete with having 
> PyMOL show red/green dots for steric clashes/matches.
> 
> Any ideas?
> 
> -Mark
> 
> 
> --
> 
> Let Crystal Reports handle the reporting - Free Crystal 
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> 
> 
> 
> 
> 

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Re: [PyMOL] help about mutation

2009-09-09 Thread Warren DeLano 
Chandan,
 
PyMOL's mutagenesis wizard is purely geometric, and is intended to offer
up Dunbrack rotamers as per:
 
http://dunbrack.fccc.edu/bbdep/bbdepdownload.php
 
Cheers,
Warren



From: Chandan Choudhury [mailto:iitd...@gmail.com] 
Sent: Wednesday, September 09, 2009 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] help about mutation



I am querious to know on what mathematical basis does the
software mutates the amino acids.
-- 
Chandan kumar Choudhury
NCL, Pune
INDIA


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Re: [PyMOL] undisplaying residues

2009-09-09 Thread Warren DeLano 
Bala,
 
The trick is to leave the phosphate displayed for those residues where
the backbone should still be shown:
 
hide everything, resi 20-40 and not elem p
 
Cheers,
Warren



From: Bala subramanian [mailto:bala.biophys...@gmail.com] 
Sent: Monday, August 31, 2009 12:05 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] undisplaying residues


Friends,

I made a cartoon representation of a DNA. now i want to
undisplay the base and sugar of certain residues in the DNA. Could
someone please write me how to do the same. When i select a residue and
choose HIDE-> EVERYTHING. It undisplays the cartoon of the backbone also
which i dnt want.

Regards,
Bala




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[PyMOL] help about mutation

2009-09-09 Thread Chandan Choudhury 
I am querious to know on what mathematical basis does the software mutates
the amino acids.
-- 
Chandan kumar Choudhury
NCL, Pune
INDIA
--
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