pymol-users Mailing List for PyMOL Molecular Graphics System

Hi PyMol-Community,

I have been looking for a PyMOL command to calculate the ribose sugar pucker information (in DNA) but have not found anything.  Thus, I began writing a simple Python script that is supposed to take a selection, determine whether or not it contains a ribose sugar ring, and then calculate the phase, amplitude, and pucker orientation for each nucleotide residue within the selection.  The completed script works just fine (see the script below) but it slows down significantly in performance when calling cmd.get_dihedral (at least, my crude debugging method using print statements has identified the culprit to be the get_dihedral command) with a LARGE protein-DNA complex (160,000 atoms) loaded.  However, if I only load the DNA (with no protein), the performance is lightning fast.  Can anybody help me improve the overall performance or suggest an alternative?  Thanks in advance!

Sean




=========================================================

from pymol.cgo import *    # get constants
from math import *
from pymol import cmd

def pucker(selection):

    # Author: Sean Law
    # Institute: Michigan State University
    # E-mail: sl...@ms...
    
    obj_name = selection
    objects = cmd.get_names(selection)
    for obj in objects:
        if (obj == selection):
            obj_name=obj
    sel=cmd.get_model(selection)
    first=1
    old=" "
    oldchain=" "
    residue={}
    count=0
    for atom in sel.atom:
        new=atom.chain+" "+str(atom.resi)
        newchain=atom.chain+" "+atom.segi
        if (not (oldchain == newchain) and first):
            print " " #Blank line to separate chain output
            print "%6s  %6s  %8s  Residue" % ("Phase", "Amp", "Pucker")
        if (not(new == old) and (not first)):
            #Check that all 5 atoms exist
            if(len(residue) == 5):
                #Calculate pucker
                info = pseudo(residue)
                print info+"  "+old
            else:
                print "There is no sugar in this residue"
            if (not (oldchain == newchain)):
                print " " #Blank line to separate chain output
                print "%6s  %6s  %8s  Residue" % ("Phase", "Amp", "Pucker")
            #Clear values
            residue={}
            #Store new value
            store_atom(atom,residue,obj_name)
        else:
            store_atom(atom,residue,obj_name)
        first=0
        old=new
        oldchain=newchain
    #Final Residue
    #Calculate dihedrals for final residue
    if (len(residue) == 5):
        #Calculate pucker for final residue
        info = pseudo(residue)
        print info+"  "+old
    else:
        print "There is no sugar in this residue"
    return

def sele_exists(sele):
    return sele in cmd.get_names("selections");

def pseudo(residue):
    other=2*(sin(math.radians(36.0))+sin(math.radians(72.0)))
    theta0=cmd.get_dihedral(residue['C4*'],residue['O4*'],residue['C1*'],residue['C2*'])
    theta1=cmd.get_dihedral(residue['O4*'],residue['C1*'],residue['C2*'],residue['C3*'])
    theta2=cmd.get_dihedral(residue['C1*'],residue['C2*'],residue['C3*'],residue['C4*'])
    theta3=cmd.get_dihedral(residue['C2*'],residue['C3*'],residue['C4*'],residue['O4*'])
    theta4=cmd.get_dihedral(residue['C3*'],residue['C4*'],residue['O4*'],residue['C1*'])
    #phase=atan2((theta4+theta1)-(theta3+theta0),2*theta2*(sin(math.radians(36.0))+sin(math.radians(72.0))))
    phase=atan2((theta4+theta1)-(theta3+theta0),theta2*other)
    amplitude=theta2/cos(phase)
    phase=math.degrees(phase)
    if (phase < 0):
        phase=phase+360 # 0 <= Phase < 360
    #Determine pucker
    if (phase < 36):
        pucker = "C3'-endo"
    elif (phase < 72):
        pucker = "C4'-exo"
    elif (phase <108):
        pucker = "O4'-endo"
    elif (phase < 144):
        pucker = "C1'-exo"
    elif (phase < 180):
        pucker = "C2'-endo"
    elif (phase < 216):
        pucker = "C3'-exo"
    elif (phase < 252):
        pucker = "C4'-endo"
    elif (phase < 288):
        pucker = "O4'-exo"
    elif (phase < 324):
        pucker = "C1'-endo"
    elif (phase < 360):
        pucker = "C2'-exo"
    else:
        pucker = "Phase is out of range"
    info = "%6.2f  %6.2f  %8s" % (phase, amplitude, pucker)
    return info
    

def store_atom(atom,residue,obj_name):
    if (atom.name == "O4'" or atom.name == "O4*"):
        residue['O4*'] = str(atom_sele(atom,obj_name))
    elif (atom.name == "C1'" or atom.name == "C1*"):
        residue['C1*'] = str(atom_sele(atom,obj_name))
    elif (atom.name == "C2'" or atom.name == "C2*"):
        residue['C2*'] = str(atom_sele(atom,obj_name))
    elif (atom.name == "C3'" or atom.name == "C3*"):
        residue['C3*'] = str(atom_sele(atom,obj_name))
    elif (atom.name == "C4'" or atom.name == "C4*"):
        residue['C4*'] = str(atom_sele(atom,obj_name))
    return

def atom_sele(atom,obj_name):
    atom_sele = ""
    if (not (obj_name == "")):
        atom_sele = atom_sele+obj_name+" & "
           if (not (atom.segi == "")):
        atom_sele = atom_sele+"segi "+atom.segi+" & "
           if (not (atom.chain == "")):
        atom_sele = atom_sele+"chain "+atom.chain+" & "
    if (not (atom.resn == "")):
        atom_sele = atom_sele+"resn "+atom.resn+" & "
    if (not (atom.resi == "")):
        atom_sele = atom_sele+"resi "+str(atom.resi)+" & "
    if (not (atom.name == "")):
        atom_sele = atom_sele+"name "+atom.name
    return atom_sele

cmd.extend("pucker",pucker)

_________________________________________________________________
Reinvent how you stay in touch with the new Windows Live Messenger.
http://go.microsoft.com/?linkid=9650731

Obviously that should read 'resn asn' in stead of 'resn asp'. Sorry for that.

Tsjerk

On Tue, Mar 31, 2009 at 9:56 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Nir,
>
> Pymol just draws bonds based on distances, not based on topological
> information. If atoms are within contact distance, a bond will be
> drawn, whatever the atoms are. If one feels need for an additional
> bond, it is possible to add them using:
>
> bond selection1, selection2
>
> This will draw bonds between all atoms of selection1 and all atoms of
> selection2. In Thierry's case it would be something like:
>
> bond resi X and resn asp and name CD, resi Y and resn lys and name NZ
>
> assuming this is about a side chain - side chain amide bond.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Tue, Mar 31, 2009 at 9:14 PM, Nir London <ni...@ro...> wrote:
>> Hi, Can anyone help thierry ?
>> http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149
>> " I would like to ask to make a special bond in pymol. Actually in my
>> protein I have a real covalent bond between an Asn and a Lys.. Obviously,
>> Pymol doesn’t know how to draw it. Can you help me ?
>> Thanks. "
>> thierry
>>
>> Nir London.
>> Rosetta Design Group.
>> http://rosettadesigngroup.com/blog/
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi Nir,

Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance, a bond will be
drawn, whatever the atoms are. If one feels need for an additional
bond, it is possible to add them using:

bond selection1, selection2

This will draw bonds between all atoms of selection1 and all atoms of
selection2. In Thierry's case it would be something like:

bond resi X and resn asp and name CD, resi Y and resn lys and name NZ

assuming this is about a side chain - side chain amide bond.

Hope it helps,

Tsjerk


On Tue, Mar 31, 2009 at 9:14 PM, Nir London <ni...@ro...> wrote:
> Hi, Can anyone help thierry ?
> http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149
> " I would like to ask to make a special bond in pymol. Actually in my
> protein I have a real covalent bond between an Asn and a Lys.. Obviously,
> Pymol doesn’t know how to draw it. Can you help me ?
> Thanks. "
> thierry
>
> Nir London.
> Rosetta Design Group.
> http://rosettadesigngroup.com/blog/
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi, Can anyone help thierry ?
http://rosettadesigngroup.com/blog/10/pymol-scripts/#comment-3149

" I would like to ask to make a special bond in pymol. Actually in my  
protein I have a real covalent bond between an Asn and a Lys..  
Obviously, Pymol doesn’t know how to draw it. Can you help me ?
Thanks. "
thierry

Nir London.
Rosetta Design Group.
http://rosettadesigngroup.com/blog/

Friends,
Someone please write to me how to resolve the following error.

 OpenGL graphics engine:
  GL_VENDOR: Mesa Project
  GL_RENDERER: Software Rasterizer
  GL_VERSION: 1.4 (2.1 Mesa 7.3-devel)
Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/pymol/__init__.py", line 400, in
launch_gui
    __import__(self.invocation.options.gui)
  File "/usr/lib/python2.5/site-packages/pmg_tk/__init__.py", line 22, in
<module>
    from PMGApp import *
  File "/usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py", line 28, in
<module>
    from Tkinter import *
  File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 38, in <module>
    import _tkinter # If this fails your Python may not be configured for Tk
ImportError: /usr/local/chimera/lib/libtk8.5.so: cannot restore segment prot
after reloc: Permission denied
 Detected 2 CPU cores.  Enabled multithreaded rendering.

thanks
bala

Hi!

Try with:

select <selection name>, <name of the object to which the selection belongs>
w. 5 of <other object>
select <other selection name>, br. <selection name>
save name.pdb, <other selection name>

The first command select the atoms at 5 Angstroms from <other object>;
the second select the whole residues to which the atoms selected belong;
the third saves the complete selection.

Hope it helps!
Annalisa

------------------------------------------------
Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano
Italy
------------------------------------------------


2009/3/31 Luca Varani <luc...@ir...>

> Hello,
>
> is it possible to generate a list of all residues within 5A of another (or
> whatever you need)
> and then save this list to a file/clipboard?
>
> Thanks a lot for the help,
> Luca
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Hello,

is it possible to generate a list of all residues within 5A of another 
(or whatever you need)
and then save this list to a file/clipboard?

Thanks a lot for the help,
Luca

Hey Wulf,

after firing up your old session, you should be able to extract any 
setting by typing 'get setting', e.g. 'get stick_radius' or 'get 
sphere_scale'.

Also, think about saving important PyMOL work as pml scripts.  I find 
them much easier to handle.


Andreas



Wulf Blankenfeldt wrote:
> Hi all,
> 
> I need to make a set of figures with a protein having different ligands 
> bound to the active site. I already have a few of them finished and now 
> I want to make the rest in a similar (identical) way.
> 
> Unfortunately, I have forgotten how I set sphere_scale, stick_radius and 
> the like for a few of the things I am showing, and I have varied these 
> settings for different parts of the plot - is there a way to get these 
> parameters listed from the old session file (which I kept)?
> 
> Thanks in advance,
> 
> 
> Wulf
> 
> 
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 

-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk

Hi all,

I need to make a set of figures with a protein having different ligands 
bound to the active site. I already have a few of them finished and now 
I want to make the rest in a similar (identical) way.

Unfortunately, I have forgotten how I set sphere_scale, stick_radius and 
the like for a few of the things I am showing, and I have varied these 
settings for different parts of the plot - is there a way to get these 
parameters listed from the old session file (which I kept)?

Thanks in advance,


Wulf

Hi,

in mac os x i have an opened session and i wonder if it is possible to 
add a new molecule from finder, just dragging the molecule to the pymol 
interface. I tried and it does not work, and it is very annoying working 
on different directories and always giving the path for the different 
molecules. Or I wonder if it exists a better method to do it

Thanks in advance

Horacio

Yes, from Python:

cmd.transform_selection( selection, 
     [m0, m1, m2, ax,
      m3, m4, m5, ay,
      m6, m7, m8, az,
      bx, by, bz,  1])

where b(xyz) is a pre-translation (applied before the rotation) and a(xyz) is a post-translation (applied after the rotation).  This is that we call a TTT matrix inside PyMOL (translate -> transform -> translate).

Note that the a/b convention of PyMOL's TTT matrices was swapped at some point in versions pre-1.0 in order to better match the homogenous transformation matrix convention of:

cmd.transform_selection( selection, 
     [m0, m1, m2, ax,
      m3, m4, m5, ay,
      m6, m7, m8, az,
      0, 0, 0, 1], homogenous=1)

which, in effect only includes a post-translation. 

Cheers,
Warren

# example

dele all

reset

fragment phe, mol1

fragment phe, mol2

cmd.transform_selection("mol1",[0,1,0,-2, -1,0,0,0, 0,0,1,0, 0,-3,0,1])
 
________________________________________
From: cedric bauvois [mailto:cba...@gm...] 
Sent: Friday, March 27, 2009 5:03 AM
To: pym...@li...
Subject: [PyMOL] moving molecules using rotation matrix

Dear All,

Is there any command to move a molecule using this type of matrix ?

 -------- rotation matrix to rotate Chain-1 to Chain-2 ------
 i          t(i)         u(i,1)         u(i,2)         u(i,3)

 1    -59.0140477207   0.5936510259  -0.4271312489   0.6820097915
 2     26.6732874752  -0.7924917102  -0.4575097139   0.4032886695
 3     86.5815155425   0.1397689115  -0.7798998384  -0.6100990849


Thanks

-- 
..................................................................
Dr. Cedric Bauvois
Cristallographie des protéines
Institut de Recherches Microbiologiques J.-M. Wiame -IRMW
Campus CERIA - Av. E. Gryson, 1
B-1070 Bruxelles, BELGIUM
e-mail: Ced...@ul...
tél: +32 (0)2 5273634
fax: +32 (0)2 5267273
.................................................................. 

Hi Warren,

I only have CRYST1, SCALE, ATOM and END lines in my pdb file. The file  
originally came out of ccp4's refmac & pdbset. I can email it and my  
conformers.pml script to you privately if  it would help.

Simon



On 27 Mar 2009, at 14:45, Warren DeLano wrote:

> Simon,
>
> You're triggering some special-purpose annotated PDB code from many  
> years back.  Are there USER records in your PDB files by chance?   
> Getting rid of those should solve the problem.
>
> Cheers,
> Warren
>
> -----Original Message-----
> From: Simon Kolstoe [mailto:s.k...@uc...]
> Sent: Fri 3/27/2009 7:16 AM
> To: pym...@li...
> Subject: [PyMOL] Scripting question
>
> Dear PyMOL list,
>
> I am trying to visualise 20 docked ligand conformations using PyMOL. I
> have been opening PyMOL as the GUI, setting up a view of my protein,
> and then running the following script to load my ligand conformations:
>
> load conformer000.pdb, conf0
> load conformer001.pdb, conf1
> load conformer002.pdb, conf2
> etc...
>
> However the script seems to also invoke the following commands which
> screw up my pretty picture:
>
> PyMOL>show cartoon
> PyMOL>util.cbac
>   Executive: Colored 9 atoms.
>   Executive: Colored 2 atoms.
> PyMOL>set cartoon_discrete_colors,1
>   Setting: cartoon_discrete_colors set to on.
> PyMOL>set cartoon_smooth_loops, 0
>   Setting: cartoon_smooth_loops set to off.
> PyMOL>set cartoon_flat_sheets, 0
>   Setting: cartoon_flat_sheets set to off.
> PyMOL>set valence,1
>   Setting: valence set to on.
> PyMOL>set stick_ball,1
>   Setting: stick_ball set to on.
> PyMOL>orient
> PyMOL>context_info=m4x.get_context_info()
> PyMOL>m4x.setup_contexts(context_info)
>
> Is there anyway of making the script JUST load the conformations and
> not change these other settings?
>
> Thanks,
>
> Simon
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
>
>
>

Simon,

You're triggering some special-purpose annotated PDB code from many years back.  Are there USER records in your PDB files by chance?  Getting rid of those should solve the problem. 

Cheers,
Warren

-----Original Message-----
From: Simon Kolstoe [mailto:s.k...@uc...]
Sent: Fri 3/27/2009 7:16 AM
To: pym...@li...
Subject: [PyMOL] Scripting question
 
Dear PyMOL list,

I am trying to visualise 20 docked ligand conformations using PyMOL. I  
have been opening PyMOL as the GUI, setting up a view of my protein,  
and then running the following script to load my ligand conformations:

load conformer000.pdb, conf0
load conformer001.pdb, conf1
load conformer002.pdb, conf2
etc...

However the script seems to also invoke the following commands which  
screw up my pretty picture:

PyMOL>show cartoon
PyMOL>util.cbac
  Executive: Colored 9 atoms.
  Executive: Colored 2 atoms.
PyMOL>set cartoon_discrete_colors,1
  Setting: cartoon_discrete_colors set to on.
PyMOL>set cartoon_smooth_loops, 0
  Setting: cartoon_smooth_loops set to off.
PyMOL>set cartoon_flat_sheets, 0
  Setting: cartoon_flat_sheets set to off.
PyMOL>set valence,1
  Setting: valence set to on.
PyMOL>set stick_ball,1
  Setting: stick_ball set to on.
PyMOL>orient
PyMOL>context_info=m4x.get_context_info()
PyMOL>m4x.setup_contexts(context_info)

Is there anyway of making the script JUST load the conformations and  
not change these other settings?

Thanks,

Simon



------------------------------------------------------------------------------
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Dear PyMOL list,

I am trying to visualise 20 docked ligand conformations using PyMOL. I  
have been opening PyMOL as the GUI, setting up a view of my protein,  
and then running the following script to load my ligand conformations:

load conformer000.pdb, conf0
load conformer001.pdb, conf1
load conformer002.pdb, conf2
etc...

However the script seems to also invoke the following commands which  
screw up my pretty picture:

PyMOL>show cartoon
PyMOL>util.cbac
  Executive: Colored 9 atoms.
  Executive: Colored 2 atoms.
PyMOL>set cartoon_discrete_colors,1
  Setting: cartoon_discrete_colors set to on.
PyMOL>set cartoon_smooth_loops, 0
  Setting: cartoon_smooth_loops set to off.
PyMOL>set cartoon_flat_sheets, 0
  Setting: cartoon_flat_sheets set to off.
PyMOL>set valence,1
  Setting: valence set to on.
PyMOL>set stick_ball,1
  Setting: stick_ball set to on.
PyMOL>orient
PyMOL>context_info=m4x.get_context_info()
PyMOL>m4x.setup_contexts(context_info)

Is there anyway of making the script JUST load the conformations and  
not change these other settings?

Thanks,

Simon

Hi Cedric,

In general terms, you can do such things with alter_state. More
specifically, you may want to start scripting, reading in the file
(assuming it's from a file) and doing the transformation. One thing
that's not directly clear is whether t is pre- or post-shifting. You
can  directly read in the matrix from the file using some Python
magic:

M=[ map(float,x.split()[1:]) for x in open("matrixfile").readlines()
if x.strip() and x.strip()[0] in "123" ]

Yes, I know this is way over the top :) List comprehensions are
definitely the way to break the inobfuscatability of Python ;) But
then again, you would be able to do:

def ip(x,y): sum( [ x[i]*y[i] for i in range( len( x ) ) ] )
alter_state 1,Chain_1,(x,y,z)=[ M[i][0]+ip((x,y,z),M[i][1:]) for i in range(3) ]

Hmm, haven't actually tested this and I don't give warranty ;)

Cheers,

Tsjerk

On Fri, Mar 27, 2009 at 10:56 AM, cedric bauvois <cba...@gm...> wrote:
> Dear All,
>
> Is there any command to move a molecule using this type of matrix ?
>
>
>  -------- rotation matrix to rotate Chain-1 to Chain-2 ------
>  i          t(i)         u(i,1)         u(i,2)         u(i,3)
>
>  1    -59.0140477207   0.5936510259  -0.4271312489   0.6820097915
>  2     26.6732874752  -0.7924917102  -0.4575097139   0.4032886695
>  3     86.5815155425   0.1397689115  -0.7798998384  -0.6100990849
>
> Thanks
>
> --
> ..................................................................
> Dr. Cedric Bauvois
> Cristallographie des protéines
> Institut de Recherches Microbiologiques J.-M. Wiame -IRMW
> Campus CERIA - Av. E. Gryson, 1
> B-1070 Bruxelles, BELGIUM
> e-mail: Ced...@ul...
> tél: +32 (0)2 5273634
> fax: +32 (0)2 5267273
> ..................................................................
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Dear All,

Is there any command to move a molecule using this type of matrix ?


 -------- rotation matrix to rotate Chain-1 to Chain-2 ------
 i          t(i)         u(i,1)         u(i,2)         u(i,3)
 1    -59.0140477207   0.5936510259  -0.4271312489   0.6820097915
 2     26.6732874752  -0.7924917102  -0.4575097139   0.4032886695
 3     86.5815155425   0.1397689115  -0.7798998384  -0.6100990849



Thanks

-- 
..................................................................
Dr. Cedric Bauvois
Cristallographie des protéines
Institut de Recherches Microbiologiques J.-M. Wiame -IRMW
Campus CERIA - Av. E. Gryson, 1
B-1070 Bruxelles, BELGIUM
e-mail: Ced...@ul...
tél: +32 (0)2 5273634
fax: +32 (0)2 5267273
..................................................................

Hi Thomas,

Joel gave some pointers using the menus. But the reason for giving
spheres and mentioning that as a generic way is that spheres will work
for connected as well as non-bonded atoms. In the case of sulphate you
probably want to have a stick representation. The hydrogen bonds can
be drawn using the 'distance' command. See

http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties

Cheers,

Tsjerk

On Fri, Mar 27, 2009 at 8:19 AM, Jhon Thomas <jho...@gm...> wrote:
> Hello Tsjerk
>
>
> Thanks for your reply...
>
> I want to show my ligand (sulpahete) in my figure and its interaction with
> the selcted atoms of the selected residues (Hbonds, ionic etc). as well as i
> want to show the interaction (hbonds) with the selected atoms of the
> selected residues. shwing sphere wouldnot be a good way. i will appreciate
> your help.
>
> Thank you
>
> Thomas
>
> On Thu, Mar 26, 2009 at 12:45 AM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
>>
>> Hi Thomas,
>>
>> You're not really specific here, so I'll give the most general reply:
>>
>> show spheres,  hetatm
>>
>> By the way, these compounds will definitely be drawn either as sticks
>> or as nonbonded upon loading of the structure. You may not easily see
>> them, but if they're in the file, they'll be drawn.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Wed, Mar 25, 2009 at 5:30 PM, Jhon Thomas <jho...@gm...>
>> wrote:
>> > Hi all
>> >
>> > I would like to know, how we can show the ligands in pymol. Although i
>> > can
>> > see the non-bonded atoms ( HOH) automatically, eacept other nonbonded
>> > atoms
>> > l;ike sulphate  and metal ions. I will appreciate the suggestions.
>> >
>> > Thanks in advance
>> >
>> > Thomas
>> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > PyMOL-users mailing list
>> > PyM...@li...
>> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>> >
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Dear Jhon,

You want to use the show sticks option. Using the sequence viewer, this will show your ligands etc. Select these by clicking on them in the sequence viewer then under selection pick show sticks. From this point once you have displayed the selected residues it would be best to use the measurement wizard. You can turn off the actual distance using the label option. Pymol will only identify H-bonds you will have to identify the rest yourself.

I hope this helps. For further information look at the pymol wiki. It is also better to post these requests to the bulletin board so others cab see the results

Regards


Joel Tyndall, PhD



Senior Lecturer in Medicinal Chemistry

National School of Pharmacy

University of Otago

PO Box 56 Dunedin 9054

New Zealand



Pukenga

Te Kura Taiwhanga Putaiao

Te Whare Wananga o Otago

Pouaka Poutapeta 913 Otepoti 9054

Aotearoa



Ph / Waea +64 3 4797293

Fax / Waeawhakaahua +64 3 4797034





________________________________
From: Jhon Thomas [mailto:jho...@gm...]
Sent: Friday, 27 March 2009 8:20 p.m.
To: Joel Tyndall
Subject: Re: [PyMOL] depiction of ligands

Hi joel

Thanks for your reply...
I want to show my ligand (sulpahete) in my figure and its interaction with the selcted atoms of the selected residues (Hbonds, ionic etc). as well as i want to show the interaction (hbonds) with the selected atoms of the selected residues. shwing sphere wouldnot be a good way. i will appreciate your help.

Thank you

Thomas
On Thu, Mar 26, 2009 at 1:51 AM, Joel Tyndall <joe...@ot...<mailto:joe...@ot...>> wrote:

Hi there,



There are many ways to do this. You can also try Action>preset>ligands. This will show the ligands (hetatms) and their interactions. Unfortunately this doesn't highlight metal ions everytime (unless it interacts with the ligands). You can usually view this using the sequence option. [show the sequence - S button bottom right, move the slider to the end of the protein (usually) and select the metal(s) show spheres of selection]



Hope this helps



J



_________________________________

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034

________________________________

From: Jhon Thomas [mailto:jho...@gm...<mailto:jho...@gm...>]
Sent: Thursday, 26 March 2009 5:30 a.m.
To: pym...@li...<mailto:pym...@li...>
Subject: [PyMOL] depiction of ligands



Hi all

I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate  and metal ions. I will appreciate the suggestions.

Thanks in advance

Thomas

Dave,

/Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL myscript.pml

Recent MacPyMOL builds come with a ./setup.sh inside the .app bundle
directory which can be used to generate a "pymol" script which works
just like the linux equivalent:

cd /Applications/MacPyMOL.app/

./setup.sh

cp ../pymol ~/bin/

cd ~

pymol myscript.pml


# the same thing can be done with PyMOLX11Hybrid.app:

cd /Applications/PyMOLX11Hybrid.app/

./setup.sh

cp ../pymol ~/bin/xpymol

cd ~

xpymol myscript.pml

Cheers,
Warren

> -----Original Message-----
> From: David Garboczi [mailto:dga...@ni...]
> Sent: Thursday, March 26, 2009 6:31 AM
> To: pym...@li...
> Subject: [PyMOL] startup options in MacPyMOL
> 
> How can I have a startup file read when I launch MacPyMOL?  For
> example, to set the background to white or load a particular pdb.
> 
> thanks,
> 
> Dave
> 
> 
> 
> --
> 
>
------------------------------------------------------------------------
--
> ----
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

How can I have a startup file read when I launch MacPyMOL?  For 
example, to set the background to white or load a particular pdb.

thanks,

Dave



-- 

Hi there,

There are many ways to do this. You can also try Action>preset>ligands. This will show the ligands (hetatms) and their interactions. Unfortunately this doesn't highlight metal ions everytime (unless it interacts with the ligands). You can usually view this using the sequence option. [show the sequence - S button bottom right, move the slider to the end of the protein (usually) and select the metal(s) show spheres of selection]

Hope this helps

J


_________________________________

Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
http://www.researcherid.com/rid/C-2803-2008

Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034

________________________________
From: Jhon Thomas [mailto:jho...@gm...]
Sent: Thursday, 26 March 2009 5:30 a.m.
To: pym...@li...
Subject: [PyMOL] depiction of ligands

Hi all

I would like to know, how we can show the ligands in pymol. Although i can see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms l;ike sulphate  and metal ions. I will appreciate the suggestions.

Thanks in advance

Thomas

Hi Thomas,

You're not really specific here, so I'll give the most general reply:

show spheres,  hetatm

By the way, these compounds will definitely be drawn either as sticks
or as nonbonded upon loading of the structure. You may not easily see
them, but if they're in the file, they'll be drawn.

Hope it helps,

Tsjerk

On Wed, Mar 25, 2009 at 5:30 PM, Jhon Thomas <jho...@gm...> wrote:
> Hi all
>
> I would like to know, how we can show the ligands in pymol. Although i can
> see the non-bonded atoms ( HOH) automatically, eacept other nonbonded atoms
> l;ike sulphate  and metal ions. I will appreciate the suggestions.
>
> Thanks in advance
>
> Thomas
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Wulf,

The source code for "presets" can be found in modules/pymol/preset.py,
but there is object, method, and housekeeping stuff in there that
distracts from its understandability.  

show surface, polymer within 5 of organic

May be all that you really need.

# example use

load $TUT/1hpv.pdb

hide

show surface, polymer within 5 of organic

set two_sided_lighting

show lines, byres polymer within 5 of organic

show sticks, organic

color auto, organic and elem c

set transparency, 0.3

Cheers,
Warren

> -----Original Message-----
> From: Wulf Blankenfeldt [mailto:wul...@mp...]
> Sent: Wednesday, March 25, 2009 10:34 AM
> To: pym...@li...
> Subject: [PyMOL] Showing only part of a surface around a ligand
> 
> Hi all,
> 
> this question may be resolvable by sufficient RTFMing, but maybe there
> is someone out there to help me...
> 
> I am trying to generate a figure in which I want to show only a part
of
> the protein surface around a ligand - pretty much like
> 
> preset --> ligand sites --> solid surface
> 
> I have already tried some amateur solutions like splitting the ligand
> into parts, placing waters to generate pseudo-ligand atoms and the
like.
> Somewhat unsatisfying. I have also realized that I can click on every
> atom of the protein and do a show surface, but this will drive me
insane
> sooner than later.
> 
> I guess it must be doable through some magic selection commands - if I
> could only see how the preset command works, I could probably work it
> out from there.
> 
> Can somebody please point me in the right direction?
> 
> Thanks in advance,
> 
> 
> Wulf
> 
> 
>
------------------------------------------------------------------------
--
> ----
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

Wulf,

suppose you have this scenario:
Protein in chain A
Ligand in chain I

Then 

create b-site, byres chain A within 5 of chain I
show sticks, chain I
show surface, b-site

should get you close.

HTH

	Carsten

BTW If you replace the "create" command with "select" your surface will be "scribed" i.e. with frizzled ends. If this is what you want then you should use select.

-----Original Message-----
From: Wulf Blankenfeldt [mailto:wul...@mp...]
Sent: Wednesday, March 25, 2009 1:31 PM
To: pym...@li...
Subject: [PyMOL] Showing only part of a surface around a ligand


Hi all,

this question may be resolvable by sufficient RTFMing, but maybe there 
is someone out there to help me...

I am trying to generate a figure in which I want to show only a part of 
the protein surface around a ligand - pretty much like

preset --> ligand sites --> solid surface

I have already tried some amateur solutions like splitting the ligand 
into parts, placing waters to generate pseudo-ligand atoms and the like. 
Somewhat unsatisfying. I have also realized that I can click on every 
atom of the protein and do a show surface, but this will drive me insane 
sooner than later.

I guess it must be doable through some magic selection commands - if I 
could only see how the preset command works, I could probably work it 
out from there.

Can somebody please point me in the right direction?

Thanks in advance,


Wulf


------------------------------------------------------------------------------
_______________________________________________
PyMOL-users mailing list
PyM...@li...
https://lists.sourceforge.net/lists/listinfo/pymol-users

Hi all,

this question may be resolvable by sufficient RTFMing, but maybe there 
is someone out there to help me...

I am trying to generate a figure in which I want to show only a part of 
the protein surface around a ligand - pretty much like

preset --> ligand sites --> solid surface

I have already tried some amateur solutions like splitting the ligand 
into parts, placing waters to generate pseudo-ligand atoms and the like. 
Somewhat unsatisfying. I have also realized that I can click on every 
atom of the protein and do a show surface, but this will drive me insane 
sooner than later.

I guess it must be doable through some magic selection commands - if I 
could only see how the preset command works, I could probably work it 
out from there.

Can somebody please point me in the right direction?

Thanks in advance,


Wulf