pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Suggestions

[Warren L. D. <wa...@su...>]

On 15 May 2002, Gareth Stockwell wrote:

> First let me say that PyMol is the most useful and powerful open-source
> software I have come across. 

> 1. There appears to be a bug in the isomesh routine (see comment
> submitted to the Sourceforge bugtracker).  I haven't tried the latest
> CVS version though.

Okay, thanks for the heads-up.

> 2. Some suggestions for improvements to PyMol:

Great!
 
> a) Automatic creation of sub-objects for protein structures
> After loading in a structure (e.g. a PDB protein file), would it be
> possible to have the option of automatically breaking it into an object
> for each chain, and one for each ligand present in the structure, so
> that the user could quickly click on/off the required components?  
> (This could be extended into a heirarchical tree-structure, in which
> chains, residues, atoms would all be available via the object list on
> the control panel)

Something like this can be easily constructed using a Python program with
the API.  I don't have time to do this myself right now, but I'd
encourage you (or someone else) to attempt it and then submit it for
inclusion.

> b) Graphical summary of density distribution for map data
> A feature which popped-up a histogram of density values, which could
> alter an isomesh contour value by clicking on it, would be extremely
> useful.

Hmm, neat idea! Very easy to implement, but how to do it with the
current GUI isn't so obvious...

> Also, is there a way to have a '.pymolrc' file containing commands which
> are run whenever PyMol starts?

Absolutely, all you need to do is create ".pymolrc" and place it in your
home directory.  Alternatively, you can instead create ".pymolrc.py" which
contains actual Python code instead of just PyMOL commands.

Cheers,
Warren

[PyMOL] Suggestions

[Gareth S. <ga...@eb...>]

First let me say that PyMol is the most useful and powerful open-source
software I have come across. 

I am running the 0.78 version, installed from RPM onto a RedHat Linux
7.3 system with an nVidia Vanta graphics card.

I have a few comments:

1. There appears to be a bug in the isomesh routine (see comment
submitted to the Sourceforge bugtracker).  I haven't tried the latest
CVS version though.

2. Some suggestions for improvements to PyMol:

a) Automatic creation of sub-objects for protein structures
After loading in a structure (e.g. a PDB protein file), would it be
possible to have the option of automatically breaking it into an object
for each chain, and one for each ligand present in the structure, so
that the user could quickly click on/off the required components?  
(This could be extended into a heirarchical tree-structure, in which
chains, residues, atoms would all be available via the object list on
the control panel)

b) Graphical summary of density distribution for map data
A feature which popped-up a histogram of density values, which could
alter an isomesh contour value by clicking on it, would be extremely
useful.

Also, is there a way to have a '.pymolrc' file containing commands which
are run whenever PyMol starts?

Please keep up the great work!
Gareth

Re: [PyMOL] 2-button mouse problems

[Warren L. D. <wa...@su...>]

> I am using a two-button mouse and have selected 2-Button Editing from 
> the mouse menu but am having trouble atom-picking etc. When I click on 
> an atom another atom somewhere else on the molecule is selected! I am 
> using v.80 and my PC is a Dell OptiPlex GX200 PIII. I have tried 
> reinstalling Pymol but this doesn't fix the problem. Any advice?
> Thank you.

This problem is unrelated to the mouse button selection.  It is due to an
insufficient color depth on your video card.  Try switching to a display
mode with the maximum number of colors (ie 24/32 bit, or 16.7 million
colors).  PyMOL uses color-keying to identify picked atoms, but some cheap
video cards don't do this well in 16 bit (65536 colors).

If this doesn't work, please email me directly with follow-up.

Cheers,
Warren
wa...@de...

[PyMOL] 2-button mouse problems

[Fergus B. <f.b...@au...>]

I am using a two-button mouse and have selected 2-Button Editing from 
the mouse menu but am having trouble atom-picking etc. When I click on 
an atom another atom somewhere else on the molecule is selected! I am 
using v.80 and my PC is a Dell OptiPlex GX200 PIII. I have tried 
reinstalling Pymol but this doesn't fix the problem. Any advice?
Thank you.

Fergus Binnie 
Chemistry 
University of Auckland

Re: [PyMOL] transparent sphere

[Warren L. D. <wa...@su...>]

On Mon, 13 May 2002, Michael Sorich wrote:

> I wish to draw a sphere with either a semi-transparent or mesh surface. 
> I can create a sphere as a cgo, however this has an opaque surface.
>  
> Any help would be appreciated 

I haven't added a transparency command to the CGO stream yet, so you'll
either need to use pyopengl (no raytracing) or create an atom with the
position and radius you'd like with sphere_transparency set to some
fraction (raytracing will work with this approach). 

Cheers,
Warren

[PyMOL] Beamtime at Cornell

[Richard G. <re...@co...>]

I realize this is a bit off topic for this list,
but I'm guessing there are a few crystallographers
out there who would be interested, who may not
subscribe to the CCP4 list. There are x-ray
beamtime slots still available before the Summer
down period (July, August). Sign up now while 
they last. PyMol is available at our facility.


Thanks 

Richard Gillilan
MacCHESS
Cornell

--------------------

  -- Protein Crystallography at MacCHESS --

MacCHESS, the macromolecular structure facility at the 
Cornell High-Energy Synchrotron Source, offers high-brightness 
x-ray beamtime to general academic and industrial users worldwide
through a fast and simple application process. Cornell is 
within a day's drive of most of the Northeast as far 
South as the Baltimore-Washington area. 

Experienced staff scientists are on duty to help you and your students 
get the most out of your crystals. We are expanding and new users are welcome.

Special experimental setups are also possible, contact the staff for details.

Can't travel? Send us your crystals. We'll send you data with no
collaborative/publishing obligation.

      o one-page, online express-mode applications for beamtime
      o small friendly academic environment
      o Ph.D. staff scientists on duty to help you
      o no collaborative publishing obligations
      o new Quantum 210 4Kx4K CCD detector with a 1 second chip readout!
      o BL-2 Containment for virus work 
      o unique dual Quantum-4 CCD detector for large unit cells/high resolution (*)
      o 60-processor supercomputer for structure solving
      o support for FireWire disks, DVD (*), tape backup
      o multi-terabyte RAID storage
      o high-speed networking (gigabit internal, 100Mb out)
      o fast turnaround FedEX Crystallography

     (*) Contact MacCHESS for availability

Visit our website:

   http://www.macchess.cornell.edu

Re: [PyMOL] transparent sphere

[Ricardo A. <apa...@if...>]

Hi,

the PyMOL Current Capabilities (v0.80) include "Transparent surfaces and 
spheres" (http://pymol.sourceforge.net/)

Another option would be use NCSMASK (ccp4) and control the 
"transparency" level by changing the GRID, it worked for me.

Good luck,

Ricardo Aparicio
PhD Student
Brazil




Michael Sorich wrote:

> Hi
> 
>  
> 
> I wish to draw a sphere with either a semi-transparent or mesh surface.
> 
> I can create a sphere as a cgo, however this has an opaque surface.
> 
>  
> 
> Any help would be appreciated
> 
>  
> 
> Michael Sorich
> 
> PhD Student
> 
> School of Pharmaceutical, Molecular and Biomedical Sciences
> 
> University of South Australia
> 
> Email: mic...@po...
> 
>            mik...@ho...
> 
>  
> 
> 
> ---
> Outgoing mail is certified Virus Free.
> Checked by AVG anti-virus system (http://www.grisoft.com).
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> 

[PyMOL] chempy/freemol docs

[Szilveszter J. <sz...@co...>]

During the weekend I gave a try to dig into pymol (ie I was thinking how
to implement a "PDB wizard" that somebody requested recently. I realized
there is no real docs about freemol/chempy so if I want to find out how
a molecule is represented I have to use the source - only. It is OK, but
wouldit would be even more pleasure to have some docs. Or am I simply
missing some URLs?

Cheers:

Szilva

[PyMOL] transparent sphere

[Michael S. <mik...@ho...>]

Hi
 
I wish to draw a sphere with either a semi-transparent or mesh surface. 
I can create a sphere as a cgo, however this has an opaque surface.
 
Any help would be appreciated 
 
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
 

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RE: [PyMOL] HOWTOS

[Warren L. D. <wa...@su...>]

Yes and no.  In principle, I'd like to include a large collection of such
files in the standard pymol distribution, but from a practical standpoint,
I don't have time to curate such a collection.  Thus, the ideal solution
would be that some PyMOL user initiates a project like this via web page,
and then provides regular "snapshots" which by default would be part of
the distro.  Somebody go for it!

On a completely unrelated note...

Are there any PyMOL users in Santa Fe, NM who would interested in getting
together for a beer between now and the 15th?  I'm on vacation down
here for a week, hanging with the Daylight crew.

Cheers,
Warren



On Thu, 9 May 2002, Frank Vondelft wrote:

> Very interested - and if it's been started, others (such as me) will
> have a formal place to make contributions.  (Or is something already set
> up???).
> 
> phx.
> 
> 
> 
> 
> 
> > -----Original Message-----
> > From: Eric Ross [mailto:ej...@bi...]
> > Sent: Thursday, May 09, 2002 12:55 PM
> > To: pym...@li...
> > Subject: [PyMOL] HOWTOS
> > 
> > 
> > I'm interesting in trying to make my little contribution to pymol.
> > 
> > I don't trust my python skills well enough to feel like I can 
> > make much
> > of a contribution through code, but I support a fair number of users
> > who would find how-to's and tutorials to be rather useful.
> > 
> > Is anyone else working on a HOWTO project?
> > 
> > Is there demand for any particular HOWTO's?
> > 
> > I'm thinking of perhaps starting with a couple of ultra 
> > simple examples
> > of making standard high-quality cartoons and basic single phase
> > rotating movies.
> > 
> > Perhaps a howto for molscript users would be worthwhile as well.
> > 
> > -- 
> > Eric Ross
> > University of Utah
> > Department of Biochemistry
> > ej...@bi...
> > 
> > 
> > 
> > _______________________________________________________________
> > 
> > Have big pipes? SourceForge.net is looking for download 
> > mirrors. We supply
> > the hardware. You get the recognition. Email Us: 
> > ban...@so...
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> 
> 
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> 

Re: [PyMOL] labels

[Robert C. <rl...@k2...>]

* Chris Rife <chr...@va...> [2002-05-10 10:47] wrote:
> I am making some stereo images and would like to put in some labels that 
> will move with the model. When I use the "label" command, the labels are 
> okay but they disappear with ray tracing. Is there any way around this, 
> other than adding in the labels in an image editing program?

You can use the cgo text (line or cylinder versions) as I mentioned in
my reply about drawing the xyz axes, but be warned that the labels
rotate with you molecule, so getting them oriented perpendicular to the
view may be a pain (unless there is something I've missed).

Warren's example from a previous reply of his:

# draw text using cgo
from pymol import cmd
from pymol.cgo import *
from pymol.vfont import plain

cgo = []

axes = [[2.0,0.0,0.0],[0.0,2.0,0.0],[0.0,0.0,2.0]]

pos = [0.0,0.0,0.0]
wire_text(cgo,plain,pos,'Hello World',axes)

pos = [0.0,-3.0,0.0]
cyl_text(cgo,plain,pos,'Hello Universe',0.10,axes=axes)

cmd.set("cgo_line_radius",0.03)
cmd.load_cgo(cgo,'txt')
cmd.zoom("all",2.0)


Cheers,
Robert

-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] labels

[Chris R. <chr...@va...>]

Hi,

I am making some stereo images and would like to put in some labels that 
will move with the model. When I use the "label" command, the labels are 
okay but they disappear with ray tracing. Is there any way around this, 
other than adding in the labels in an image editing program?

Thanks,
Chris

Re: [PyMOL] direction vectors

[Robert C. <rl...@k2...>]

* Tommy Wang <che...@im...> [2002-05-10 19:52] wrote:
> How do I view the direction vectors i.e. x,y,z in pymol?
> 

This is how I would do it.  Create a python script (I call it axes.py):

# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain

# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z

obj = [
   CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
   CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
   CYLINDER, 0., 0., 0., 0., 0., 10., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
   ]

# add labels to axes object (requires pymol version 0.8 or greater, I
# believe

cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[10.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,10.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,10.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])

# then we load it into PyMOL
cmd.load_cgo(obj,'axes')

################### end of script

Then you just need to do "run axes.py" from the pymol command line.

You can modify the "3" in the above description of the text labels to
change the size of the labels.  If you are running a version of pymol
older the 0.8, then you cannot add the text (that's why I included
colour coding of the axes).  You can also use just lines instead of
cylinders if you wish:

obj = [
   BEGIN, LINES,
   COLOR, 1.0, 0.0, 0.0,
   VERTEX, 0.0, 0.0, 0.0, VERTEX, 10.0, 0.0, 0.0,
   COLOR, 0.0, 1.0, 0.0,
   VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 10.0, 0.0,
   COLOR, 0.0, 0.0, 1.0,
   VERTEX, 0.0, 0.0, 0.0, VERTEX, 0.0, 0.0, 10.0,
   END,
   ]

would work as well to define the axes object.

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] direction vectors

[Tommy W. <che...@im...>]

How do I view the direction vectors i.e. x,y,z in pymol?

tommy wang

RE: [PyMOL] HOWTOS

[Frank V. <Fra...@sy...>]

Very interested - and if it's been started, others (such as me) will
have a formal place to make contributions.  (Or is something already set
up???).

phx.





> -----Original Message-----
> From: Eric Ross [mailto:ej...@bi...]
> Sent: Thursday, May 09, 2002 12:55 PM
> To: pym...@li...
> Subject: [PyMOL] HOWTOS
> 
> 
> I'm interesting in trying to make my little contribution to pymol.
> 
> I don't trust my python skills well enough to feel like I can 
> make much
> of a contribution through code, but I support a fair number of users
> who would find how-to's and tutorials to be rather useful.
> 
> Is anyone else working on a HOWTO project?
> 
> Is there demand for any particular HOWTO's?
> 
> I'm thinking of perhaps starting with a couple of ultra 
> simple examples
> of making standard high-quality cartoons and basic single phase
> rotating movies.
> 
> Perhaps a howto for molscript users would be worthwhile as well.
> 
> -- 
> Eric Ross
> University of Utah
> Department of Biochemistry
> ej...@bi...
> 
> 
> 
> _______________________________________________________________
> 
> Have big pipes? SourceForge.net is looking for download 
> mirrors. We supply
> the hardware. You get the recognition. Email Us: 
> ban...@so...
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


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result of e-mail transmission. If verification is required please
request a hard-copy version.


----------
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delete this e-mail from your system. E-mail transmission cannot be
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contain viruses. The sender therefore does not accept liability for any
errors or omissions in the contents of this message, which arise as a
result of e-mail transmission. If verification is required please
request a hard-copy version. 

[PyMOL] HOWTOS

[Eric R. <ej...@bi...>]

I'm interesting in trying to make my little contribution to pymol.

I don't trust my python skills well enough to feel like I can make much
of a contribution through code, but I support a fair number of users
who would find how-to's and tutorials to be rather useful.

Is anyone else working on a HOWTO project?

Is there demand for any particular HOWTO's?

I'm thinking of perhaps starting with a couple of ultra simple examples
of making standard high-quality cartoons and basic single phase
rotating movies.

Perhaps a howto for molscript users would be worthwhile as well.

-- 
Eric Ross
University of Utah
Department of Biochemistry
ej...@bi...

[PyMOL] Wizard and External GUI documenation

[Michael S. <mik...@ho...>]

Is there any documentation (or self-explanatory examples) on how to make
a Wizard and/or External GUI?
 
Thanks
 
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
 

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[PyMOL] Creating separate objects from a starting structure

[Lieven B. <li...@ul...>]

  Hello all,

  I am working with a PDB file that contains a protein molecule
(chain id A) and three different ligands in its binding site (as
chains B, C and D). This file was made by combining three 
superimposed complex structures to illustrate the relationsips 
between the modes of binding of the different ligands. 

I used PyMol and the following script to create an overview
figure: 

----[ PyMol script ]-----------------------------------------

# Load the PDB file containing all the elements
load combination.pdb

# Separate structure into different objects
# chain A is the protein
create lectin,(A//)
# chains B,C and D contain three different ligands
create one,(B//)
create two,(C//)
create three,(D//)
# delete the original structure
delete combination

# Set view
hide lines,all
zoom one,3
# set orientation,...

# Color atoms according to functon
color white,lectin
# site 1
color green,(/lectin///85,86,106,132,138,220/)     
# site 2
color bluegreen,(/lectin///104,45/)                
# Generate van der Waals surface
show surface,lectin

# Ligands in different colors
set stick_radius,0.05
color magenta,one
show sticks,one
color yellow,two
show sticks,two
color red,three
show sticks,three

----------------------------------------------------------------


This works very well. Maybe a wizard could be created to automatically 
split a structure into separate objects for the different chains?



-- 
Lieven Buts
Vrije Universiteit Brussel

[PyMOL] problem loading molecule using commands

[Michael S. <mik...@ho...>]

Hi,
I am having a little trouble loading a molecule from the command line
 
PyMOL>load "test/dat/pept.pdb"
ObjectMoleculeLoadPDBFile-Error: Unable to open file!
 
I can load the molecule using the external GUI, though. What have I done
wrong?
 
Thanks
 
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
 

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RE: [PyMOL] util.mroll & movie rate

[Byron D. <by...@SL...>]

Hi Ricardo -

You can install this open-source contribution to pymol.  It was distributed
with v.80, but isn't working in the publicly available distribution I think
because of some changes Warren made to the pymol code.

The command is 'movie.tdroll' so type help movie.tdroll for advice on how to
use it after you install it.  The code below will work with pymol v.80
(currently only available for windows release, I think...).

Put the code in the movie.py file ([installation root]/DeLano
Scientific/python/modules/python/ ) directory.

Make sure you remove the tdroll routine that is currently in the movie.py
code before adding this new piece of code.

Alternatively, just replace your movie.py file with the one I've attached to
this email (hope it makes it through the maillist server...)


Now how to use it -

movie.tdroll ('Three-Dimensional roll') will allow you to use make a quick
movie of rotation along multiple axes of whatever is showing on the pymol
screen.  You can speed it up or slow it down by changing the 'skip' value.
Play with setting different axes to 0 until you achieve what you want.  I
like movie.tdroll 180,180,0,5 for a cool display of the molecule.

If your movies are still too fast, you can alter the fps setting in pymol to
be whatever you want.  Otherwise, you will have to change the playback rate
with whatever you are using to generate your movies.  I use bink&smacker
software (freely available, just google the name) for generating avi's - it
allows pseudo-control over the playback speed.

Good luck -

Byron

--->start below here---->
def tdroll(rangex,rangey,rangez,skip=1):
   '''
AUTHOR

   Byron DeLaBarre

USAGE

   movie.tdroll(rangex,rangey,rangez,skip=1,mset=0)

   This is an extension of the roll command along other axes (3d-roll)

   rangex/y/z = rotation range on respective axis
   enter 0 for no rotation on the particular axis.

   skip is angle increment in each frame

   Use skip to reduce final movie size or to speed up rotation.

EXAMPLE

   movie.tdroll 360,360,360,5

'''
   rangex = float(rangex)
   rangey = float(rangey)
   rangez = float(rangez)
   skip = int(skip)
   axis=['x','y','z']
   rangel=[rangex,rangey,rangez]
   axpos=0
   frpos=1
   tot_frames=(((rangex+rangey+rangez)/skip) + (rangex % skip) + (rangey %
skip)  + (rangez % skip))
   cmd.mset ("1 x%d" %((int(tot_frames))))
   for ax in axis:
      range = int(rangel[axpos])
      if range:
         leftover = divmod(range,skip)
         print leftover[1]
         if leftover[1]:
           range = range + int(leftover[1])
         a = 0
         while a<=range:
            cmd.mdo("%d" % (int(frpos)),"turn %s,%8.3f" % (ax,skip))
            a = a + skip
            frpos+=1
         axpos+=1
      else:
         axpos+=1
   print (" tdroll: defined rotations for %s frames" %(int(frpos) - 1))
<----- cut above here

> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...]On Behalf Of Ricardo
> Aparicio
> Sent: Monday, May 06, 2002 10:36 AM
> To: pym...@li...
> Subject: [PyMOL] util.mroll & movie rate
>
>
> Dear users:
>
> Sorry if these are trivial questions for you but I am in trouble and any
> help is very welcomed:
>
> 1) How to use util.mroll to rotate around another axis other than Y axis ?
>
> 2) how to control the speed of a movie?
> (it is possible to change size and number of images but I think there is
> an easier answer to this question)
>
> Thank you in advance,
>
>
> Ricardo Aparicio
> PhD Student
> Brazil
>
>
> _______________________________________________________________
>
> Have big pipes? SourceForge.net is looking for download mirrors. We supply
> the hardware. You get the recognition. Email Us: ban...@so...
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] extract molecule information

[Robert C. <rl...@k2...>]

Dear Warren and fellow pymol hackers,

How would I go about getting information that has been stored about a
molecule when it is read in.  For example, say I do:

   load protein.pdb

and the PDB file contains crystallographic symmetry information.  Is
there some easy way of getting at the values for a,b,c,alpha,beta,gamma
and the space group from the protein object?  

I'm almost finished a project to draw all of the crystallographic axes
within the unit cell (using CGO objects), but it would be nice if the
user didn't have to enter the unit cell information if it is already
stored from reading the PDB file.  When I get it slightly more perfected
I'll make it available on my web site for downloading.

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rl...@k2...                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

[PyMOL] util.mroll & movie rate

[Ricardo A. <apa...@if...>]

Dear users:

Sorry if these are trivial questions for you but I am in trouble and any 
help is very welcomed:

1) How to use util.mroll to rotate around another axis other than Y axis ?

2) how to control the speed of a movie?
(it is possible to change size and number of images but I think there is 
an easier answer to this question)

Thank you in advance,


Ricardo Aparicio
PhD Student
Brazil

RE: [PyMOL] problem importing pymol.cmd module

[DeLano, W. <wa...@su...>]

Michael,

   A present, you can't simply "import" the PyMOL program as a module.  =
You need to use PyMOL as your Python interpreter.

You can use "Run" from the File menu or the "run" command from within =
PyMOL.

PyMOL>cd c:\some_directory
PyMOL>run myscript.py

Since you are under windows, you can use the DOS/Win command shell:

"C:\Program Files\DeLano Scientific\PyMOL\pymolwin.exe" myscript.py

# command-line only scripts

"C:\Program Files\DeLano Scientific\PyMOL\pymolwin.exe" -qc myscript.py

- Warren

--=20
mailto:wa...@su...=20
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606  FAX:(650)-266-3501=20

-----Original Message-----
From: Sorich, Michael Joseph - SORMJ001 =
[mailto:Mic...@po...]

Subject: [PyMOL] problem importing pymol.cmd module

I have just started to use PyMol. I wish link some scripts I have =
written in python with PyMol using PyMol=92s API. From what I =
understand, all I need to do is import the module pymol.cmd and call the =
functions contained within.
=20
However, when I attempt to import this module, I get the following =
error:
=20
>>> from pymol import cmd
Traceback (most recent call last):
  File "<pyshell#0>", line 1, in ?
    from pymol import cmd
  File "C:\Program Files\DeLano =
Scientific\PyMOL/modules\pymol\__init__.py", line 137, in ?
    import _cmd
ImportError: No module named _cmd
=20
Where have I gone wrong? Any help would be appreciated.
=20

[PyMOL] problem importing pymol.cmd module

[Sorich, M. J. - S. <Mic...@po...>]

Hi,
=20
I have just started to use PyMol. I wish link some scripts I have =
written in
python with PyMol using PyMol=92s API. From what I understand, all I =
need to do
is import the module pymol.cmd and call the functions contained within.
=20
However, when I attempt to import this module, I get the following =
error:
=20
>>> from pymol import cmd
Traceback (most recent call last):
  File "<pyshell#0>", line 1, in ?
    from pymol import cmd
  File "C:\Program Files\DeLano =
Scientific\PyMOL/modules\pymol\__init__.py",
line 137, in ?
    import _cmd
ImportError: No module named _cmd
=20
Where have I gone wrong? Any help would be appreciated.
=20
=20
Michael Sorich
PhD Student
School of Pharmaceutical, Molecular and Biomedical Sciences
University of South Australia
Email: mic...@po...
           mik...@ho...
=20

---
Outgoing mail is certified Virus Free.
Checked by AVG anti-virus system (http://www.grisoft.com).
Version: 6.0.351 / Virus Database: 197 - Release Date: 19/04/2002
=20

RE: [PyMOL] Let's Introduce Your Company To China Government

[DeLano, W. <wa...@su...>]

> From: Marc Saric [mailto:mar...@mp...]

> >    2. Let's Introduce Your Company To China Government=20
> (inv...@ya...)
>       ^ ^ ^ ^
> Shouldn't that have been filtered out?

Absolutely.  After digging into the settings, I found that SourceForge =
doesn't protect these lists by default (grumble), but I changed the =
settings so only list members will be able to post from now on.  Contact =
me directly if you have any trouble posting.  We lost about 5 =
subscribers from that PRC spam.=20

- Warren

--

mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501