pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] fofc map

[S. S. S. R. <ra...@ya...>]

Hi,

I tried to show the fofc map by using the following lines:

load fofc.map, fofc
isomesh fo1, fofc,3.0, (chain D), buffer=2.0

but it gives the error as, Isomesh: map or brick object "fofc" not found.

i would like to show at different  contour  levels.

Thanks in advance
Raj 

		
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 What are the most popular cars? Find out at Yahoo! Autos 

[PyMOL] thick c-alpha trace?

[Jose B. <bor...@gm...>]

I have a pdb with only CA entries. I did "set ribbon_trace,1" and "show
ribbon" to see the c-alpha trace, but is there a way to control the
thickness of the lines connecting the CA's ?

jose

RE: [PyMOL] viewing multi-sdf files

[<gre...@un...>]

Hi Joel,

Have you tried the frame control commands at the lower right corner of =
your
main PyMOL window?=20
Cheers,

Greg


-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Joel =
Tyndall
Sent: jeudi, 16. f=E9vrier 2006 03:48
To: pym...@li...
Subject: [PyMOL] viewing multi-sdf files

Hi folks,

hopefully an easy solution but how do I read all the molecules (scroll=20
thru) in a multi-sdf file or mol file. I have tried the split states=20
command but that only reads the first molecule.

Any help would be appreciated.

J

--=20
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                    =20

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293=20
Fax / Waeawhakaahua     +64 3 4797034

[PyMOL] viewing multi-sdf files

[Joel T. <joe...@ot...>]

Hi folks,

hopefully an easy solution but how do I read all the molecules (scroll 
thru) in a multi-sdf file or mol file. I have tried the split states 
command but that only reads the first molecule.

Any help would be appreciated.

J

-- 
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand                     

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

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

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

[<Mat...@im...>]

pym...@li... wrote on 02/15/2006 05:36:51 PM:

> Hi all,
>
> There is a beautiful ball-and-stick image on pymol-wiki that I am
> trying to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick).
>
> The wiki image has grey bonds and light blue balls for carbon, dark
> blue for nitrogen, and red balls for oxygen.  My problem is that all
> my bonds and balls are the same color, and I can't figure out how to
> make the bonds a grey color, distinct from the atom ball colors.
> And I'm trying to script this.
>



Hi Marilyn -

You probably can't do it all with one object.  Create another object which
is a duplicate of the one you're working with, then show spheres on object
#1 and sticks on object #2.  You can then color the balls and the sticks
separately, since each object gets its own set of colors.

For example:

PyMOL>create obj1, 1FLT and chain w
 Selector: found 797 atoms.
 Executive: object "obj1" created.
PyMOL>create obj2, 1FLT and chain w
 Selector: found 797 atoms.
 Executive: object "obj2" created.
PyMOL>color gray, obj2
 Executive: Colored 797 atoms and 1 object.
PyMOL>color green, obj1
 Executive: Colored 797 atoms and 1 object.
PyMOL>show spheres, obj1
PyMOL>show sticks, obj2
PyMOL>set stick_radius, 0.1
 Setting: stick_radius set to 0.10000.
PyMOL>set sphere_scale, 0.25
 Setting: sphere_scale set to 0.25000.


This gives a ball-and-stick of one chain where the balls are all green and
the sticks are all gray.  Modify as needed....

- Matt


--
Matthew Franklin                     phone:(917)606-4116
Senior Scientist, ImClone Systems      fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014



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[PyMOL] Pymol 0.99 stereo on SGI Fuel

[Ken S. <sat...@sp...>]

Pymol 0.99 stereo works well on our system in the Med school.

SGI Fuel, R16K MIPS
V12 graphics board, C220 Dimandtron Monitor
Stereographics Z-Screen Monitor Cover, and $20 glasses.
kas


--
Kenneth A. Satyshur, M.S., Ph.D.
Associate Scientist,Department of Bacteriology
University of Wiscosin, Madison, WI 53706
608-265-9282

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

[Yoder, M. <Yo...@um...>]

Hi all,
=20
There is a beautiful ball-and-stick image on pymol-wiki that I am trying
to replicate (http://www.pymolwiki.org/index.php/Ball_and_Stick).
=20
The wiki image has grey bonds and light blue balls for carbon, dark blue
for nitrogen, and red balls for oxygen.  My problem is that all my bonds
and balls are the same color, and I can't figure out how to make the
bonds a grey color, distinct from the atom ball colors.  And I'm trying
to script this.
=20
Part of my current script is below.  I'm superimposing three molecules,
and showing sidechain atoms for three residues (which are Args).  The
carbons from each molecule I want to be distinct colors, but I want the
bonds in all to be grey.  The ball-and-stick is displaying nicely, I
just don't know how to color the thing.  I suspect my problem is from
earlier commands in coloring the whole molecule, and the selections
below are showing these same colors.
=20
--------------- what I'm currently doing ------------
=20
select ec_RR, resi 191-192+208 and eccdtb
select hd_RR, resi 249-250+232 and 1sr4b
select aa_RR, resi 249-250+232 and aacdtb
=20
cmd.show("sticks","ec_RR+hd_RR+aa_RR")
cmd.show("spheres","ec_RR+hd_RR+aa_RR")
set stick_radius=3D0.2
set sphere_scale=3D0.25
----------------end-----------------
=20
Hope this is clear,
Marilyn
=20
Marilyn D. Yoder
Division of Cell Biology and Biophysics
University of Missouri-Kansas City
5007 Rockhill Rd.
Kansas City, MO  64110-2499
phone: 816-235-1986
fax: 816-235-1503
=20

[PyMOL] PyMOL/O stereo 3D on G5 Quad with Quadro FX 4500

[Luca J. <luc...@bi...>]

Dear PyMOL & O users,

This is just a short feedback note to let you know that the stereo 3D =20=

feature of recent builds of both programs works really well with the =20
following combination:

	Apple PowerMac G5 Quad with NVIDIA Quadro FX 4500 card
	Philips 202P73 22" CRT monitor
	NuVision 60GX emitter/glasses

This is both at 1280 x 960 @ 120 Hz and 1280 x 1024 @ 100 Hz. The =20
former is perhaps marginally better, but both are essentially flicker-=20=

free.
Hope this will be of some help to people who might be considering =20
such a system,

Luca

-----------------------------------------------------
Luca Jovine, Ph.D.
Karolinska Institutet
Department of Biosciences and Nutrition
Center for Structural Biochemistry (CSB)
H=E4lsov=E4gen 7-9, S-141 57 Huddinge, Sweden
Voice: +46.(0)8.6083-301  FAX: +46.(0)8.6089-290
E-mail: luc...@bi...
W3: http://www.biosci.ki.se/groups/ljo/
-----------------------------------------------------

[PyMOL] Re: PymolX11Hybrid problems (Avram Slovic)

[William S. <wg...@ch...>]

>
> I am having a hard time getting PymolX11Hybrid properly installed on
> my G4 powerbook.  My goal is to make molecular surfaces with
> elctrostatic potentials. What am I doing wrong?  I installed the
> newest version of MacPymol, duplicated it, renamed it
> PymolX11Hybrid.  Then I downloaded the APBS and put it in the folder:


You can do this with pymol that comes with fink. You can also use it to
install apbs and its dependencies.  I am about to stick the very latest
version of pymol into fink, but if you can live with 0.98 for now, it is
ready to go.  I've described the process on the pymol wiki, upon which I
have just frittered away the last 6 or 8 hours....

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


It needs some more input on stereo on mac, for example.

[PyMOL] PymolX11Hybrid problems

[Avram S. <as...@co...>]

Hi,

I am having a hard time getting PymolX11Hybrid properly installed on  
my G4 powerbook.  My goal is to make molecular surfaces with  
elctrostatic potentials. What am I doing wrong?  I installed the  
newest version of MacPymol, duplicated it, renamed it   
PymolX11Hybrid.  Then I downloaded the APBS and put it in the folder:

PYMOLX11Hybrid.app/pymol/modules/pmg_tk/startup

and also downloaded apbs_tools.py, and put it in the folder:

$PYMOL_PATH/modules/pmg_tk/startup/,

but I don' think that this was correct.  Can someone help?

thanks

Avram Slovic

Re: [PyMOL] gui-programming

[Charlie M. <cw...@gm...>]

radiovar.get() seems to work fine for me with the code you provided.=20
You mention .get() but you never say radiovar.get(), so is that what
you meant?  Also, radiovar.set(2) works as well for changing the
selection.

- Charlie

On 2/13/06, Martin Weisel <Mar...@gm...> wrote:
> Hi folks,
>
> I figured out how to preselect a Radiobutton in a Tkinter-GUI. One ought =
to
> use .select() instead of .set().
> But now I've come up with another problem: How do I get the actual value =
of
> that Radiobutton? For some reason .get() is returning 0 all the times.
>
> from Tkinter import *
> radio =3D Tk()
>
> radiovar =3D IntVar()
> Yes =3D Radiobutton(radio, text=3D'Yes', value =3D1, variable =3D radiova=
r)
> Yes.pack(side =3D LEFT)
> Yes.select()
> No =3D Radiobutton(radio, text=3D'No', value =3D2, variable =3D radiovar)
> No.pack(side=3DLEFT)
>
> Although .get() does not work, displaying the actual value of radiovar as=
 a
> dynamic label on the GUI works very well:
>
> Label(radio, textvariable=3Dradiovar).pack(side =3D RIGHT)
>
> How do I get the actual value of that Radiobutton? In case .get() doesn't
> work at all, is there a way of reading out the textvariable of the Label?
>
> I would appreciate any help.
> Regards,
> Martin
>
>
> --
> DSL-Aktion wegen gro=DFer Nachfrage bis 28.2.2006 verl=E4ngert:
> GMX DSL-Flatrate 1 Jahr kostenlos* http://www.gmx.net/de/go/dsl
>
>
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[PyMOL] gui-programming

[Martin W. <Mar...@gm...>]

Hi folks,

I figured out how to preselect a Radiobutton in a Tkinter-GUI. One ought to
use .select() instead of .set().
But now I've come up with another problem: How do I get the actual value of
that Radiobutton? For some reason .get() is returning 0 all the times. 

from Tkinter import *
radio = Tk()

radiovar = IntVar()
Yes = Radiobutton(radio, text='Yes', value =1, variable = radiovar)
Yes.pack(side = LEFT)
Yes.select()
No = Radiobutton(radio, text='No', value =2, variable = radiovar)
No.pack(side=LEFT)

Although .get() does not work, displaying the actual value of radiovar as a
dynamic label on the GUI works very well:

Label(radio, textvariable=radiovar).pack(side = RIGHT)

How do I get the actual value of that Radiobutton? In case .get() doesn't
work at all, is there a way of reading out the textvariable of the Label?

I would appreciate any help.
Regards,
Martin


-- 
DSL-Aktion wegen großer Nachfrage bis 28.2.2006 verlängert:
GMX DSL-Flatrate 1 Jahr kostenlos* http://www.gmx.net/de/go/dsl

RE: [PyMOL] movie of diffusion of atoms/molecules

[EPF \(E. P. Friis\) <EP...@no...>]

Hi Satya

You can use the command "translate" to move the individual objects in =
pymol. Is takes a list of 3 floating points numbers as the translational =
vector.=20

I don't know how Pymol would handle 4000 objects, but an alternative =
might be to load them as states within one object, and then use the =
"show all states" command from the "Movie" menu. The "translate" command =
can also move the individual states independently. (If you also need to =
rotate the molecules, it gets more difficult :-)

Another suggestion: If you have 4000 proteins, you may not need a very =
high level of detail for each molecule. You could save a lot by loading =
only the alpha carbon atoms and then increase their vdw-size to make =
them "stick" together:

pymol> alter my_object, vdw=3D3.0
pymol> show spheres, my_object
pymol> sort


Cheers,

Esben


-----Original Message-----
From: pym...@li... on behalf of Satya Arjunan
Sent: Sat 2006-02-11 03:56
To: pym...@li...
Subject: [PyMOL] movie of diffusion of atoms/molecules
=20
Hi all,

I would like to use Pymol to visualize 3D simulation of lattice-based=20
diffusion of molecules. The simulator provides the 3D coordinates (or=20
the translational direction since they have fixed diffusion distance) of =

the molecules at everytime step. At the end of the simulation, I would=20
like to feed the coordinates (or the translational direction) to Pymol=20
using a python script and make a movie of this.

What is a good way of implementing this with Pymol with lowest=20
computational cost because there are about 4000 protein molecules=20
altogether? I have come across a sample script at=20
http://www.rubor.de/bioinf/tips_python.html#chempy which I think I can=20
use to place the atoms/molecules in pymol. I am wondering if there is=20
any other cost effective way of implementing this? Is it possible just=20
to provide the translational angle and distance for certain molecules=20
already in the model?

Thanks in advance.
satya


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RE: [PyMOL] NAMD/dcd

[EPF \(E. P. Friis\) <EP...@no...>]

Hi Arturas!


A - relatively - easy way to read DCDs into PyMOL is:=20

* Convert the .dcd to .trr using "catdcd 4.0" =
(http://www.ks.uiuc.edu/Development/MDTools/catdcd/). At the same time =
you can concatenate multiple .dcd files, remove solvent, skip frames, =
etc.

* Convert the .trr file to a multi-model .pdb file using "trjconv" from =
the Gromacs package (http://www.gromacs.org/) Here you can select eg. =
desired residues (using make_ndx), skip frames, and align each frame to =
a reference structure before writing the pdb file.

Using two programs may seem a bit complicated, but most likely you want =
to concatenate files, remove solvent or do other processing anyway, so I =
think it is ok :-) =20

This works quite nicely for me. If you want to look at every single =
frame of a long MD with many atoms, you may run into problems with very =
large pdb files, though.=20

Having the trajectory as a .trr file also gives the possibility of using =
Gromacs' analysis tools, such as g_rms or g_rmsf.=20


There are some examples below...


Cheers,

Esben


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

# the structure is in "system.pdb", "system.psf" and trajectories in =
0000-0100.dcd ... 0900-1000.dcd.=20

# creating the stripped pdb file (removing solvent (residues called =
TIP3)):
grep -v TIP ../system.pdb > solute.pdb

# creating the index file for catdcd (for removing solvent):
awk '/ATOM/ {print $2-1}' solute.pdb > solute.idx

# making the stripped file in gromacs format.
/z/linux/catdcd4/LINUX/bin/catdcd4.0/catdcd -o wt_strip.trr -otype trr =
-i solut.idx ../0000-0100.dcd ../0100-0200.dcd ../0200-0300.dcd =
../0300-0400.dcd ../0400-0500.dcd ../0500-0600.dcd ../0600-0700.dcd =
../0700-0800.dcd ../0800-0900.dcd ./0900-1000.dcd

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

# The per-residue rms and pdb file for putty cartoon
g_rmsf -f wt_strip.trr -s solute.pdb -oq test.pdb
# select group 4 for backbone
# load "test.pdb" in PyMOL and show it as putty cartoon:

pymol> load "test.pdb"
pymol> cartoon putty, test
pymol> show cartoon, test
pymol> hide lines, test


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

# The overall rmsd as a function of time
g_rms -f wt_strip.trr -s solute.pdb
# selecet group 0, compare to 1, and select group 0 again
# The resulting "rmsd.xvg" can be shown directly with xmgrace =
(http://plasma-gate.weizmann.ac.il/Grace/):

xmgrace rmsd.xvg

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

#Showing MD ensemble of specific residues (here =
100,101,102,103,200,201):

# run make_ndx

make_ndx -f solute.pdb -o site.ndx
# make a new group
r 100 101 102 103 200 201
# delete the other groups:
keep 14
# call it "site"
name 0 site
# save and quit:
q

# run trjconv to get a pdb file with every 100th frame for the site =
residues:
trjconv -f wt_strip.trr -o site.pdb -s solute.pdb -n site.ndx -fit =
rot+trans-skip 100

# load site.pdb and solute.pdb in pymol

pymol> load site.pdb
pymol> load solute.pdb

# use a similar selection in pymol to align it to the reference =
structure:
pymol> select solute and resi 100+101+102+103+200+201
pymol> align site////CA, sele////CA




-----Original Message-----
From: pym...@li... on behalf of Warren DeLano
Sent: Fri 2006-02-10 20:08
To: zie...@os...; pym...@li...
Subject: RE: [PyMOL] NAMD/dcd
=20
Arturas,

DCD suppot?  Not yet -- we need someone to either donate, develop, or
fund code to support this key MD trajectory format.=20

Cheers,
warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> zi...@ec...
> Sent: Friday, February 10, 2006 10:59 AM
> To: pym...@li...
> Subject: [PyMOL] NAMD/dcd
>=20
> HI !
>=20
> I new one with PyMol and found it very promising for my=20
> works. However, I need analyze MD trajectories DCD from NAMD.=20
>=20
> Is there any clue to load DCD's, as manual talks only abaout=20
> Amber format ?
>=20
> Best
> Arturas Z.
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
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> dat=3D121642
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>=20
>=20
>=20
>=20


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[PyMOL] movie of diffusion of atoms/molecules

[Satya A. <sa...@sf...>]

Hi all,

I would like to use Pymol to visualize 3D simulation of lattice-based 
diffusion of molecules. The simulator provides the 3D coordinates (or 
the translational direction since they have fixed diffusion distance) of 
the molecules at everytime step. At the end of the simulation, I would 
like to feed the coordinates (or the translational direction) to Pymol 
using a python script and make a movie of this.

What is a good way of implementing this with Pymol with lowest 
computational cost because there are about 4000 protein molecules 
altogether? I have come across a sample script at 
http://www.rubor.de/bioinf/tips_python.html#chempy which I think I can 
use to place the atoms/molecules in pymol. I am wondering if there is 
any other cost effective way of implementing this? Is it possible just 
to provide the translational angle and distance for certain molecules 
already in the model?

Thanks in advance.
satya

[PyMOL] French PyMOL tutorial

[<pan...@ch...>]

Dear PymOL users,

The first release of the french PyMOL tutorial is available on this web
page:
http://www.pansanel.org/index.php?page=3Dchemistry&sub_page=3Dpymol

It's released under a Creative Common Attribution License.

Do not hesitate to send me any comments !

Cheers,

Jerome Pansanel




--------------------------------------------
Mail sent through IMP: http://horde.org/imp/

Re: [PyMOL] delete/create bonds in pymol

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

Hi Vanessa,

* Vanessa Oklejas <vok...@st...> [2006-02-10 11:18] wrote:
> Hi All,
> 
> Does anyone know how to delete bonds between atoms in PyMol?

You can use the "unbond" command:

  PyMOL>unbond ?
  Usage: unbond [ atom1 [, atom2 ]]

You can pick the two atoms with the mouse (such that they are selected
and named pk1 and pk2 and then just type "unbond", or you can explicitly
specify the atom selections in the typed command.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.                         <rl...@po...>
Senior Research Associate                            phone: 613-533-6821
Dept. of Biochemistry, Queen's University,             fax: 613-533-2497
Kingston, ON K7L 3N6  Canada       http://adelie.biochem.queensu.ca/~rlc
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

RE: [PyMOL] pymol 0.99 msvcr71.dll startup crash

[Warren D. <wa...@de...>]

Just FYI,

According to Microsoft's own web site, developers can indeed include =
this file in the distribution, so we are just going to include in a =
Windows 0.99 release candidate 2 (0.99rc2), instead of taking the more =
dramatic step of rebuilding Python from source, which could potentially =
create other compatibility issues between PyMOL and the official win32 =
Python 2.4 build.

Hopefully that will resolve this issue -- apologies to everyone for the =
inconvience!  Microsoft pulled a bit of a fast one with respect to this =
DLL, which was a standard part of Windows up until now.
=20
Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Charlie Moad
> Sent: Friday, February 10, 2006 11:11 AM
> To: Yusuf Tanrikulu
> Cc: Guillaume LETELLIER; pym...@li...
> Subject: Re: [PyMOL] pymol 0.99 msvcr71.dll startup crash
>=20
> I want to reiterate you don't need this file at linking time,=20
> so hopefully future builds of pymol won't use it and=20
> hopefully no one will run into this problem.
>=20
> On 2/10/06, Yusuf Tanrikulu=20
> <tan...@bi...> wrote:
> > Hi,
> >
> > I had the same problem with the new release of PyMOL. Just=20
> search for=20
> > the requested file "msvcr71.dll" on your windows computer=20
> and copy it=20
> > into the folder "c:\windows\system\". PyMOL will do its job=20
> on next startup.
> >
> > If you do not have the file, just google for it. There are a lot of=20
> > pages who are offering dll-files.
> >
> > Cheers
> >
> > YT
> >
> >
> > Guillaume LETELLIER wrote:
> > > Hi pymol user
> > >
> > >
> > >
> > > I have been unable to run the new 0.99 version of pymol=20
> on a windows=20
> > > xp laptop.
> > > The app crash at startup saying it has been unable to=20
> find "msvcr71.dll".
> > > Il reinstalled, old beta version 0.99beta32 and everything run=20
> > > perfectly ...
> > >
> > > Any idea ?
> > >
> > >
> > > Thank you
> > >
> > > Guillaume
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: Splunk Inc. Do you=20
> grep through=20
> > > log files for problems?  Stop!  Download the new AJAX=20
> search engine=20
> > > that makes searching your log files as easy as surfing the  web. =20
> > > DOWNLOAD SPLUNK!
> > >=20
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=3D=
12
> > > 1642 _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> > --
> > Yusuf Tanrikulu
> > Bioinformatics PhD student
> > Johann Wolfgang Goethe-Universit=E4t Frankfurt Department of=20
> Biosciences=20
> > Siesmayerstrasse 70
> > 60323 Frankfurt
> > Tel: (+49) 069/79824879
> > Fax: (+49) 069/79824880
> > tan...@bi...
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log=20
> > files for problems?  Stop!  Download the new AJAX search=20
> engine that=20
> > makes searching your log files as easy as surfing the  web.=20
>  DOWNLOAD SPLUNK!
> >=20
> =
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=3D=
1216
> > 42 _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=103432&bid#0486&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] delete/create bonds in pymol

[Vanessa O. <vok...@st...>]

Hi All,

Does anyone know how to delete bonds between atoms in PyMol?

Thanks,
Vanessa

RE: [PyMOL] NAMD/dcd

[Warren D. <wa...@de...>]

Arturas,

DCD suppot?  Not yet -- we need someone to either donate, develop, or
fund code to support this key MD trajectory format.=20

Cheers,
warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> zi...@ec...
> Sent: Friday, February 10, 2006 10:59 AM
> To: pym...@li...
> Subject: [PyMOL] NAMD/dcd
>=20
> HI !
>=20
> I new one with PyMol and found it very promising for my=20
> works. However, I need analyze MD trajectories DCD from NAMD.=20
>=20
> Is there any clue to load DCD's, as manual talks only abaout=20
> Amber format ?
>=20
> Best
> Arturas Z.
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] pymol 0.99 msvcr71.dll startup crash

[Charlie M. <cw...@gm...>]

I want to reiterate you don't need this file at linking time, so
hopefully future builds of pymol won't use it and hopefully no one
will run into this problem.

On 2/10/06, Yusuf Tanrikulu <tan...@bi...> wrot=
e:
> Hi,
>
> I had the same problem with the new release of PyMOL. Just search for
> the requested file "msvcr71.dll" on your windows computer and copy it
> into the folder "c:\windows\system\". PyMOL will do its job on next start=
up.
>
> If you do not have the file, just google for it. There are a lot of
> pages who are offering dll-files.
>
> Cheers
>
> YT
>
>
> Guillaume LETELLIER wrote:
> > Hi pymol user
> >
> >
> >
> > I have been unable to run the new 0.99 version of pymol on a windows xp
> > laptop.
> > The app crash at startup saying it has been unable to find "msvcr71.dll=
".
> > Il reinstalled, old beta version 0.99beta32 and everything run perfectl=
y
> > ...
> >
> > Any idea ?
> >
> >
> > Thank you
> >
> > Guillaume
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> > files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>
> --
> Yusuf Tanrikulu
> Bioinformatics PhD student
> Johann Wolfgang Goethe-Universit=E4t Frankfurt
> Department of Biosciences
> Siesmayerstrasse 70
> 60323 Frankfurt
> Tel: (+49) 069/79824879
> Fax: (+49) 069/79824880
> tan...@bi...
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] dash transparency

[Warren D. <wa...@de...>]

Desiree,

No, this isn't possible yet, but thank you for the request -- it'll be
easy, so I've added this item into the "to do" list.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Desiree Fong
> Sent: Friday, February 10, 2006 10:59 AM
> To: pym...@li...
> Subject: [PyMOL] dash transparency
>=20
> Is it possible to adjust the dash transparency?  I would like=20
> to incorporate it into a movie so that the bond would fade in=20
> and out with the cartoon/stick of the protein.
>=20
> Thanks.
> Desiree Fong
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] pymol 0.99 msvcr71.dll startup crash

[Alexei K. <avk...@uc...>]

I always include msvcr71.dll
with my python distributives to avoid this exact problem.

get  msvcr71.dll 
http://www.google.com/search?hl=en&q=msvcr71.dll&btnG=Google+Search

and place it in *the same* directory as your python app. In this case, within PyMol.
Python 2.4 apps seem to ignore this dll if it's in system folders on some machines. 

From my experience, one can never see this issue on a machine that has Python installed; so 
a clean PC should be used for APP testing before distribution.

Alexei.








Warren DeLano wrote:

>Guillaume,
>
>It is not clear why this is happening -- and note that it doesn't happen
>on every machine.  Regardless, I believe you can fix it by searching for
>"msvcr71.dll" and making sure that it appears in the 
>
>   C:\windows\system32
>
>directory.
>
>Please let me know if that solves the issue with 0.99.
>
>Cheers,
>Warren
>
>--
>Warren L. DeLano, Ph.D.                     
>Principal Scientist
>
>. DeLano Scientific LLC  
>. 400 Oyster 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:wa...@de...      
> 
>
>  
>
>>-----Original Message-----
>>From: pym...@li... 
>>[mailto:pym...@li...] On Behalf Of 
>>Guillaume LETELLIER
>>Sent: Friday, February 10, 2006 5:06 AM
>>Cc: pym...@li...
>>Subject: [PyMOL] pymol 0.99 msvcr71.dll startup crash
>>
>>Hi pymol user
>>
>>
>>
>>I have been unable to run the new 0.99 version of pymol on a 
>>windows xp laptop.
>>The app crash at startup saying it has been unable to find 
>>"msvcr71.dll".
>>Il reinstalled, old beta version 0.99beta32 and everything 
>>run perfectly ...
>>
>>Any idea ?
>>
>>
>>Thank you
>>
>>Guillaume
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: Splunk Inc. Do you grep 
>>through log files for problems?  Stop!  Download the new AJAX 
>>search engine that makes searching your log files as easy as 
>>surfing the  web.  DOWNLOAD SPLUNK!
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&
>>dat=121642
>>_______________________________________________
>>PyMOL-users mailing list
>>PyM...@li...
>>https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>>    
>>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
>for problems?  Stop!  Download the new AJAX search engine that makes
>searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
>http://sel.as-us.falkag.net/sel?cmd=k&kid3432&bid#0486&dat1642
>_______________________________________________
>PyMOL-users mailing list
>PyM...@li...
>https://lists.sourceforge.net/lists/listinfo/pymol-users
>  
>

Re: [PyMOL] pymol 0.99 msvcr71.dll startup crash

[Charlie M. <cw...@gm...>]

     This is a long shot but we ran into this error with matplotlib
and python2.4 using MingW.  Basically we removed the linking
references to msvcr71 in "distutils/cygwinccompiler.py", specifically
in the Mingw32CCompiler class.  The link is not needed, and this
removed the error mentioned below.  I don't know how pymol is built in
windows, but this sounded familiar enough to mention.  Python2.3 does
not suffer from the same problem btw.

- Charlie

On 2/10/06, Warren DeLano <wa...@de...> wrote:
> Guillaume,
>
> It is not clear why this is happening -- and note that it doesn't happen
> on every machine.  Regardless, I believe you can fix it by searching for
> "msvcr71.dll" and making sure that it appears in the
>
>    C:\windows\system32
>
> directory.
>
> Please let me know if that solves the issue with 0.99.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster 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:wa...@de...
>
>
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of
> > Guillaume LETELLIER
> > Sent: Friday, February 10, 2006 5:06 AM
> > Cc: pym...@li...
> > Subject: [PyMOL] pymol 0.99 msvcr71.dll startup crash
> >
> > Hi pymol user
> >
> >
> >
> > I have been unable to run the new 0.99 version of pymol on a
> > windows xp laptop.
> > The app crash at startup saying it has been unable to find
> > "msvcr71.dll".
> > Il reinstalled, old beta version 0.99beta32 and everything
> > run perfectly ...
> >
> > Any idea ?
> >
> >
> > Thank you
> >
> > Guillaume
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep
> > through log files for problems?  Stop!  Download the new AJAX
> > search engine that makes searching your log files as easy as
> > surfing the  web.  DOWNLOAD SPLUNK!
> > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> > dat=3D121642
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> >
> >
> >
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmdlnk&kid=103432&bid#0486&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

RE: [PyMOL] pymol 0.99 msvcr71.dll startup crash

[Warren D. <wa...@de...>]

Guillaume,

It is not clear why this is happening -- and note that it doesn't happen
on every machine.  Regardless, I believe you can fix it by searching for
"msvcr71.dll" and making sure that it appears in the=20

   C:\windows\system32

directory.

Please let me know if that solves the issue with 0.99.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
. 400 Oyster Point Blvd., Suite 213          =20
. South San Francisco, CA 94080 USA  =20
. Biz:(650)-872-0942  Tech:(650)-872-0834    =20
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:wa...@de...     =20
=20

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Guillaume LETELLIER
> Sent: Friday, February 10, 2006 5:06 AM
> Cc: pym...@li...
> Subject: [PyMOL] pymol 0.99 msvcr71.dll startup crash
>=20
> Hi pymol user
>=20
>=20
>=20
> I have been unable to run the new 0.99 version of pymol on a=20
> windows xp laptop.
> The app crash at startup saying it has been unable to find=20
> "msvcr71.dll".
> Il reinstalled, old beta version 0.99beta32 and everything=20
> run perfectly ...
>=20
> Any idea ?
>=20
>=20
> Thank you
>=20
> Guillaume
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D103432&bid=3D230486&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20