pymol-users Mailing List for PyMOL Molecular Graphics System (Page 670)

> Maybe the path where pymol expects other 
> packages is hardcoded into its source?
GNU-Darwin has a unique PyMOL installation method, but it follows
standards, and I'm expecting that
it will be adopted by the other distributions eventually. The pymol
executable is actually a shell script (pymol.com) that is installed in
/usr/local/bin. 
I believe that you can edit this script to change the PYTHON_PATH
variable to the Fink installation path. 
If you really want to use Python from the Fink with PyMOL, then you might
consider copying this file to your home directory and editing it there, so
that it
does not get overwritten when you upgrade PyMOL. 
> 
> I also had to install py-pmw with pkg_add and I then moved it to the 
> site-packages directory from python.
I'd be surprised if the Fink
doesn't provide Megawidgets ;-}. Sorry, but I also find all of this a
little
amusing, because it seems like alot of work to use the Fink in this case,
when
GNU-Darwin was truly built as a PyMOL installer. You should note
that the PyMOL developer, Warren Delano, intends to base his OSX
development efforts on some of the GNU-Darwin tools. The situation is
somewhat
similar with CCP4, Raster3D, and many other major projects as well.
http://www.ccp4.ac.uk/problems/ccp4onMacs.html
http://www.ccp4.ac.uk/ccb/
http://www.bmsc.washington.edu/raster3d/r3d_FAQ.html#PC
Although GNU-Darwin is a free software distribution, it was founded to
build the infrastructure for molecular graphics and crystallographic
computing. 
http://www.newsforge.com/article.pl?sid=00/12/01/2028254&mode=thread
http://www.gnu.org/brave-gnu-world/issue-25.en.html
PyMOL provided the impetus for GNU-Darwin to go Beta so that users would
have a user friendly way to install PyMOL. I believe that our distribution
will emerge as the primary free software distribution for biotechnology in
general, and PyMOL support will be a crucial part of that emergence. I
have the utmost respect for the Fink project and their free software
offerings, but it will never meet the standards that we have set in this
arena, which is mission-critical for GNU-Darwin. The Fink has nothing like
this...
http://gnu-darwin.sourceforge.net/gdc/mol.html
or this,
http://gnu-darwin.sourceforge.net/art.html
or this,
http://gnu-darwin.sourceforge.net/gdc/ccp4.html
and it probably never will. (Heh, I bet there will be Fink PyMOL and
Megawidgets right away now! ;-).
> Finally, I installed povray with Fink, 
> if I give the command 'ray' in pymol it works.
Here again is a problem. ray by itself invokes PyMOL's own internal
rendering
engine. You need to add an argument to ray to invoke POV-ray as an
external rendering engine. PyMOL-0.7.3 is requred for this. Type "help
ray". I believe that PyMOL looks for x-povray in the PATH variable, so
that the Fink's non-standard installation directory should not matter in
this case.
Sorry, if this seems tedious. I really love the Fink as a fellow free
software project, although I do not use it myself for anything. GNU-Darwin
is sufficient without the Fink. TDC is sufficient. It gets tiresome
answering questions about the Fink all the time, and I do not believe that
the others on the GNU-Darwin list are interested. The GNU-Darwin
infrastructure was built expressly for projects like PyMOL. If you want to
use GNU-Darwin PyMOL, then I highly recommend using the GNU-Darwin packages
that were built to support it (instead of the Fink). 
Be sure to consult the PyMOL documentation. Warren has done an
excellent job with the PyMOL website. I printed out a color copy of the
manual.
It's so beautiful.
http://pymol.sourceforge.net/
Regards,
Michael L. Love
MacCHESS
Cornell University
http://www.gnu-darwin.org/
-- 
Visit proclus realm! http://proclus.tripod.com/
-----BEGIN GEEK CODE BLOCK-----
Version: 3.1
GMU/S d+@ s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O
M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++
h--- r+++ y++++
------END GEEK CODE BLOCK------

Dear PyMOL Users:
 Happy New Year! 2001 was a great year for PyMOL, with the following
developments: cartoon ribbons, improved rendering quality, transparency,
CCP4 maps, concise atom selections, increased stability, bug fixes, and
many other minor improvements. According to SourceForge's updated
statistics, PyMOL has accumulated about 75,000 web-page hits, 15,000
file downloads, and 72 subscribers to the mailing list. Hooray!
 Given this wonderful response, I intend to continue developing PyMOL as
a hobby in 2002 under the same unrestricted software license. Some of my
goals include: updated documentation, tutorials, a better user interface
and API, an improved builder with structure clean-up, MOL2 file support,
electrostatic potential display, generalized volumetric rendering, a
native OSX version, and an ActiveX control (to replace Chime). 
 Although PyMOL is free and unrestricted, the reality of software
development is that it takes substantial time and money. If you
haven't yet considered whether it would be in your interest to support
PyMOL with a monetary donation, then please do so today! DeLano
Scientific can now take donations via credit card or check, or we can even
sell your company or institution a standard software license -- whatever
is most convenient.
 
 Details at http://www.pymol.org/donate.html 
 Even if you are cash-poor, there are many others ways in which you
can advance the PyMOL vision. See the "contribute" section of the
home page for more information on what you can do.
 As an individual scientist, I am striving to make the PyMOL vision a
reality, but it will not happen unless many other scientists join me in
this quest. As of today, only 2 parties have made donations, and 3 more
have made pledges. Less than ten people have directly contributed to 
development. This is a good start, but let us turn this promising little
snowball into a roaring avalanche which validates the PyMOL approach for
developing free and unrestricted research software.
 Join me in taking a stand against outrageously expensive commercial
research tools. Working together as individual scientists, we can create
free and unrestricted alternatives. Please support PyMOL today!
 Cheers,
 Warren L. DeLano, Ph.D.
 PyMOL Creator
 DeLano Scientific
 San Carlos, CA, USA

That's the spirit Jason -- don't hold back with those questions!
> From: Jason Yano [mailto:jk...@br...]
> 1) Is there a way to find out what secondary strucuture has been=20
> assigned by the automatic algorythem?
> I assume there must be a python command that will dump the=20
> output of the=20
> utility to the screen or to a file.
util.ss
iterate (name ca),print resn,resi,chain,ss
# or to a file (using the persistent global object "stored")
stored.file =3D open("secondary.txt","w")
iterate (name ca),stored.file.write("%s %s %s
%s\n"%(resn,resi,chain,ss))
stored.file.close()
# but remember, that SS algorithm is bogus -- it was cooked up in a few
hours based on what I thought "looked right".=20
> 2) Is there any information available for any of the other=20
> util programs?
The menu module makes use of the util module, so you will see some
example code there. So far there isn't much else in the way of
documention.=20
=20
> 3) Is it possible to color the chain by B-factor?
# yes, but it's weak.=20
color br0
color br1,(b>5)
color br2,(b>10)
color br3,(b>15)
color br4,(b>20)
color br5,(b>25)
color br6,(b>30)
color br7,(b>35)
color br8,(b>40)
color br9,(b>45)
# You can create a python loop which does the same thing.
# Try colors, s000, s001, ... up through s999 for more subtle shading.
=20
> 4) I have a heme moiety, I can get the program to display the=20
> FE atom,=20
> but I'm not sure how to increase the sphere size of the atom=20
> so that I=20
> can exagerate it, it is possibe? something close to the set=20
> atomradius=20
> command in molscript.
alter (elem fe),vdw =3D 4.0
rebuild
# should work, but just in case you might need to use the
# atom name (whatever it is)
alter (name fe),vdw =3D 4.0
rebuild
> 5) For some strange reason it recognizes the Nitrogens on the heme=20
> differently and colors some of them blue and others pink. I tried to=20
> manually set it like I could for the Fe, but I think that I am not=20
> getting the atom type/name correct. Is there a list of atom names?
PyMOL is probably getting confused. Please send a copy of the PDB file
to warren@delanoscientific to debug.
> 6) Is there a way to make a C-alpha trace? other than ribbons=20
> something=20
> that will draw straight bonds between C-alpha's?
#ala midas "chain" command?
set ribbon_sampling=3D1
show ribbon
> 7) Is it possible to change the color of the mesh (not the isomesh)=20
> relatve to helix color ie what are the command line commands. I have=20
> tied color red, mesh and that didn't seem to work, same=20
> question for the=20
> surfaces as well.
set mesh_color=3Dblue
set surface_color=3Dgreen
> 8) Is it possible to have a "ball and stick" representation?
yes, but right now is it kludgy...you will need to create multiple
copies of an object if you want to simultaneously adjust vdw and show
surfaces.
alter (all),vdw=3Dvdw*0.25
set stick_radius=3D0.15
rebuild
> 9) What is the command to output a pov ray file?
You'll need to use Python for this.
cmd.get_povray() returns a tuple of two strings (header and data).
Write these to a file in order to get a povray input file.
=20
> 10) How do you get two color helicies, ie the equivalent to=20
> planecolour2=20
> in molescript?
sorry can't do this, but 8.5 out of 10 aint bad ; ) PyMOL's secondary
structures are unicolor for now.
> So far the program is running great. The stereo works very=20
> well for me.=20
> I have it running on a dual AMD athlon 1.4GHz, with an Oxygen GVX1=20
> graphics card and 1 gig of DDR ram under the Windows 2000 pro OS.
I envy you. That's pretty much the machine I'd like to buy except that
I'd run Linux on it at +200 mhz. Athlon's are definitely the way to go
-- Python really flies on them.
- Warren

Hello All,
 I had a few questions:
1) Is there a way to find out what secondary strucuture has been 
assigned by the automatic algorythem?
I assume there must be a python command that will dump the output of the 
utility to the screen or to a file.
2) Is there any information available for any of the other util programs?
3) Is it possible to color the chain by B-factor?
4) I have a heme moiety, I can get the program to display the FE atom, 
but I'm not sure how to increase the sphere size of the atom so that I 
can exagerate it, it is possibe? something close to the set atomradius 
command in molscript.
5) For some strange reason it recognizes the Nitrogens on the heme 
differently and colors some of them blue and others pink. I tried to 
manually set it like I could for the Fe, but I think that I am not 
getting the atom type/name correct. Is there a list of atom names?
6) Is there a way to make a C-alpha trace? other than ribbons something 
that will draw straight bonds between C-alpha's?
7) Is it possible to change the color of the mesh (not the isomesh) 
relatve to helix color ie what are the command line commands. I have 
tied color red, mesh and that didn't seem to work, same question for the 
surfaces as well.
8) Is it possible to have a "ball and stick" representation?
9) What is the command to output a pov ray file?
10) How do you get two color helicies, ie the equivalent to planecolour2 
in molescript?
So far the program is running great. The stereo works very well for me. 
I have it running on a dual AMD athlon 1.4GHz, with an Oxygen GVX1 
graphics card and 1 gig of DDR ram under the Windows 2000 pro OS.
Thanks,
Jason Yano

Danny,
 I think your problem is one of two possibilities: either your
LD_LIBRARY_PATH is not being set correctly by pymol.com, or your
python1.5.so shared object isn't valid. =20
You might try using linking against a static Python library as described
in http://pymol.sourceforge.net/workarounds.html
Good luck!
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
> -----Original Message-----
> From: Danny G Smith [mailto:dg...@om...]
> Sent: Tuesday, December 18, 2001 12:52 PM
> To: pym...@li...
> Subject: [PyMOL] pymol on SGI
>=20
>=20
> I have complied pymol-0_73, with ext-0_51, useing the following
> build.com in the ext subdirectory. When I try to run pymol.com I get
> the following message:
>=20
> omega[272]:/misc/local/src/pymol/pymol % ./pymol.com
> Traceback (innermost last):
> File "/misc/local/src/pymol/pymol/modules/launch_pymol.py",=20
> line 6, in
> ?
> import pymol
> File=20
> "/misc/local/src/pymol/pymol/modules/pymol/__init__.py", line 24,
> in ?
> import _cmd
> ImportError: 4192945:/misc/local/src/pymol/pymol/ext/bin/python: rld:
> Fatal Error: Cannot Successfully map soname 'libpython1.5.so'=20
> under any
> of the filenames
> /usr/local/lib/libpython1.5.so:/usr/lib32/libpython1.5.so:/usr
> /lib32/internal/libpython1.5.so:/lib32/libpython1.5.so:/opt/li
> b32/libpython1.5.so:
> omega[273]:/misc/local/src/pymol/pymol %
>=20
>=20
> Any help would be appreciated.
>=20
>=20
> # build.com in ext directory
> #!/bin/csh
> #
> #---------------------------------------------------------------------
> # Build script for making PyMOL External dependencies
> #---------------------------------------------------------------------
> # (can't do this stuff in a makefile cause we need to define
> # some important environmental variables)
> #
> #- Paths -------------------------------------------------------------
> #
> # --- Base
> #setenv BASE /home/local/export/ext
> setenv BASE /misc/local/src/pymol/pymol/ext
> #
> #- Targets=20
> -------------------------------------------------------------
> # -- Linux with just Tcl/Tk
> # setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy=20
> pmw png-linux
> glut-linux"
> #
> # -- Linux with Tcl/Tk and wxPython
> # setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw=20
> png-linux
> glut-linux glib gtk wxgtk wxpython"
> #
> # -- SGI/IRIX with just Tcl/Tk
> # setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy=20
> pmw png-irix
> glut-irix"
> #
> # -- SGI/IRIX with Tcl/Tk and wxPython
> setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy pmw png-irix
> glut-irix glib gtk wxgtk wxpython"
> #---------------------------------------------------------------------
> #
> #- For creation of a shared python library --------------------------
> # --- Linux
> #setenv LDALLFLAGS "--whole-archive"
> # --- SGI/IRIX
> setenv LDALLFLAGS "-n32 -all"
> #---------------------------------------------------------------------
> #
> #- Misc --------------------------------------------------------------
> #
> # --- SGI/IRIX
> setenv SGI_ABI -n32
> setenv MAKE gmake
> setenv CXX CC
> #
> # --- Linux
> #setenv MAKE make
> #
> #- Path pre-emption critical for building gtk/wx ---------------------
> #
> setenv PATH ${BASE}/bin:$PATH
> setenv LD_LIBRARY_PATH ${BASE}/lib
> #
> #- Build=20
> --------------------------------------------------------------
> $MAKE -f Makefile.in 1ドル
>=20
>=20
>=20
>=20
> --=20
> thanks,
> Danny G Smith =20
>=20
> UNIX Systems Administrator
> Crystallography Dept Oklahoma Medical Research Foundation
> phone 271-8954 fax 271-7953
>=20
> =
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
> UNIX air conditioned environment, keep the windows closed
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

I have complied pymol-0_73, with ext-0_51, useing the following
build.com in the ext subdirectory. When I try to run pymol.com I get
the following message:
omega[272]:/misc/local/src/pymol/pymol % ./pymol.com
Traceback (innermost last):
 File "/misc/local/src/pymol/pymol/modules/launch_pymol.py", line 6, in
?
 import pymol
 File "/misc/local/src/pymol/pymol/modules/pymol/__init__.py", line 24,
in ?
 import _cmd
ImportError: 4192945:/misc/local/src/pymol/pymol/ext/bin/python: rld:
Fatal Error: Cannot Successfully map soname 'libpython1.5.so' under any
of the filenames
/usr/local/lib/libpython1.5.so:/usr/lib32/libpython1.5.so:/usr/lib32/internal/libpython1.5.so:/lib32/libpython1.5.so:/opt/lib32/libpython1.5.so:
omega[273]:/misc/local/src/pymol/pymol %
Any help would be appreciated.
# build.com in ext directory
#!/bin/csh
#
#---------------------------------------------------------------------
# Build script for making PyMOL External dependencies
#---------------------------------------------------------------------
# (can't do this stuff in a makefile cause we need to define
# some important environmental variables)
#
#- Paths -------------------------------------------------------------
#
# --- Base
#setenv BASE /home/local/export/ext
setenv BASE /misc/local/src/pymol/pymol/ext
#
#- Targets -------------------------------------------------------------
# -- Linux with just Tcl/Tk
# setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy pmw png-linux
glut-linux"
#
# -- Linux with Tcl/Tk and wxPython
# setenv PYMOL_TARGETS tcl tk zlib python distutils numpy pmw png-linux
glut-linux glib gtk wxgtk wxpython"
#
# -- SGI/IRIX with just Tcl/Tk
# setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy pmw png-irix
glut-irix"
#
# -- SGI/IRIX with Tcl/Tk and wxPython
setenv PYMOL_TARGETS "tcl tk zlib python distutils numpy pmw png-irix
glut-irix glib gtk wxgtk wxpython"
#---------------------------------------------------------------------
#
#- For creation of a shared python library --------------------------
# --- Linux
#setenv LDALLFLAGS "--whole-archive"
# --- SGI/IRIX
setenv LDALLFLAGS "-n32 -all"
#---------------------------------------------------------------------
#
#- Misc --------------------------------------------------------------
#
# --- SGI/IRIX
setenv SGI_ABI -n32
setenv MAKE gmake
setenv CXX CC
#
# --- Linux
#setenv MAKE make
#
#- Path pre-emption critical for building gtk/wx ---------------------
#
setenv PATH ${BASE}/bin:$PATH
setenv LD_LIBRARY_PATH ${BASE}/lib
#
#- Build --------------------------------------------------------------
$MAKE -f Makefile.in 1ドル
-- 
thanks,
Danny G Smith 
UNIX Systems Administrator
Crystallography Dept Oklahoma Medical Research Foundation
phone 271-8954 fax 271-7953
=========================================================
UNIX air conditioned environment, keep the windows closed

> From: Mirek Cygler [mailto:mir...@br...]
>=20
> 	I am trying my first steps with PyMOL. I have tried to=20
> display a XPLOR map.
> It worked well but the isomesh command displayed the entire=20
> map. How can I
> display only a part of the map (box or sphere) around a=20
> specific point (say,
> the center of the screen) if I do not have a model yet (ie, no atoms).
Mirek,
 That exactly functionality isn't yet implemented, but you can kludge
it by:
1. creating a model on the fly
2. setting the atom coordinates in the model to the location
3. creating a mesh around the model
4. and deleting the model.
The following .pml example script shows you how to get a 10 A brick
(msh1) or a sphere (msh2) about (2.0,21.0,4.0). If you plan to use this
functionality often, you should convert the following script into a
Python function with four arguments and place its definition in your
PyMOL start-up file. This is how you can customize PyMOL to suit your
needs...
# begin example
fragment methane,_pos
alter_state 1,(_pos),x=3D2.0;y=3D21.0;z=3D4.0
isomesh msh1,map1,1.0,(_pos),10.0
isomesh msh2,map1,1.0,(_pos),carve=3D10.0
del _pos
zoom msh1
# end example
Cheers,
Warren
cc: PyMOL mailing list
--
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
>=20

On 2001年12月15日, Manfred W. Baumstark wrote:
> I would like to display an electron density as a surface instead of a mesh.
> Is this somehow possible with PyMOL?
> 
> Thanks in advance for any help
This is planned but not yet possible.
Cheers,
Warren

On 2001年12月15日, Mirek Cygler wrote:
> 	The images produced by PyMOL are really nice. Is there a way to define the
> resolution of the image file? Say I would like to get an image with a
> resolution of 1600 x 1200 pixels but my screen is only 1400 x 1050?
ray 1600,1200
png image.png
I've even used PyMOL to generate poster sized images at 4800 by 3600,
Warren

Hi,
	The images produced by PyMOL are really nice. Is there a way to define the
resolution of the image file? Say I would like to get an image with a
resolution of 1600 x 1200 pixels but my screen is only 1400 x 1050?
 Mirek

I would like to display an electron density as a surface instead of a mesh.
Is this somehow possible with PyMOL?
Thanks in advance for any help
Manfred

Charles,
 ".dat" is a hopefully oversubscribed file extension, and the .dat
which PyMOL currently recognizes is for Macromodel. If you are have
some development skills, consider writing a Python-based CSD file parser
for the Chemical Python portion of PyMOL. Any ChemPy model can be
loaded straight into PyMOL. This approach doesn't have quite the
performance as native C reads but, it will suffice for
moderate-throughput applications.
 Example Python code for reading MOL files can be found in
modules/chempy/mol.py. The code is just over 105 lines and supports
both reads and writes. One should be able to add a CSD reader with just
an hour or two starting with a description of the CSD file format. Just
focus on the atom symbols, coordinates, bonds, and bond orders...the
rest can be dealt with later on.
 I propose using the extension ".csd" for csd structure files.
Cheers,
Warren
--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
> From: Ross, Charles [mailto:Cha...@st...]
>=20
> I am running latest version (0.73) on an SGI Octane running=20
> IRIX 6.5.14m.
> Structures extracted from the Cambridge Structural Database have the
> extension .dat. This extension is recognized by PyMol,=20
> although perhaps not
> as a structure file - when I read it, I get no errors, but I get no
> structure either. Does PyMol recognize CSD structure files,=20
> and if so, what
> is the proper extension?
>=20
> thanks
> Charles Ross
>=20
> Department of Structural Biology
> St. Jude Children's Research Hospital
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

I am running latest version (0.73) on an SGI Octane running IRIX 6.5.14m.
Structures extracted from the Cambridge Structural Database have the
extension .dat. This extension is recognized by PyMol, although perhaps not
as a structure file - when I read it, I get no errors, but I get no
structure either. Does PyMol recognize CSD structure files, and if so, what
is the proper extension?
thanks
Charles Ross
Department of Structural Biology
St. Jude Children's Research Hospital

Dear all:
I tried to install pymol in my Linux box (Mandrake 8.0) and I've been having 
some problems downloading the external dependencies packages (both the 
required and the optional one). When I try to untar them I get a message 
saying that the packages are not complete or corrupted. 
I don't know if the problem resides in my school connection (10,000 students 
and a very narrow bandwidth) or with the files (shouldn't the req one be 
10MB? when I'm downloading I get the information it is only 3,6...)
Thanks
Palmira

Dear PyMol users:
I recently upgraded to WindowsXP from WindowsMe, in doing so I had some =
problems that ultimately resulted in wiping out my hard drive. I have =
tried to downlad and reinstall PyMol and I am experiencing some difficulty.=
 I have ben able to download and install Python-2.1 successfully; however, =
I have been unable to install PyMol. I downloaded pymol-0_68-bin-win32-py2=
1 and also pymol-0_73-bin-win32-py21, when I try to unzip these files I =
get an error that says the file is corrupt or there are no files to unzip. =
 I have tried several times. Is this a conflict with XP or a problem with =
my computer or a problem with the files? Thanks ion advance for your =
feedback. Sue

Addis,
 Yes, I am aware of this issue and plan to address it in later
versions. Hydrogen adding needs to become residue-aware. =20
Note that when you are building amino acids, they do start out with
qausi-correct hydrogen names. There is still some ambituity as to which
convention is followed for 4-letter names 2HH1 vs. HH12. Unfortunately,
certain packages make assumptions about this, so PyMOL should probably
support both, as well as on-the-fly interconversion.
Cheers,
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
> -----Original Message-----
> From: Addis [mailto:ad...@ds...]
> Sent: Thursday, December 13, 2001 10:13 AM
> To: pym...@li...
> Subject: [PyMOL] add hydrogens
>=20
>=20
> I start to work in computational chemistry and I use as imput=20
> file of my=20
> algorithm a pdb standard format, I need all atoms for my calculation=20
> (also hydrogens), but frequently the examples I found are without=20
> hydrogens. I have used the command h_add and it works: it add=20
> hydrogens,=20
> but the names are diffrent from the standard pdb format. I explain in=20
> pdb format the name of hydrogen depends on the position that=20
> it has in=20
> the aminoacyd structure ( for example 1HB is the first=20
> hydrogen linked=20
> to C-beta , but if I add hydrogens with h_add I obtain a sequence of=20
> hydrogens labeled as H01,H02,...
> Is it possible to obtain labels in standard pdb format?
> Thank you very much,
> 	Bernardetta Addis
>=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

I start to work in computational chemistry and I use as imput file of my 
algorithm a pdb standard format, I need all atoms for my calculation 
(also hydrogens), but frequently the examples I found are without 
hydrogens. I have used the command h_add and it works: it add hydrogens, 
but the names are diffrent from the standard pdb format. I explain in 
pdb format the name of hydrogen depends on the position that it has in 
the aminoacyd structure ( for example 1HB is the first hydrogen linked 
to C-beta , but if I add hydrogens with h_add I obtain a sequence of 
hydrogens labeled as H01,H02,...
Is it possible to obtain labels in standard pdb format?
Thank you very much,
	Bernardetta Addis

Dear PyMOL users,
in case that you may find the current stereo parameters not optimal, here
are my suggestions:
put the following lines in your .pymolrc file (copy from
<yourinstallation>/pymol/sample.pymolrc):
set stereo_angle=6.0
set stereo_shift=0.0
At least on our SGIs these settings produce a significantly better stereo
picture than the default values 2.1 and 2.0, respectively.
Many thanks to Warren who told me which parameters to change and their
default values.
Regards,
Dirk.
*****************************************************
Dirk Kostrewa
Paul Scherrer Institut e-mail: dir...@ps...
Life Sciences phone: +41-56-310-4722
OSRA/007 fax: +41-56-310-4556
CH-5232 Villigen PSI WWW: http://sb.web.psi.ch
Switzerland
*****************************************************

Leslie,=20
 Well it seems a mis-spoke. I tried to write a script which does what
you layed out, but it turns out that the current the API functions for
moving moleculs don't have quite enough power to do this efficiently
(even in version 0.73). My time is probably better spent refining
"rotate" and "translate" than describing some kind of elaborate
work-around which would enable you to do this right now. Can we
revisit this in a month or two?
 Electrostatic surfaces are also a few months away still, unless
someone can provide me with source code for a drop-in PB solver.
Cheers,
Warren
> From: Leslie Hall [mailto:HA...@ut...]
> I am trying to make these changes automatically. =20
> Essentially, I would
> like to have a script to make a movie where;
>=20
> First, I want to load pdb files that contain four molecules=20
> (A, A, B, and
> B). Initially, I what to hide all four molecules. Then=20
> show the dimer AA
> in the center of the screen. Have this dimer rotate around=20
> X. Then show a
> conformational change in this dimer where you hold one of the=20
> molecules (A)
> stationary, while you rotate the other molecule A in X by 100 degrees.
> After this is done, I then want to show one molecules of B on=20
> the left side
> and the other molecule B on the right side of the dimer of=20
> AA. Finally I
> want to show the molecule B's moving and docking with the=20
> dimer (AA) in its
> new conformation.
>=20
> Also, is it posible to make this movie showing electrostatic surface?
>=20
> Les
>=20
>=20
>=20

> Marc,
> 
> I'm the person, who build the rpm. I'm using Red Hat and package works
> flawlessly (as far as I need).
Actually that might be the problem. As Warren has pointed out, rpm's are 
not neccessarily interchangeable between distributions. Therefore 
something might be broken if installed on SuSE (for example it seems 
that the package expects python to be in a different path or under a 
different name (I have a working python 2.1.1, but one package 
complains, that python > 2.1 is neccessary).
Pymol now runs (compiled from source) so anyway.
-- 
Bye, Marc Saric
Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

Marc,
"MS" == Marc Saric wrote:
 MS> Bottomline: The precompiled rpm-binaries seem to be broken -at least
 MS> they don't for SuSE 7.3.
They work for me :)
-- 
Andrey V Khavryuchenko http://www.kds.com.ua/
Offshore Software Development

Hi,
disregard my message from yesterday.
Today I downloaded the pymol 0.73-sources and the ext-req-package and 
now it works (I also sorted out some problems with rpm-packages of 
Numeric and other external stuff not directly related to Pymol).
But still I had some problems compiling:
1. glut complained that glutbitmap.h was not there (but should'nt it be 
there, otherwise downloading a complete ext-package does not make 
sense???). I installed mesaglut-devel from SuSE 7.3, and after that, it 
worked.
2. after compilation (apparently without error, but with some warnings) 
of both the required ext-packages (I excluded png1 because I have the 
png2-lib installed, as described in the INSTALL-manual) and pymol, I 
tried to start pymol, but got an error from _cmd complaining, that 
python 152.so-something had an undefined symbol "stat".
I changed the Makefile-scripts to use my preinstalled SuSE 7.3 Python 
2.1 (why use 1.52 anyway) and after that it worked (i.e. demos ran 
without problems and program did not crash for 10 minutes or so ;-) ).
So now I need to test-check it a bit more and see if everything is ok.
Any hints for ready-made self-tests or so?
Bottomline: The precompiled rpm-binaries seem to be broken -at least 
they don't for SuSE 7.3.
There is a missing (really??) header-file in glut in the ext-package.
The default compilation of Python 1.52 as in the ext-package does not 
work either (for me -don't know why) but with a precompiled Python 2.1.1 
it is ok.
Cheers!
-- 
Bye, Marc Saric
Max-Planck-Institut fuer molekulare Physiologie
Otto-Hahn-Str.11 44227 Dortmund phone:0231/133-2168

Marc,
I'm the person, who build the rpm. I'm using Red Hat and package works
flawlessly (as far as I need).
"MS" == Marc Saric wrote:
 MS> Hi all,
 MS> I recently downloaded the rpm-packages available from the
 MS> pymol-sourceforge-site
 MS> (i.e.
 MS> Numeric-20.2.1-1.i386.rpm
 MS> Pmw-0.8.5-1.i386.rpm
 MS> pymol-0_68-1.i386.rpm
 MS> )
 MS> and installed them, but after starting pymol, I got the following error:
 MS> -------------------------------
 MS> saric@m99106:/home/saric> pymol
 MS> Traceback (most recent call last):
 MS> File "/usr/lib/pymol/launch_pymol.py", line 6, in ?
 MS> import pymol
 MS> File "/usr/lib/python2.1/site-packages/pymol/__init__.py", line 24, in ?
 MS> import _cmd
 MS> File "/usr/lib/python2.1/site-packages/pymol/_cmd.py", line 57, in ?
That line is strange. Do you really have _cmd.py file???
There's no such file in rpm. Neither in my site-packages/pymol.
This might be the cause of malfunction.
 MS> import parsing
 MS> File "/usr/lib/python2.1/site-packages/pymol/parsing.py", line 592, in ?
 MS> import cmd
 MS> File "/usr/lib/python2.1/site-packages/pymol/cmd.py", line 97, in ?
 MS> lock_api = pymol.lock_api
 MS> AttributeError: 'pymol' module has no attribute 'lock_api'
Other generic recommendation would be to rebuild rpm from src.rpm. That's
simple: just issue
 rpm --rebuild pymol-xxx.src.rpm
-- 
Andrey V Khavryuchenko http://www.kds.com.ua/
Offshore Software Development

vim (Improved Vi editor) which is on RedHat and probably most other
Linux, also is python-sensitive. It does pretty colours and stuff, so
for all you vi loyalists, there's no need to go over to the Dark Side.
:)
phx.
> -----Original Message-----
> From: DeLano, Warren [mailto:wa...@su...]
> Sent: Monday, December 10, 2001 9:13 AM
> To: David J. Schuller
> Cc: pym...@li...
> Subject: [PyMOL] Learning Python for PyMOL
>=20
>=20
>=20
> David Schuller asked about the best books for learning Python. There
> are two key resources:
>=20
> (1) Guido's online tutorial is a good starting point for learning the
> language.
>=20
> http://www.python.org/doc/current/tut/tut.html
>=20
> and (2) "Python Essential Reference" by David M. Beazley, (New Riders)
> is a must-have reference for writing Python code.
>=20
> These tare what got me going a couple years back along with the other
> documentation files on the Python web site.=20
> http://www.python.org/doc/current/
>=20
> NOTE: In order to write Python effectively, you need an editor which
> supports its indentation scheme. The top choices are (1)=20
> emacs running
> python-mode, or (2) IDLE, the editor included with most Python
> distributions. =20
>=20
> Writing Python without a Python-aware editor is a thankless=20
> task due to
> Python's sensitive block structures which would be a chore to=20
> maintain.
> I recommend that you use spaces instead of tabs to indent=20
> Python code --
> PyMOL's convention is 3 spaces per block.
>=20
> The relavent portions of my .emacs file are included below in case
> anyone is interested. I think most modern Linux=20
> distrubutions include a
> python mode in emacs by default.
>=20
> For simple tasks, the PyMOL command language (.pml files) is=20
> easier than
> Python because you can ignore the identation issue. However,=20
> .pml files
> are suited for real programming.
>=20
> Cheers,
> Warren
>=20
> -- BEGIN .emacs excerpt
>=20
> (setq-default visible-bell t)
> (setq-default backup-inhibited t)
> (setq-default auto-save-default nil)
>=20
> (global-set-key "\C-c\C-w" 'goto-line)
>=20
> (setq-default tab-stop-list '(3 6 9 12 15 18 21 24 27 30 33=わ20
> 36 39 42) )
>=20
> (setq-default tab-width 3)
> (setq-default py-indent-offset 3)
> (setq-default indent-tabs-mode nil)
>=20
> (setq auto-save-default nil)
> (setq auto-save nil)
> (setq load-path (cons "/usr/share/emacs/site-lisp/" load-path))
> (autoload 'python-mode "python-mode" "Python editing mode." t)
> (setq auto-mode-alist
> 	 (cons '("\\.py$" . python-mode) auto-mode-alist))
> (setq auto-mode-alist
> 	 (cons '("\\.pym$" . python-mode) auto-mode-alist))
> (setq interpreter-mode-alist
> 	 (cons '("python" . python-mode) interpreter-mode-alist))
> (global-font-lock-mode)
>=20
> -- END .emacs excerpt
>=20
> --
> 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
>=20
>=20
>=20
> > -----Original Message-----
> > From: DeLano, Warren=20
> > Sent: Monday, December 10, 2001 7:40 AM
> > To: Glen L. Prosise
> > Cc: pym...@li...
> > Subject: [PyMOL] PyMOL 0.73 Released (Win,Linux)
> >=20
> >=20
> >=20
> > Gang,
> >=20
> > Last night I posted binaries of PyMOL 0.73 for Windows and=20
> > Linux to the
> > downloads page. Read more at http://www.pymol.org
> >=20
> > This is the first version to support fragment and residue-based
> > molecular building. However, you may find the process=20
> > challenging with
> > the current rudimentary interface. =20
> >=20
> > Cheers,
> > Warren
> >=20
> >=20
> >=20
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >=20
>=20
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20

"DeLano, Warren" wrote:
> > From: Leslie Hall [mailto:HA...@ut...]
>
> > I have just started using PyMol and had a question about
> > moving selected
> > objects in an animation.
> > Here is basically what I want to do.
> >
> > 1. Load two separate pdb files.
> > 2. Be able to move the two molecules independently of each other.
> > 3. Show a conformational change in one of the molecules.
> > 4. Move the two molecules independently and show them docking with
> > each other.
>
> Leslie,
>
> Are you trying to perform these changes manually using the mouse, or
> automatically using the Python API? The manual approach is documented
> in the manual, but the Python API approach was neither documented nor
> complete in 0.68.
>
> It is complete now in version (0.73) but still isn't well documented.
> If you provide some more details about how you're planning on doing
> this, I could probably post a couple examples for you.
Warren,
 I am trying to make these changes automatically. Essentially, I would
like to have a script to make a movie where;
First, I want to load pdb files that contain four molecules (A, A, B, and
B). Initially, I what to hide all four molecules. Then show the dimer AA
in the center of the screen. Have this dimer rotate around X. Then show a
conformational change in this dimer where you hold one of the molecules (A)
stationary, while you rotate the other molecule A in X by 100 degrees.
After this is done, I then want to show one molecules of B on the left side
and the other molecule B on the right side of the dimer of AA. Finally I
want to show the molecule B's moving and docking with the dimer (AA) in its
new conformation.
Also, is it posible to make this movie showing electrostatic surface?
Les