pymol-users Mailing List for PyMOL Molecular Graphics System

Hello I am trying to make a movie from saved scenes using the  
template posted by Seth :


mset 1 x180
scene 001, animate=0
mview store, 1
scene 002, animate=0
mview store, 60
mview interpolate
mdo 1: scene 001, view=0
mdo 2: scene 002, view=0


Basically the scenes that I have show some rotations and then hide  
and show objects and maps. It appears that the hiding and showing of  
objects is proceeding faster then the transitions and so the frames  
dont always correspond to the scene I have stored.  basically I was  
wondering if one must use a wait command to allow the scene  
transitions to occur before showing/hiding objects??? If so what is  
this command?

sean

Hi all,

On Wednesday 30 August 2006 23:54, Peter Adrian Meyer wrote:
> Which version of gcc are you using?  
gcc (GCC) 4.1.1 20060525 (Red Hat 4.1.1-1)
> A quick check of google for the 
> unterminated argument list in macro error makes it look like that could be
> an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's
> using  make instead of python distutils).  It looks to me like a c
> preprocessor issue, rather than something in Crystal.c; specifically
> dealing with the PRINTF macro in Feedback.h (although it does seem a
> little strange seeing special characters in a logfile...).
Tried doing the make using the Rules.linux . (did not use the ext package)
In the Rule.linux file I changed 2.3 -> 2.4 and added the location of the 
python .h file etc:
PYTHON_EXE = /usr/bin/python
PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.4 \
	-I$(PYMOL_PATH)/ext/include/python2.4/Numeric
	-I/usr/include/python2.4/ \
	-I/usr/include/python2.4/Numeric

I copied Rules.linux to Rules.make under the base pymol dir.
It seemed to have compiled ok.

In the pymol file I needed to change line 43 to /usr/bin/python 
$PYMOL_PATH/modules/pymol/__init__.py "$@"

so it's poining to the right place for python

However when I run it the following errors are thrown:
Traceback (most recent call last):
  File "/home/fauxn/software/pymol-0.99rc6/modules/pymol/__init__.py", line 
209, in exec_str
    exec s in globals(),globals()
  File "<string>", line 1, in ?
  File "/home/fauxn/software/pymol-0.99rc6/modules/pymol/__init__.py", line 
325, in launch_gui
    __import__(invocation.options.gui)
  File "/home/fauxn/software/pymol-0.99rc6/modules/pmg_tk/__init__.py", line 
22, in ?
    from PMGApp import *
  File "/home/fauxn/software/pymol-0.99rc6/modules/pmg_tk/PMGApp.py", line 27, 
in ?
    from Tkinter import *
ImportError: No module named Tkinter

Have I missed something?

The main graphics windows appears.  I can load a pdb and view it, but when I 
try to select an atom/residue an error is thrown:
*** glibc detected *** /usr/bin/python: double free or corruption (!prev): 
0x087de808 ***

Back to square one!!!

>
> You could try 1. checking that you've got all of your development packages
> installed (you probably do, but it never hurts to check);

yum search <for devel packages>

python-devel.i386                        2.4.3-8.FC5            installed

python-numeric.i386                      23.7-2.2.1             installed

tcl-devel.i386                           8.4.13-1.1             installed

freetype-devel.i386                      2.1.10-5.2.1           installed

freeglut-devel.i386                      2.4.0-4                installed

libpng-devel.i386                        2:1.2.8-2.2.1          installed

libgcc.i386                              4.1.1-1.fc5            installed

can't find pmw or the zlib-gcc packages through yum.

> 2. upgrading (or  downgrading) gcc; 
I'm unsure how to downgrade.

> 3. customize setup/rules.generic for your system, and 
> build with make (personal preference is for building ext dependencies from
> ext-0_99rc1-src.tgz as well, but this shouldn't make a difference).
Tried to build the ext package but got constant problems:

./build.com tcl
...
checking system version (for dynamic loading)... ./configure: line 7624: 
syntax error near unexpected token `)'
./configure: line 7624: `       OSF*)'
make: *** [tcl] Error 2

./build.com tk
...
checking for Tcl configuration... configure: 
error: /home/fauxn/software/pymol-0.99rc6/ext/src/build/tcl8.4.11/unix 
directory doesn't contain tclConfig.sh
make: *** [tk] Error 1

./build.com zlib-gcc
...
cp: target `/home/fauxn/software/pymol-0.99rc6/ext/include' is not a directory
make: *** [zlib-gcc] Error 1

I'm now at a complete loss as how to get pymol running stability on my 
machine.  I'm begining to feel that the best and simplest option is to 
upgrade my card.  Is that really going to fix things if it's a gcc problem?

Many Thanks,
Noel

-- 
PhD Student
Department of Biochemistry and Molecular Biology
Monash University
Clayton, Victoria
Australia

Ph: +61 3 9905 1418
e-mail: noe...@me...
website: http://vbc.med.monash.edu.au/~fauxn

Hi Noel,

Which version of gcc are you using?  A quick check of google for the
unterminated argument list in macro error makes it look like that could be
an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's
using  make instead of python distutils).  It looks to me like a c
preprocessor issue, rather than something in Crystal.c; specifically
dealing with the PRINTF macro in Feedback.h (although it does seem a
little strange seeing special characters in a logfile...).

You could try 1. checking that you've got all of your development packages
installed (you probably do, but it never hurts to check); 2. upgrading (or
downgrading) gcc; or 3. customize setup/rules.generic for your system, and
build with make (personal preference is for building ext dependencies from
ext-0_99rc1-src.tgz as well, but this shouldn't make a difference).

Good luck,

Pete

> Hi all,
>
> As suggested by Peter, I tried compiling PyMol from src
> (pymol-0_99rc6-src.tgz).  Unfortunately it fell over :(
>
> Attached is the output.
>
> The error  occurs in layer0/Crystal.c.  I've look at the file in vim and
> there
> does not seem to be anything untowards (weird characters etc...) in it.
>
> I tried to compile from pymol-0_99rc1-src.tgz and got the same error.
>
> Any pointers??
>
> Many thanks
>
> Noel

<snip>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Hi Orla,

You're not making clear what kind of effects you want to investigate.
Basically, it is possible to delete amino acids using pymol, but you
could as well use a text editor. If the purpose is to have a 'correct'
starting structure for further study (e.g. MD simulation), it's
unlikely to work. You won't know whether the result is reasonable
enough. Initially, you will create a long bond, which you might fix up
with an energy minimizer, but this is likely to screw up the structure
anyway. This said, if the residue(s) you want to delete are located in
an extended loop, you could probably get away with it, and yes, you
can do such modeling in Pymol.

Hope it helps,

Tsjerk

On 8/29/06, Orla O'Sullivan <Orl...@te...> wrote:
>
>
>
>
>
>
> Hi
>
>
>
> I have a PDB file and I want to look at the effects of deleting certain
> amino acids on the structure. Is this possible in pymol??
>
>
>
> Orla
>
> Dr. Orla O'Sullivan
>
> Research Officer
>
> Teagasc
>
> Moorepark Food Research Centre
>
> Fermoy
>
> Co. Cork
>
> Ireland
>
> Phone: 353 25 42344
>
> Fax: 353 25 42340
>
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
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>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hi all,

As suggested by Peter, I tried compiling PyMol from src 
(pymol-0_99rc6-src.tgz).  Unfortunately it fell over :(

Attached is the output.

The error  occurs in layer0/Crystal.c.  I've look at the file in vim and there 
does not seem to be anything untowards (weird characters etc...) in it.

I tried to compile from pymol-0_99rc1-src.tgz and got the same error.

Any pointers??

Many thanks

Noel

On Friday 25 August 2006 23:49, you wrote:
> <snip>
>
> > Dose anyone have any idea's?  This occurs when I single click left or
> > right in
> > the main display.
>
> If you're using the binary distribution, try using the source distribution
> and see if the problem persists (if compilation fails, then the error
> message might provide some information as to what's going on).  You could
> also try different graphics drivers (if possible).
>
> Failing that, it sounds like an issue w\ the mouse event listener in the
> glut stuff.  Unfortunately I don't know of an easy fix or work-around if
> this is the case (hopefully Warren will chime in on this).
>
> Good luck,
>
> Pete

-- 
PhD Student
Department of Biochemistry and Molecular Biology
Monash University
Clayton, Victoria
Australia

Ph: +61 3 9905 1418
e-mail: noe...@me...
website: http://vbc.med.monash.edu.au/~fauxn

=20

Hi=20

=20

I have a PDB file and I want to look at the effects of deleting certain
amino acids on the structure. Is this possible in pymol??

=20

Orla

Dr. Orla O'Sullivan

Research Officer=20

Teagasc

Moorepark Food Research Centre

Fermoy=20

Co. Cork

Ireland

Phone: 353 25 42344

Fax: 353 25 42340

=20

=20

Hi OJ,

I don't know if someone has implemented it already, but it's not a
hard thing to do if you know a little python. You basically need to
fetch the coordinates of the OCNH atoms from a selection and build
planes with CGO (you can have a look at Gareth Stockwells walls.py:
http://www.ebi.ac.uk/~gareth/pymol/downloads/scripts/walls.py).

Hope it helps,

Tsjerk

On 8/27/06, O. J. Ganesh <ojg...@mb...> wrote:
> Hey everyone,
>
> I checked the pymol wiki for this one, but didn't find it.   Is there an easy way to create/show the OCNH peptide plane throughout a protein (or maybe in certain sections of a protein)?   I'd like to make planes that look like the ones from Ramachandran Plot Explorer:
> http://bosco.infogami.com/rama
>
> Thanks.
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hey everyone,
=20
I checked the pymol wiki for this one, but didn't find it.   Is there an =
easy way to create/show the OCNH peptide plane throughout a protein (or =
maybe in certain sections of a protein)?   I'd like to make planes that =
look like the ones from Ramachandran Plot Explorer:
http://bosco.infogami.com/rama
=20
Thanks.

Hi everyone,

I 'd like to display the substrate binding cavity inside an enzyme.  I don't
know how to calculate it.  It seems to me there is no command as in Swiss
PdbViewer to do it.  However, I did read some paper in that this kind of cavity
was displayed using PyMol.

Thank you very much!

Yours sincrely,

Fayi

HI all,

This is a follow on from the e-mail below.  Frequently I'm also getting this 
error when pymol crashes:

*** glibc detected *** /home/fauxn/software/pymol/pymol.exe: double free or 
corruption (!prev): 0x0aaef170 ***
======= Backtrace: =========
/lib/libc.so.6[0xc69d88]
/lib/libc.so.6(__libc_free+0x78)[0xc6d25f]
/usr/lib/libGL.so.1[0x5bd8e5a]
======= Memory map: ========
00101000-001fa000 r-xp 00000000 fd:00 11326935   /usr/lib/libX11.so.6.2.0
001fa000-001fe000 rwxp 000f9000 fd:00 11326935   /usr/lib/libX11.so.6.2.0
001fe000-00200000 rwxp 00000000 00:0f 1254       /dev/zero
00200000-00214000 r-xp 00000000 fd:00 
12931879   /home/fauxn/software/pymol/ext/lib/python2.4/site-packages/Numeric/_numpy.so
00214000-00216000 rwxp 00013000 fd:00 
12931879   /home/fauxn/software/pymol/ext/lib/python2.4/site-packages/Numeric/_numpy.so
00216000-00219000 r-xp 00000000 fd:00 
12905453   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/time.so
00219000-0021b000 rwxp 00002000 fd:00 
12905453   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/time.so
0021b000-00224000 r-xp 00000000 fd:00 
12905473   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_socket.so
00224000-00227000 rwxp 00009000 fd:00 
12905473   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_socket.so
00227000-0022c000 r-xp 00000000 fd:00 
12905440   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/struct.so
0022c000-0022d000 rwxp 00004000 fd:00 
12905440   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/struct.so
0022d000-00231000 r-xp 00000000 fd:00 
12905478   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/operator.so
00231000-00232000 rwxp 00004000 fd:00 
12905478   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/operator.so
00232000-00234000 rwxp 00000000 00:0f 1254       /dev/zero
00234000-00236000 rwxp 00000000 00:0f 1254       /dev/zero
00236000-00238000 rwxp 00000000 00:0f 1254       /dev/zero
00238000-0023a000 rwxp 00000000 00:0f 1254       /dev/zero
0023a000-0023c000 rwxp 00000000 00:0f 1254       /dev/zero
0023c000-0023e000 rwxp 00000000 00:0f 1254       /dev/zero
0023e000-00240000 rwxp 00000000 00:0f 1254       /dev/zero
00240000-00242000 rwxp 00000000 00:0f 1254       /dev/zero
00242000-0024b000 rwxp 00000000 00:0f 1254       /dev/zero
0027c000-00280000 r-xp 00000000 fd:00 
12905441   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/collections.so
00280000-00281000 rwxp 00003000 fd:00 
12905441   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/collections.so
002b3000-002b6000 r-xp 00000000 fd:00 
12905457   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_random.so
002b6000-002b7000 rwxp 00002000 fd:00 
12905457   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/_random.so
002f3000-002f4000 r-xp 002f3000 00:00 0          [vdso]
002f4000-0030d000 r-xp 00000000 fd:00 1669685    /lib/ld-2.4.so
0030d000-0030e000 r-xp 00018000 fd:00 1669685    /lib/ld-2.4.so
0030e000-0030f000 rwxp 00019000 fd:00 1669685    /lib/ld-2.4.so
00311000-00a87000 r-xp 00000000 fd:00 
11326754   /usr/lib/libGLcore.so.1.0.7182
00a87000-00aa3000 rwxp 00775000 fd:00 
11326754   /usr/lib/libGLcore.so.1.0.7182
00aa3000-00ab8000 rwxp 00aa3000 00:00 0
00aba000-00abb000 r-xp 00000000 fd:00 
15615182   /usr/lib/tls/libnvidia-tls.so.1.0.7182
00abb000-00abc000 rwxp 00000000 fd:00 
15615182   /usr/lib/tls/libnvidia-tls.so.1.0.7182
00ad3000-00ad7000 r-xp 00000000 fd:00 
12905474   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/strop.so
00ad7000-00ad9000 rwxp 00003000 fd:00 
12905474   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/strop.so
00b14000-00b17000 r-xp 00000000 fd:00 
12905449   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/math.so
00b17000-00b18000 rwxp 00003000 fd:00 
12905449   /home/fauxn/software/pymol/ext/lib/python2.4/lib-dynload/math.so
00b4a000-00b52000 r-xp 00000000 fd:00 11326936   /usr/lib/libXrender.so.1.3.0
00b52000-00b53000 rwxp 00007000 fd:00 11326936   /usr/lib/libXrender.so.1.3.0
00b60000-00b64000 r-xp 00000000 fd:00 11327016   /usr/lib/libXfixes.so.3.0.0
00b64000-00b65000 rwxp 00003000 fd:00 
11327016   /usr/lib/libXfixes/home/fauxn/software/pymol/pymol: line 14: 10660 
Aborted                 $PYMOL_PATH/pymol.exe "$@"


Dose anyone have any idea's?  This occurs when I single click left or right in 
the main display.

On Tuesday 22 August 2006 13:46, Noel Faux wrote:
> Hi all,
>
> Recently I finally managed to install the Nvidia driver
> (NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2
> Pro/AGP/SSE2) on my Fedora Core 5 box.  When I try and run pymol it crashed
> after I load a pdb file and try and either right or left click on the main
> display.
>
> Here is the output from the pymol run:
>
> PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
>
>  A current PyMOL Maintenance and/or Support Subscription may be required
>  for legal use of this Build beyond a finite honor-system evaluation
> period. Please visit http://www.pymol.org/funding.html for more
> information.
>
>  This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
>  OpenGL graphics engine:
>   GL_VENDOR: NVIDIA Corporation
>   GL_RENDERER: Quadro2 Pro/AGP/SSE2
>   GL_VERSION: 1.5.3 NVIDIA 71.82
>  Adapting to Quadro hardware.
>
>  PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.
>
>  A current PyMOL Maintenance and/or Support Subscription may be required
>  for legal use of this Build beyond a finite honor-system evaluation
> period. Please visit http://www.pymol.org/funding.html for more
> information.
>
>  This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
> HEADER    SCOP/ASTRAL domain d1a5ug2 [29269]      08-MAY-03   0000
>  CmdLoad: "/home/fauxn/results/SCOP_90_results/d1a5ug2.pdb" loaded
> as "d1a5ug2".
> /home/fauxn/software/pymol/pymol: line 14:  7203 Segmentation fault
> $PYMOL_PATH/pymol.exe "$@"
>
> Any pointers welcome!
>
> Cheers
> Noel

-- 
PhD Student
Department of Biochemistry and Molecular Biology
Monash University
Clayton, Victoria
Australia

Ph: +61 3 9905 1418
e-mail: noe...@me...
website: http://vbc.med.monash.edu.au/~fauxn

I'm trying to create a smooth surface representation of a set of 6.5A  
diameter spheres read in as CA atoms. Is there a way to override  
PyMol's assignment of atomic radii? Also, if I were using a  
conventional molecular surface algorithm I would turn up the "probe"  
radius so that the surface had a smoother appearance. Any way to do  
this?

Richard

You can also check if there is connecting electron density, see for example
the electron density server at http://eds.bmc.uu.se/eds/ . This of course
only works if the authors have deposited the experimental data. 

I hope this helps.

Best regards,

Anne

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Tsjerk
Wassenaar
Sent: 24. august 2006 13:36
To: mahesh kulharia
Cc: pym...@li...
Subject: Re: [PyMOL] Problem

Hi Mahesh,

There is no way to see whether two atoms are connected. Pymol guesses
the connectivity based on the distances between the particles. But to
be certain whether atoms are bonded, you have to look in the PDB file,
which should mention covalent attachment of a ligand. At the end of
the pdb file there will also often be CONECT statements, indicating
which bonds to create explicitly. Pymol also reads those records.
Alternatively, you can look up the original paper regarding the pdb
structure, in which you should be able to find out more about the
nature of the system.

Hope it helps,

Tsjerk

On 8/24/06, mahesh kulharia <kul...@go...> wrote:
> Hi
> I need help. Can some one tell me a way to find out whether 2 molecules
are
> connected by covalent linkage or not. Say for example in pdb files we have
> ligand and protein molecules and I wish to know a way to find out if the
> ligand is connected to the protein via a covalent bond or not, The problem
> is I cannot use covalent radius values for specific bonds as the
resolution
> is not good in pdb.
> I wonder how does the program in pymol does that. I would be very grateful
> if someone could tell me a way out. Please help.
> need_help
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
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>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

-------------------------------------------------------------------------
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_______________________________________________
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Hi Mahesh,

There is no way to see whether two atoms are connected. Pymol guesses
the connectivity based on the distances between the particles. But to
be certain whether atoms are bonded, you have to look in the PDB file,
which should mention covalent attachment of a ligand. At the end of
the pdb file there will also often be CONECT statements, indicating
which bonds to create explicitly. Pymol also reads those records.
Alternatively, you can look up the original paper regarding the pdb
structure, in which you should be able to find out more about the
nature of the system.

Hope it helps,

Tsjerk

On 8/24/06, mahesh kulharia <kul...@go...> wrote:
> Hi
> I need help. Can some one tell me a way to find out whether 2 molecules are
> connected by covalent linkage or not. Say for example in pdb files we have
> ligand and protein molecules and I wish to know a way to find out if the
> ligand is connected to the protein via a covalent bond or not, The problem
> is I cannot use covalent radius values for specific bonds as the resolution
> is not good in pdb.
> I wonder how does the program in pymol does that. I would be very grateful
> if someone could tell me a way out. Please help.
> need_help
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>


-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

Hi
I need help. Can some one tell me a way to find out whether 2 molecules are
connected by covalent linkage or not. Say for example in pdb files we have
ligand and protein molecules and I wish to know a way to find out if the
ligand is connected to the protein via a covalent bond or not, The problem
is I cannot use covalent radius values for specific bonds as the resolution
is not good in pdb.
I wonder how does the program in pymol does that. I would be very grateful
if someone could tell me a way out. Please help.
need_help

Dear Selvaraj,

You will find useful resources about hydrogen bonding with PyMOL on:
http://www.rubor.de/bioinf/tips_modeling.html#addhbond

Regards,

Jerome Pansanel

Le mercredi 23 ao=C3=BBt 2006 22:48, selva raj a =C3=A9crit=C2=A0:
> Dear Pymol users,
>        Would anyone tell me how to draw hydrogen bonds between interacting
> atoms in a crystal structure of small molecule using Pymol. An attempt to
> do it through mentioning cutoff distance as 3.0, and mode as 0, failed.
> Command:
>        distance (selection1),(selection2)[,3.0[,0]]
>        This command is showing all possible distances from the selected
> atoms Thanking you,
>
>   yours friendly.
>   Selvaraj,
>
>
>
> ---------------------------------
>  Here's a new way to find what you're looking for - Yahoo! Answers
>  Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. G=
et
> it NOW

Take a look at this link:
http://www.rubor.de/bioinf/tips_modeling.html#addhbond
It contains two simple examples and one python script.

On 8/23/06, selva raj <cry...@ya...> wrote:
>
> Dear Pymol users,
>      Would anyone tell me how to draw hydrogen bonds between interacting
> atoms in a crystal structure of small molecule using Pymol. An attempt to do
> it through mentioning cutoff distance as 3.0, and mode as 0, failed.
> Command:
>      distance (selection1),(selection2)[,3.0[,0]]
>      This command is showing all possible distances from the selected atoms
>                                              Thanking you,
>
> yours friendly.
> Selvaraj,
>
>
>
>  ________________________________
>  Here's a new way to find what you're looking for - Yahoo! Answers
>  Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get
> it NOW
>
>
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>
>

Hi Siv,

Try giving each chain a unique identifier.   As pymol might believe that all 
the fragments belong to chain ' '.

Cheers
Noel

On Wednesday 23 August 2006 22:40, Siv Midtun Hollup wrote:

> Hi,
>
> Hope this is the correct place for this question :)
>
> I have a pdb file with many small fragments in addition to a longer chain.
> These are not numerated in any way, only separated by TER (example
> below). In pymol, only two 'chains' appear, one with the long chain, and
> the other with all the fragments mixed together.
>
> Do chains need to be separated by anything else than lines containing
> TER? If I try to visualise the same pdb file in rasmol, the separate
> chains are drawn up (for instance with ribbon).
>
> Also, is there a limit to how many chains pymol can handle? I might have
> 1000 shorter chains in one pdb file.
>
> I run pymol 0.99rc6 for linux.
>
> Any help appreciated :)
>
> Sincerly,
> Siv Hollup
>

-- 
PhD Student
Department of Biochemistry and Molecular Biology
Monash University
Clayton, Victoria
Australia

Ph: +61 3 9905 1418
e-mail: noe...@me...
website: http://vbc.med.monash.edu.au/~fauxn

Dear Pymol users,
       Would anyone tell me how to draw hydrogen bonds between interacting atoms in a crystal structure of small molecule using Pymol. An attempt to do it through mentioning cutoff distance as 3.0, and mode as 0, failed.  
  Command:
       distance (selection1),(selection2)[,3.0[,0]]
       This command is showing all possible distances from the selected atoms
                                               Thanking you,
   
  yours friendly.
  Selvaraj,
   

 				
---------------------------------
 Here's a new way to find what you're looking for - Yahoo! Answers 
 Send FREE SMS to your friend's mobile from Yahoo! Messenger Version 8. Get it NOW

>> I think he means for you to have a "Load" button as part of your
>> plugin.  That button would first record the path to the file and then
>> call through to cmd.load().
>
> Perhaps what Ron needs to do is not use the cmd.load() function but
> use his own file reading procedure.  The lines containing coordinates
> could be extracted from the file (by recognizing them with a  
> regexp) and
> passed to the cmd.read_pdbstr() function.  The CGO commands could be
> read separately.  Then there is no need to worry about where  
> cmd.load()
> thinks file is.


Rob, thanks for the response.  I'm currently using a variation of  
what you wrote above.  It's just that the primary "use case" in my  
lab is to load multiple structures at once when starting pymol on the  
command line.
$ pymol 1AAA.pdb 1AAB.pdb 1AAC.pdb  or, more frequently
$ pymol *.pdb

I then want the user to be able to click on my plugin in the Plugin  
menu and have it run without the need for a GUI asking where to find  
the files (so I can reread them for the extra info I need).  In the  
example above, there's no problem: The files are all located in the  
current working directory so I know where to find them.  I start  
having problems when users do things as below:

$ pymol ../1AAD.pdb ~/jsmith/1AAE.pdb ./structures/1AAF.pdb

When PyMOL loads these structures, it drops the path information to  
create the object name and none of these structures are in the  
current working directory.  Hence, my plugin can't find the files.

For the time being, I'm going to instruct users in my lab that the  
structures they load must be in the same directory as the one from  
which they execute pymol.  At some point I will (hopefully) release  
the plugin to the public.  If I see that it's being used, I'll  
consider adding some preprocessing step that checks to see if the  
files can be found and if not, maybe execute a restricted "find"  
command up and down one or two directories or pop up a GUI that asks  
users to specify where to find the files (that couldn't be found).

I don't want to beat/flog a dead horse here, but other suggestions  
are always welcome.

Best,
-Ron

Hi folks,

* Michael Lerner <mgl...@gm...> [2006-08-21 12:26] wrote:
> I think he means for you to have a "Load" button as part of your
> plugin.  That button would first record the path to the file and then
> call through to cmd.load().

Perhaps what Ron needs to do is not use the cmd.load() function but
use his own file reading procedure.  The lines containing coordinates
could be extracted from the file (by recognizing them with a regexp) and
passed to the cmd.read_pdbstr() function.  The CGO commands could be
read separately.  Then there is no need to worry about where cmd.load()
thinks file is.

> On 8/19/06, Ron Jacak <ro...@em...> wrote:
>
> > Peter,
> >
> > >> I'm working on a plugin that reads information appended to the
> > >> end of PDB files to draw CGO objects.  Right now, I have the
> > >> user specify the filesystem path to the currently loaded objects
> > >> through the plugin GUI so that I know where to go to find the
> > >> file.  For one object, this isn't so bad.  But if users load
> > >> multiple objects that are in different directories, I will have
> > >> to change the GUI so that the user has to specify the path to
> > >> each object loaded.  This kind of situation would quickly become
> > >> tedious.  Does PyMOL store the paths for objects that are loaded
> > >> somewhere?  I know I can get the current working directory using
> > >> getcwd(), so I'm hoping there's a way to get the path to the
> > >> loaded objects as well.
> >
> > > I don't know of a way to get file information from a pymol object,
> > > but you could work around this by using a python dictionary (when
> > > the pdb file is loaded, store the full path to the file in a
> > > dictionary using the pymol object name as the key).
> >
> > I'm not sure I fully understand your suggestion.  It sounds to
> > me like what you're saying is that I should add code (e.g. a
> > dictionary) to the importing.py load() function which saves the
> > file information of objects as they're loaded.  But then instead of
> > just distributing my plugin, I would have to get users to change
> > their PyMOL source, as well (which I'm not willing to do).  Am I
> > understanding correctly?
> >
> > Any other ways around this problem?

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Department of Biochemistry, Queen's University
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>         http://adelie.biochem.queensu.ca/~rlc

Hi,

Hope this is the correct place for this question :)

I have a pdb file with many small fragments in addition to a longer chain.
These are not numerated in any way, only separated by TER (example
below). In pymol, only two 'chains' appear, one with the long chain, and
the other with all the fragments mixed together. 

Do chains need to be separated by anything else than lines containing
TER? If I try to visualise the same pdb file in rasmol, the separate
chains are drawn up (for instance with ribbon). 

Also, is there a limit to how many chains pymol can handle? I might have
1000 shorter chains in one pdb file. 

I run pymol 0.99rc6 for linux. 

Any help appreciated :) 

Sincerly, 
Siv Hollup

Example file: 

ATOM      1  CA  ALA A   2      39.866  21.059   8.959  1.00  0.000
ATOM      2  CA  ASP A   3      43.425  19.735   8.836  1.00  0.000
ATOM      3  CA  LYS A   4      44.119  17.105   6.147  1.00  0.000
ATOM      4  CA  GLU A   5      45.918  15.101   8.820  1.00  0.000
ATOM      5  CA  LEU A   6      42.800  14.764  10.998  1.00  0.000
ATOM      6  CA  LYS A   7      42.788  11.087  12.105  1.00  0.000
ATOM      7  CA  PHE A   8      39.620   9.225  11.057  1.00  0.000
ATOM      8  CA  LEU A   9      38.249   5.964  12.522  1.00  0.000
ATOM      9  CA  VAL A  10      36.051   4.078   9.925  1.00  0.000
ATOM     10  CA  VAL A  11      33.741   1.537  11.645  1.00  0.000
ATOM     11  CA  ASP A  12      31.811  -1.156   9.804  1.00  0.000
ATOM     12  CA  ASP A  13      31.552  -4.975   9.930  1.00  0.000
ATOM     13  CA  PHE A  14      32.160  -5.228   6.162  1.00  0.000
ATOM     14  CA  SER A  15      35.826  -4.868   5.227  1.00  0.000
ATOM     15  CA  THR A  16      34.876  -3.922   1.618  1.00  0.000
ATOM     16  CA  MET A  17      32.758  -0.963   2.790  1.00  0.000
ATOM     17  CA  ARG A  18      35.630   0.118   5.108  1.00  0.000
ATOM     18  CA  ARG A  19      37.960   0.012   2.052  1.00  0.000
ATOM     19  CA  ILE A  20      35.480   2.111   0.006  1.00  0.000
ATOM     20  CA  VAL A  21      35.304   4.818   2.693  1.00  0.000
ATOM     21  CA  ARG A  22      39.075   4.807   3.161  1.00  0.000

<znip long chain>

ATOM    121  CA  LYS A 122      28.602  20.659   6.335  1.00  0.000
ATOM    122  CA  ILE A 123      29.836  19.118   9.608  1.00  0.000
ATOM    123  CA  PHE A 124      33.045  21.152   9.650  1.00  0.000
ATOM    124  CA  GLU A 125      30.917  24.274   9.124  1.00  0.000
ATOM    125  CA  LYS A 126      28.302  23.283  11.765  1.00  0.000
ATOM    126  CA  LEU A 127      31.094  22.603  14.304  1.00  0.000
ATOM    127  CA  GLY A 128      33.194  25.622  13.408  1.00  0.000
ATOM    128  CA  MET A 129      36.197  23.497  12.226  1.00  0.000
TER
REMARK next fragment
ATOM      1  CA  ASP   928      42.867  13.075  13.193  1.00   1.00
ATOM      2  CA  VAL   929      41.607   9.565  12.506  1.00   2.00
ATOM      3  CA  ILE   930      38.318   8.385  11.059  1.00   4.00
ATOM      4  CA  LEU   931      37.131   4.823  11.752  1.00   8.00
ATOM      5  CA  LEU   932      34.886   4.133   8.729  1.00   4.00
ATOM      6  CA  LEU   933      32.669   1.190   9.618  1.00   2.00
ATOM      7  CA  ASP   934      30.966  -1.045   7.090  1.00   1.00
ATOM      8  CA  LYS   948      31.343  -1.115  17.238  1.00   1.00
ATOM      9  CA  SER   949      33.588  -3.020  19.694  1.00   2.00
ATOM     10  CA  PHE   950      36.575  -2.337  17.454  1.00   3.00
ATOM     11  CA  ALA   951      35.721   1.386  17.478  1.00   4.00
ATOM     12  CA  LYS   952      35.265   1.425  21.266  1.00   3.00
ATOM     13  CA  ALA   953      38.537  -0.417  21.936  1.00   2.00
ATOM     14  CA  PHE   954      40.407   1.905  19.558  1.00   1.00
ATOM     15  CA  ALA   951      35.721   1.386  17.478  1.00   1.00
ATOM     16  CA  LYS   952      35.265   1.425  21.266  1.00   2.00
ATOM     17  CA  ALA   953      38.537  -0.417  21.936  1.00   3.00
ATOM     18  CA  PHE   954      40.407   1.905  19.558  1.00   4.00
ATOM     19  CA  ILE   955      38.981   4.961  21.371  1.00   3.00
ATOM     20  CA  SER   956      39.800   3.586  24.844  1.00   2.00
ATOM     21  CA  LYS   957      43.410   2.919  23.826  1.00   1.00
ATOM     22  CA  LYS   952      35.265   1.425  21.266  1.00   1.00
ATOM     23  CA  ALA   953      38.537  -0.417  21.936  1.00   2.00
ATOM     24  CA  PHE   954      40.407   1.905  19.558  1.00   3.00
ATOM     25  CA  ILE   955      38.981   4.961  21.371  1.00   4.00
ATOM     26  CA  SER   956      39.800   3.586  24.844  1.00   3.00
ATOM     27  CA  LYS   957      43.410   2.919  23.826  1.00   2.00
ATOM     28  CA  ALA   958      43.936   6.085  21.764  1.00   1.00
TER
<znip many more fragments>

-- 
Siv Midtun Hollup 
PhD Student
Dept. of Informatics
University of Bergen, Norway
si...@ii... (NOTE: new email adress)
- Blessed are the flexible, for they can be tied into knots. -

Hello,
There are plenty examples of how to create frames by loading several
structures (i.e one file, one frame).
What I want is to do something like this:
 - load a structure
 - set it as frame 1
 - change representation and coloring
 - set the view as frame 2
 - show/hide several atoms,
 - set t he view as frame 3
 - add labels
 - set the view as frame 4
..... you get the point.

Is this possible? Can anyone give a simple example or give a link?

Thank you

I've tested two Kensington PilotMouse Laser Wireless mice and the  
middle button only works occassionally.  I returned them for refund.   
I think the problem is what you said -- pressing activates the side- 
to-side scroll which overrides the middle click.  I've also tried an  
MS Notebook Laser Mouse and the button didn't work either.

I know that many other mice work --- probably the ones without the  
horizontal scroll.

-Mark


On Aug 22, 2006, at 5:07 PM, pymol-users- 
re...@li... wrote:

> From: Ramachandran Murali <mu...@xr...>
> Date: August 21, 2006 8:43:00 PM GMT-04:00
> To: pym...@li...
> Subject: [PyMOL] kensington three button mouse in mac book pro-issue
>
>
> Hi,
> I am using Kensington three-button mouse on a Mac book pro (17")  
> laptop. In pymol,
> when i press the middle button (for translation), it switches to  
> horizontal scroll. The translation function is not working!
>
> Has anyone experienced similar problem?. Any fix or work around?
>
> Thanks
> Murali

Ron,

> I'm not sure I fully understand your suggestion.  It sounds to me
> like what you're saying is that I should add code (e.g. a dictionary)
> to the importing.py load() function which saves the file information
> of objects as they're loaded.  But then instead of just distributing
> my plugin, I would have to get users to change their PyMOL source, as
> well (which I'm not willing to do).  Am I understanding correctly?

Well, I may have been misunderstanding you...I'd though you mentioned you
were using a gui to load the pdb files, which would be the natural place
to add additional code.  I'd assumed the gui you were talking about was
specific to your plugin (if this isn't the case, then my suggestion
doesn't help that much).

> Any other ways around this problem?

You could try turning on logging, and scan through the logfile looking for
load events (on my system, using the standard gui menus to open a pdb,
this stores the full path to the input pdb file; although it does not
associate it with the object name).  Of course then you're stuck with the
problem of getting the name/path of the logfile...

Good luck,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Hi all,

Recently I finally managed to install the Nvidia driver 
(NVIDIA-Linux-x86-1.0-7182-pkg1) for the graphics card (Quadro2 Pro/AGP/SSE2) 
on my Fedora Core 5 box.  When I try and run pymol it crashed after I load a 
pdb file and try and either right or left click on the main display.

Here is the output from the pymol run:

PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.

 A current PyMOL Maintenance and/or Support Subscription may be required
 for legal use of this Build beyond a finite honor-system evaluation period.
 Please visit http://www.pymol.org/funding.html for more information.

 This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro2 Pro/AGP/SSE2
  GL_VERSION: 1.5.3 NVIDIA 71.82
 Adapting to Quadro hardware.

 PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC.

 A current PyMOL Maintenance and/or Support Subscription may be required
 for legal use of this Build beyond a finite honor-system evaluation period.
 Please visit http://www.pymol.org/funding.html for more information.

 This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6.
HEADER    SCOP/ASTRAL domain d1a5ug2 [29269]      08-MAY-03   0000
 CmdLoad: "/home/fauxn/results/SCOP_90_results/d1a5ug2.pdb" loaded 
as "d1a5ug2".
/home/fauxn/software/pymol/pymol: line 14:  7203 Segmentation fault     
$PYMOL_PATH/pymol.exe "$@"

Any pointers welcome!

Cheers
Noel
-- 
PhD Student
Department of Biochemistry and Molecular Biology
Monash University
Clayton, Victoria
Australia

Ph: +61 3 9905 1418
e-mail: noe...@me...
website: http://vbc.med.monash.edu.au/~fauxn