pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Problems in using PyMol plugins

[Forlani R. <rob...@ni...>]

Dear all,
I am trying to use PyMol plugins but I have some problems.
In the reported case the Caver plugin was considered (following usage
notes reported in http://loschmidt.chemi.muni.cz/caver/examples.php),
for your information similar problems were encountered with builtin
PyMol plugins (e.g PDB Loader). I think theres something wrong with my
configuration/environment variables, can you give me some hints?

PyMol version is 0.99 beta 33 (binary) on Windows XP Pro sp2.

Thank you in advance for your help.

Regards,
Roberto


-- 8< --
IOError Exception in Tk callback
  Function: <function <lambda> at 0x0C25CEB0> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "C:\Programmi\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in
__call__
    return apply(self.func, args)
  File "C:\Programmi\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwDialog.py", line 153, in
<lambda>
    command=3Dlambda self=3Dself, name=3Dname: self._doCommand(name))
  File "C:\Programmi\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwDialog.py", line 132, in
_doCommand
    return command(name)
  File "C:\Programmi\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\caver.py", line 650, in execute
    self.prepareinput(self.selection.getvalue(),startpoint)
  File "C:\Programmi\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\caver.py", line 489, in
prepareinput
    f =3D open(self.pymol_generated_trj_filename.getvalue(), "w")
IOError: [Errno 2] No such file or directory: 'C:/Program
Files/MasarykUniversity-Ncbr/Caver/Temp/pymol-generated.trj'

[PyMOL] load *only one* state for NMR ensemble ..

[Andrea S. <and...@gm...>]

Hi all,
I have more then 200 pdb files and each file represents an ensemble of
NMR calculated structure (ca. 30). If I try to load all together, my
system goes terribly slowly and pymols seems crashing (the windows
freeze). Is there any way to load only the first structure for each
file rather than all the ensemble??
Thanks to all

Regards

andrea


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

Re: [PyMOL] alpha carbon trace

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

On Thursday 30 March 2006 11:24, Daniel Gutmann wrote:
> I was recently looking at the 1JSQ a structure containing only the
> alpha carbon trace. However pymol seems to be unable to join them
> together for proper rendering. If anyone knows the required command
> or plugin, I would be very grateful!

There is a setting called "cartoon_trace". By default it is set to zero and 
PyMOL will not connect Calpha atoms when the other atoms are absent. You can 
change the setting in the corresponding menu, or with the command

set cartoon_trace,1

PyMOL should now draw cartoons through the Calpha positions, although it might 
get confused if there are multiple chains in the PDB file and connect the 
last atom of one chain to the first of antoher. In that case it will be 
necessary to create separate objects for the different chains.

There is an analogous setting "ribbon_trace" for the ribbon representation. In 
this case, separate chains do not appear to get connected.

-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

RE: [PyMOL] Updated PyMOL v0.99 Release Candidate

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

Michael,

A couple of minor and easily-fixed glitches have cropped up in in =
0.99rc6, so there will be at least one more patch applied to the 0.99 =
release branch before it is finalized.  Other than that, rc6 is quite =
solid.

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
> Michael Banck
> Sent: Thursday, March 30, 2006 5:08 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Updated PyMOL v0.99 Release Candidate
>=20
> On Fri, Mar 03, 2006 at 06:00:03PM -0800, Warren DeLano wrote:
> > These may be infamous last words, but I do believe that the latest=20
> > PyMOL
> > v0.99 release candidate has reached a level of stability,=20
> performance,=20
> > and bug containment such that most everyone should feel comfortable=20
> > downloading and updating to version 0.99.
>=20
> So that means that contrary to the PyMOL webpage, 0.99 isn't=20
> officially released yet?  I was looking for official 0.99=20
> tarballs in order to upload them to Debian/Ubuntu, but I=20
> could only find release candidates on Sourceforge's download site.
>=20
>=20
> Michael
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] Updated PyMOL v0.99 Release Candidate

[Michael B. <mb...@gm...>]

On Fri, Mar 03, 2006 at 06:00:03PM -0800, Warren DeLano wrote:
> These may be infamous last words, but I do believe that the latest PyMOL
> v0.99 release candidate has reached a level of stability, performance,
> and bug containment such that most everyone should feel comfortable
> downloading and updating to version 0.99.

So that means that contrary to the PyMOL webpage, 0.99 isn't officially
released yet?  I was looking for official 0.99 tarballs in order to
upload them to Debian/Ubuntu, but I could only find release candidates
on Sourceforge's download site.


Michael

[PyMOL] alpha carbon trace

[Daniel G. <dan...@im...>]

Hello,

I was recently looking at the 1JSQ a structure containing only the  
alpha carbon trace. However pymol seems to be unable to join them  
together for proper rendering. If anyone knows the required command  
or plugin, I would be very grateful!

Best

Dan

[PyMOL] nt_gly.pkl wrong

[Alan <ala...@gm...>]

Hi List!

It is just to inform that the nt_gly.pkl is wrong.

Look the pdb output for the file:

ATOM      1  N   GLY    22      58.491  32.332  -1.281  1.00  0.00         =
  N
ATOM      2  CA  GLY    22      59.916  32.449  -1.577  1.00  0.00         =
  C
ATOM      3  C   GLY    22      60.745  31.741  -0.533  1.00  0.00         =
  C
ATOM      4  O   GLY    22      60.231  31.156   0.424  1.00  0.00         =
  O
ATOM      5 3HA  GLY    22      60.168  33.468  -1.589  0.00  0.00         =
  H
ATOM      6  HA  GLY    22      60.120  31.972  -2.554  1.00  0.00         =
  H
ATOM      7 1HT  TYR    22      58.066  32.699  -0.358  1.00  0.00         =
  H
ATOM      8 2HT  TYR    22      58.065  32.977  -1.992  0.00  0.00         =
  H
ATOM      9 3HT  TYR    22      58.265  31.307  -1.322  0.00  0.00         =
  H
END

There TYR H in a GLY ;-)

Cheers,
Alan
--
Alan Wilter S. da Silva, D.Sc. - Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

RE: [PyMOL] exact molecule duplication keeping its spacial orientation

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

Michael,

Yes, that is what the create command does:=20

load prot.pdb
create prot_cpy, prot

Should generate an identical copy.

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
> Michael Weber
> Sent: Tuesday, March 28, 2006 5:04 AM
> To: PyM...@li...
> Subject: [PyMOL] exact molecule duplication keeping its=20
> spacial orientation
>=20
> Hello,
> is there a possibility in PyMOL to duplicate a molecule that=20
> is present in the currently loaded PyMOL session file such=20
> that is exactly placed on its "parent"? I have to color the=20
> same residue in two or more colors.
> I ask this because reloading the same molecule requires=20
> subsequent alignment and - strangely - these alignments are=20
> often not performed properly (my files contain many other=20
> molecules as well) although the same molecule is already present.
> =20
> Thanks for your help,
> Michael.
>=20

Re: [PyMOL] exact molecule duplication keeping its spacial orientation

[Andrew C. <aco...@gm...>]

I think that the create command will do this

create newM, select statement

if I have a molecule named mol1 with three chains and I  want to make
a copy of chain c I would use

create new_C, mol1 & c. C

Andrew



On 3/28/06, Michael Weber <we...@st...> wrote:
>
> Hello,
> is there a possibility in PyMOL to duplicate a molecule that is present i=
n
> the currently loaded PyMOL session file such that is exactly placed on it=
s
> "parent"? I have to color the same residue in two or more colors.
> I ask this because reloading the same molecule requires subsequent alignm=
ent
> and - strangely - these alignments are often not performed properly (my
> files contain many other molecules as well) although the same molecule is
> already present.
>
> Thanks for your help,
>
> Michael.

[PyMOL] many thanks

[Chandra <ch...@bi...>]

wonderful. many thanks andrea!!

to my question:
If I have two chains in a structure how can i draw a surface on each
> chain separately (as though the other chain did not exist).
> currently i have to separate the structure file into two different files
> with a chain each and read them both and draw teh surface on each.

andrea replied:
Hi
I think you should select the chain A and then create the object for
this selection. Then you can manipulate as standalone object.
select A, chain A
create A_obj, A
show A_obj,surface
I hope this help

Regards

andrea

Re: [PyMOL] surfaces

[Andrea S. <and...@gm...>]

Hi
I think you should select the chain A and then create the object for
this selection. Then you can manipulate as standalone object.
select A, chain A
create A_obj, A
show A_obj,surface
I hope this help

Regards

andrea

2006/3/28, Chandra <ch...@bi...>:
> If I have two chains in a structure how can i draw a surface on each
> chain separately (as though the other chain did not exist).
> currently i have to separate the structure file into two different files
> with a chain each and read them both and draw teh surface on each.
>
> thanks
>
> chandra
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
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=3D121642
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

[PyMOL] surfaces

[Chandra <ch...@bi...>]

If I have two chains in a structure how can i draw a surface on each 
chain separately (as though the other chain did not exist).
currently i have to separate the structure file into two different files 
with a chain each and read them both and draw teh surface on each.

thanks

chandra

[PyMOL] exact molecule duplication keeping its spacial orientation

[Michael W. <we...@st...>]

Hello,
is there a possibility in PyMOL to duplicate a molecule that is present =
in the currently loaded PyMOL session file such that is exactly placed =
on its "parent"? I have to color the same residue in two or more colors.
I ask this because reloading the same molecule requires subsequent =
alignment and - strangely - these alignments are often not performed =
properly (my files contain many other molecules as well) although the =
same molecule is already present.

Thanks for your help,
Michael.

RE: [PyMOL] Saving PDB with CONECT information

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

Hi Alan,

Hmm...you need to use "nt_arg" and "ct_glu" fragment names.  Otherwise, =
you won't get the C-terminal oxygen.

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 Alan
> Sent: Monday, March 20, 2006 12:16 PM
> To: Warren DeLano
> Cc: Pymol
> Subject: Re: [PyMOL] Saving PDB with CONECT information
>=20
> Thanks a lot Warren.
>=20
> If you allow me, my script to build sequences of 3 peptides=20
> is almost done. I could even use sculpt to improve my=20
> molecules structures.
>=20
> For the moment I am missing just one thing. I want to make=20
> the N-term and C-term (NH3+ and COO-) automatically for all=20
> 20 tripeptide. I know how to to do it by mouse, but how to=20
> 'add hydrogens' and 'make pk1 positive', e. g., by command?
>=20
> Thanks a lot for PyMol.
>=20
> Cheers,
> Alan
>=20
> On 20/03/06, Warren DeLano <wa...@de...> wrote:
> > Alan,
> >
> > > Is PyMol able to save the built protein/molecule in a PDB=20
> file with=20
> > > CONECT information. If so, how to do it?
> >
> > Yes,
> >
> > set pdb_conect_all
> >
> > before saving the pdb file in order to get a PDB file with explicit=20
> > connectivity and valences for all atoms.
> >
> > 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 =20
> > Cell:(650)-346-1154 . mailto:wa...@de...
> >
> >
> > > -----Original Message-----
> > > From: pym...@li...
> > > [mailto:pym...@li...] On Behalf Of Alan
> > > Sent: Monday, March 20, 2006 11:39 AM
> > > To: Pymol
> > > Subject: [PyMOL] Saving PDB with CONECT information
> > >
> > > Hello List!
> > >
> > > Is PyMol able to save the built protein/molecule in a PDB=20
> file with=20
> > > CONECT information. If so, how to do it?
> > >
> > > Thanks in advance for any help.
> > >
> > > Cheers,
> > > Alan
> > > --
> > > Alan Wilter S. da Silva, D.Sc. - Research Associate Department of=20
> > > Biochemistry, University of Cambridge.
> > > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting=20
> > > language that extends applications into web and mobile=20
> media. Attend=20
> > > the live webcast and join the prime developer group breaking into=20
> > > this new coding territory!
> > > =
http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyM...@li...
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >
> > >
> > >
> > >
> >
>=20
>=20
> --
> Alan Wilter S. da Silva, D.Sc. - Research Associate=20
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dk&kid=110944&bid$1720&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] (no subject)

[Andrea S. <and...@gm...>]

Hi,
for this purpose I have used caver program. You can download it free
of charge from here  http://loschmidt.chemi.muni.cz/caver/download.php

I hope this help

Regards

andrea

2006/3/27, Sri...@ju... <Sri...@ju...>:
> dear sir
>             iam a pymol user, do we can find area & volume of active site=
 in
> pymol
> if we can, just tell me how to do it
> thanking you
> srilatha
> Thanks & Regards
> srilatha potlapelly
> MSc Biotechnology
>  -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting langua=
ge
> that extends applications into web and mobile media. Attend the live webc=
ast
> and join the prime developer group breaking into this new coding territor=
y!
> http://sel.as-us.falkag.net/sel?cmdlnk&kid=110944&bid$1720&dat=121642
> _______________________________________________ PyMOL-users
> mailing list PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users


--
"La conoscenza libera il genere umano dalla superstizione"
J. Watson

[PyMOL] (no subject)

[<Sri...@ju...>]

<FONT face=3D"Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=
=3D2><DIV>dear sir </DIV><DIV>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;iam a pymol user, do we can find area &amp; volu=
me of active site in pymol </DIV><DIV>if we can, just tell me how to do it =
</DIV><DIV>thanking you </DIV><DIV>srilatha<BR></DIV><DIV>Thanks&nbsp;&amp;=
&nbsp;Regards<BR>srilatha&nbsp;potlapelly<BR>MSc&nbsp;Biotechnology<BR></DI=
V></FONT>=

Re: [PyMOL] sporadic pymol/X-server freezes?

[Sabuj P. <sab...@va...>]

> No consistent pattern.  Both machines are x86, non-nvidia graphics cards
> (which probably isn't helping).  But, score at least one working setup
> (yours) as a fully functional combination.

Yes always go with nvidia on linux x86/x86_64 if you can. Do you have an 
ati/sis/3dlabs/intel product?

RE: [PyMOL] sporadic pymol/X-server freezes?

[Soisson, S. M. <ste...@me...>]

My new laptop has an ATI FireGLV3200 card, and I am using the fglrx driver.
I was having problems with seg faults, but using "set use_display_lists"
fixed the problem.  I did try using the "set nvidia" option that Warren
suggested and it crashed my X-server.  Had to do a hard reboot.  So far so
good though with the display_lists option.  There clearly are some issues
with the ATI GL implementation and pymol, at some level.

Cheers,

Steve

-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Tim Fenn
Sent: Friday, March 24, 2006 3:30 AM
To: Peter Adrian Meyer
Cc: Warren DeLano; pym...@li...
Subject: Re: [PyMOL] sporadic pymol/X-server freezes?


On Thu, Mar 23, 2006 at 08:56:27PM -0500, Peter Adrian Meyer wrote:
> 
> I guess it shouldn't supprise me that there are issues with proprietary
> OpenGL on linux (FYI the two machines I've seen this on are using ATI and
> intel graphics cards).  I'll try out the options you mentioned.
> 

So the ATI card is using the fglrx driver, I'm assuming (right?), and
is the intel card using the Intel graphics drivers from intel.com?
I've been told i810 that comes with XOrg is actually better (besides
having full 3d support)... but what intel chipset are you using?  Have
you tried the NON-proprietary drivers?

> Your idea about known-working (and non-working) combinations of hardware
> seems like a very good thing to do.
> 

If its a proprietary driver, my money is on a buggy driver that
doesn't cooperate with the kernel.

> >
> >
> >> Has anyone else run into cases where pymol will freeze the
> >> X-server (pymol doesn't repond to mouse or keyboard input;
> >> keyboard non-responsive to caps-lock on/off)?  The system is
> >> still stable, I'm able to login remotely and see that pymol
> >> is running at 100% CPU.  Killing pymol results in xorg
> >> running at 100% CPU (killing the xorg process as root doesn't
> >> do anything).

So xorg quits, but the monitor stays frozen?  Or the xorg process
doesn't die?  If its the latter, can you just send it a KILL (try an
INT signal first, of course)?  Anything in dmesg or the XOrg logs?
Can you grab the XOrg pid with gdb and get a stack trace?  Can you
switch over to a console (ctrl-alt-f1, typically)?

-Tim

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

        Tim Fenn
        fe...@st...
        Stanford University, School of Medicine
        James H. Clark Center
        318 Campus Drive, Room E300
        Stanford, CA  94305-5432
        Phone:  (650) 736-1714
        FAX:  (650) 736-1961

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



-------------------------------------------------------
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that extends applications into web and mobile media. Attend the live webcast
and join the prime developer group breaking into this new coding territory!
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Re: [PyMOL] sporadic pymol/X-server freezes?

[Tim F. <fe...@st...>]

On Thu, Mar 23, 2006 at 08:56:27PM -0500, Peter Adrian Meyer wrote:
> 
> I guess it shouldn't supprise me that there are issues with proprietary
> OpenGL on linux (FYI the two machines I've seen this on are using ATI and
> intel graphics cards).  I'll try out the options you mentioned.
> 

So the ATI card is using the fglrx driver, I'm assuming (right?), and
is the intel card using the Intel graphics drivers from intel.com?
I've been told i810 that comes with XOrg is actually better (besides
having full 3d support)... but what intel chipset are you using?  Have
you tried the NON-proprietary drivers?

> Your idea about known-working (and non-working) combinations of hardware
> seems like a very good thing to do.
> 

If its a proprietary driver, my money is on a buggy driver that
doesn't cooperate with the kernel.

> >
> >
> >> Has anyone else run into cases where pymol will freeze the
> >> X-server (pymol doesn't repond to mouse or keyboard input;
> >> keyboard non-responsive to caps-lock on/off)?  The system is
> >> still stable, I'm able to login remotely and see that pymol
> >> is running at 100% CPU.  Killing pymol results in xorg
> >> running at 100% CPU (killing the xorg process as root doesn't
> >> do anything).

So xorg quits, but the monitor stays frozen?  Or the xorg process
doesn't die?  If its the latter, can you just send it a KILL (try an
INT signal first, of course)?  Anything in dmesg or the XOrg logs?
Can you grab the XOrg pid with gdb and get a stack trace?  Can you
switch over to a console (ctrl-alt-f1, typically)?

-Tim

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

        Tim Fenn
        fe...@st...
        Stanford University, School of Medicine
        James H. Clark Center
        318 Campus Drive, Room E300
        Stanford, CA  94305-5432
        Phone:  (650) 736-1714
        FAX:  (650) 736-1961

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

Re: [PyMOL] sporadic pymol/X-server freezes?

[Peter A. M. <pa...@co...>]

> same here, how big are your map files in MB, how much ram and swap space
> do you have?

~5MB/map, 512MB RAM, ~2GB swap.  I'd expect a segfault (or an exception at
least) if I was overloading the memory/swap, and CPU would drop if it was
running out of physical RAM and swapping too much.

> I haven't the slightest clue. Does this happen immediately after loading
> the map or while rotating or what? But I can tell you that I'm running
> gentoo, w/vanilla sources 2.6.15 running in x86_64 mode (straight from
> kernel.org), 1.0.8178 nvidia drivers on a quadro4 980xgl video card.

No consistent pattern.  Both machines are x86, non-nvidia graphics cards
(which probably isn't helping).  But, score at least one working setup
(yours) as a fully functional combination.

> You might try as was suggested to upgrade your kernel. You can get
> 2.6.16 from kernel.org, copy your current .config into the root of the
> source directory, run make oldconfig, hit enter a bunch of times, then
> compile the kernel with make && make modules_install. You will have to
> recompile the nvidia drivers for the new kernel too.

It might come to that, but it'll be a last resort.  I'm reluctant to make
major modifications to a system that I'm using to do research in the
middle of a project (I've had 2 independent backups fail me at the same
time).  Particularly for a problem that isn't predictably reproducable, so
I wouldn't know if an upgraded kernel/module had actually fixed the
problem or not (it could be done w\ testing livecd distributions or within
a vm, or trying to get a debug build of pymol talking happily to a
debugger, but at a certain point it becomes more trouble to track down and
fix the bug than it does to deal with it).

Thanks for the suggestions,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

RE: [PyMOL] sporadic pymol/X-server freezes?

[Peter A. M. <pa...@co...>]

Warren,

Thanks for getting back to me so quickly.  It's good to hear that this
problem has been seen before (it's been one of those weeks for strange
computer issues).

I guess it shouldn't supprise me that there are issues with proprietary
OpenGL on linux (FYI the two machines I've seen this on are using ATI and
intel graphics cards).  I'll try out the options you mentioned.

Your idea about known-working (and non-working) combinations of hardware
seems like a very good thing to do.

Pete

> Pete,
>
> We have been suffering this same exact symptom with our nVidia-base
64-bit RHEL workstation for over a year.  I have spent enough time
troubleshooting the issue to have convinced myself that the problem
isn't PyMOL -- it is an inability of certain combinations of hardware,
Linux kernels, and proprietary OpenGL drivers to handle the vast
quantity of immediate mode rendering geometry that PyMOL generates.  It
seems to be either a sporadic buffer overflow or a race condition within
the kernel layer.
>
> The proprietary nature of the OpenGL drivers prevents anyone other than
the hardware vendor from being able to actually understand and solve the
problem.  Plus, the problem is sporadic -- most of the time everything
works fine, but sometimes PyMOL hangs, sometimes all of X11 freezes, and
sometimes the whole system comes crashing down.  The intractable nature
of these Linux stability problems is one of the primary reasons why I
recommend Mac OS X over Linux for unix-based PyMOL visualization.
>
> Note that the settings "nvidia_bugs" and "use_display_lists"  may reduce
the frequency of the problem on your system.  Other than that, my
suggestion would be to try different Linux kernels and OpenGL driver
versions.
>
> The combinatorial matrix of possibilities is huge, but maybe we should
create a table on the Wiki for people to post working and non-working
combinations of Linux kernels, cpu and graphics hardware, and opengl
drivers?  That's how we used to do things in the old days.  I suspect
only 5-10% of configurations are truly unworkable, and once enough data
is collected from enough people, meaningful patterns would likely
emerge.
>
> 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
>> Peter Adrian Meyer
>> Sent: Thursday, March 23, 2006 9:32 AM
>> To: pym...@li...
>> Subject: [PyMOL] sporadic pymol/X-server freezes?
>> Hi everyone,
>> Has anyone else run into cases where pymol will freeze the
>> X-server (pymol doesn't repond to mouse or keyboard input;
>> keyboard non-responsive to caps-lock on/off)?  The system is
>> still stable, I'm able to login remotely and see that pymol
>> is running at 100% CPU.  Killing pymol results in xorg
>> running at 100% CPU (killing the xorg process as root doesn't
>> do anything).
>> I've only seen this while looking at several maps/masks (but
>> that's most of what I use pymol for, so I'm not sure if
>> that's the cause).  I've seen this error on both suse 10.0
>> and kubuntu (3.10?  whatever the lastest apt-get dist upgrade
>> got me; two different machines) using source builds of
>> pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95. Any
suggestions on how to fix this (or get debugging
>> information out of pymol to narrow down the problem)?
>> Thanks,
>> Pete
>> Pete Meyer
>> Fu Lab
>> BMCB grad student
>> Cornell University
>> -------------------------------------------------------
>> This SF.Net email is sponsored by xPML, a groundbreaking
>> scripting language that extends applications into web and
>> mobile media. Attend the live webcast and join the prime
>> developer group breaking into this new coding territory!
>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&
>> dat=121642
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Re: [PyMOL] sporadic pymol/X-server freezes?

[Sabuj P. <sab...@va...>]

Hi,

>>Has anyone else run into cases where pymol will freeze the 
>>X-server (pymol doesn't repond to mouse or keyboard input; 
>>keyboard non-responsive to caps-lock on/off)? 

no.

>>I've only seen this while looking at several maps/masks (but 
>>that's most of what I use pymol for, so I'm not sure if 
>>that's the cause). 

same here, how big are your map files in MB, how much ram and swap space
do you have?

 I've seen this error on both suse 10.0
>>and kubuntu (3.10?  whatever the lastest apt-get dist upgrade 
>>got me; two different machines) using source builds of 
>>pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95.
>>
>>Any suggestions on how to fix this (or get debugging 
>>information out of pymol to narrow down the problem)?
I haven't the slightest clue. Does this happen immediately after loading
the map or while rotating or what? But I can tell you that I'm running
gentoo, w/vanilla sources 2.6.15 running in x86_64 mode (straight from
kernel.org), 1.0.8178 nvidia drivers on a quadro4 980xgl video card.

You might try as was suggested to upgrade your kernel. You can get
2.6.16 from kernel.org, copy your current .config into the root of the
source directory, run make oldconfig, hit enter a bunch of times, then
compile the kernel with make && make modules_install. You will have to
recompile the nvidia drivers for the new kernel too.

Hope that helps,
Sabuj Pattanayek

RE: [PyMOL] sporadic pymol/X-server freezes?

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

Pete,

We have been suffering this same exact symptom with our nVidia-base
64-bit RHEL workstation for over a year.  I have spent enough time
troubleshooting the issue to have convinced myself that the problem
isn't PyMOL -- it is an inability of certain combinations of hardware,
Linux kernels, and proprietary OpenGL drivers to handle the vast
quantity of immediate mode rendering geometry that PyMOL generates.  It
seems to be either a sporadic buffer overflow or a race condition within
the kernel layer. =20

The proprietary nature of the OpenGL drivers prevents anyone other than
the hardware vendor from being able to actually understand and solve the
problem.  Plus, the problem is sporadic -- most of the time everything
works fine, but sometimes PyMOL hangs, sometimes all of X11 freezes, and
sometimes the whole system comes crashing down.  The intractable nature
of these Linux stability problems is one of the primary reasons why I
recommend Mac OS X over Linux for unix-based PyMOL visualization.
 =20
Note that the settings "nvidia_bugs" and "use_display_lists"  may reduce
the frequency of the problem on your system.  Other than that, my
suggestion would be to try different Linux kernels and OpenGL driver
versions. =20

The combinatorial matrix of possibilities is huge, but maybe we should
create a table on the Wiki for people to post working and non-working
combinations of Linux kernels, cpu and graphics hardware, and opengl
drivers?  That's how we used to do things in the old days.  I suspect
only 5-10% of configurations are truly unworkable, and once enough data
is collected from enough people, meaningful patterns would likely
emerge. =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
> Peter Adrian Meyer
> Sent: Thursday, March 23, 2006 9:32 AM
> To: pym...@li...
> Subject: [PyMOL] sporadic pymol/X-server freezes?
>=20
> Hi everyone,
>=20
> Has anyone else run into cases where pymol will freeze the=20
> X-server (pymol doesn't repond to mouse or keyboard input;=20
> keyboard non-responsive to caps-lock on/off)?  The system is=20
> still stable, I'm able to login remotely and see that pymol=20
> is running at 100% CPU.  Killing pymol results in xorg=20
> running at 100% CPU (killing the xorg process as root doesn't=20
> do anything).
>=20
> I've only seen this while looking at several maps/masks (but=20
> that's most of what I use pymol for, so I'm not sure if=20
> that's the cause).  I've seen this error on both suse 10.0=20
> and kubuntu (3.10?  whatever the lastest apt-get dist upgrade=20
> got me; two different machines) using source builds of=20
> pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95.
>=20
> Any suggestions on how to fix this (or get debugging=20
> information out of pymol to narrow down the problem)?
>=20
> Thanks,
> Pete
>=20
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking=20
> scripting language that extends applications into web and=20
> mobile media. Attend the live webcast and join the prime=20
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&
> dat=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] sporadic pymol/X-server freezes?

[Peter A. M. <pa...@co...>]

Hi everyone,

Has anyone else run into cases where pymol will freeze the X-server (pymol
doesn't repond to mouse or keyboard input; keyboard non-responsive to
caps-lock on/off)?  The system is still stable, I'm able to login remotely
and see that pymol is running at 100% CPU.  Killing pymol results in xorg
running at 100% CPU (killing the xorg process as root doesn't do
anything).

I've only seen this while looking at several maps/masks (but that's most
of what I use pymol for, so I'm not sure if that's the cause).  I've seen
this error on both suse 10.0 and kubuntu (3.10?  whatever the lastest
apt-get dist upgrade got me; two different machines) using source builds
of pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95.

Any suggestions on how to fix this (or get debugging information out of
pymol to narrow down the problem)?

Thanks,
Pete


Pete Meyer
Fu Lab
BMCB grad student
Cornell University

Subject: Re: [PyMOL] Producing publication quality images

[Jason V. <jav...@ut...>]

Just a quick note: we've had a "Publication Quality Images" page on the wiki 
for a while (http://www.pymolwiki.org/index.php/Publication_Quality_Images).  
We just didn't -- and still don't -- have the documentation for the new 
internal DPI setting that Warren told us about.

Feel free to add any PyMol hints or tips to the wiki if you have one.

-- Jason

-- 
Jason Vertrees
BSCB Graduate Student @ UTMB, Galveston
jav...@ut... :: http://www.bscb.utmb.edu
PyMol Wiki        :: http://www.pymolwiki.org
Vertrees dot Org  :: http://www.vertrees.org