pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] saving multiple object in one pdb file

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

FYI: In the development code, I've added a new "segi" option to "symexp"
that will automatically assign a unique segment ID to symmetry-generated
molecules.

This will allow a use case such as follows:

% pymol

load $PYMOL_PATH/test/dat/1tii.pdb
symexp s, 1tii, 1tii, 20.0, segi=3D1
save packing.pdb, all
quit

% pymol

packing.pdb

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: Monday, November 21, 2005 11:45 AM
> To: kosa
> Cc: pym...@li...
> Subject: Re: [PyMOL] saving multiple object in one pdb file
>=20
>=20
>=20
> > My question is: how to save multiple objects from pymol as one nice=20
> > pdb file, for instance with each object with different chain name?
>=20
> alter SymgenObject,chain 'X'
>=20
> and repeat as needed for all objects (changing the chain as=20
> needed).  Then use all of your objects as the selection for=20
> save (aka save
> AllObjects.pdb,(original,sym1,sym2) )
>=20
> Pete
>=20
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
> 2005. For more info visit:
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] saving multiple object in one pdb file

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

> My question is: how to save multiple objects from pymol as one nice pdb
> file, for instance with each object with different chain name?

alter SymgenObject,chain 'X'

and repeat as needed for all objects (changing the chain as needed).  Then
use all of your objects as the selection for save (aka save
AllObjects.pdb,(original,sym1,sym2) )

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

RE: [PyMOL] Slowwwww ray

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

Michele,=20

Did you just migrate from an older version?  We switched PyMOL over to
perspective-based rendering (WYSIWYG with OpenGL) as the default at some
point in the past year.  You can still render orthoscopically if you'd
prefer:

load 1alk.pdb
show surface
set orthoscopic
set hash_max=3D160
ray

=3D>2.58 seconds on 2 X 2 Ghz opteron

load 1alk.pdb
show surface
set hash_max=3D160
ray

=3D>10.7 seconds on 2 x 2 Ghz opteron

In other words, raytracing taking into account the perspective
transformation can require almost 5X more time than orthoscopic
rendering.

FYI: on a quad-core G5 Quad 2.5 Ghz, the times are 1.78 seconds and 4.82
seconds respectively.  Those Mac G5 Quads are PyMOL raytracing monsters!

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
> Stuart Endo-Streeter
> Sent: Monday, November 21, 2005 11:13 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Slowwwww ray
>=20
> Default view, white with black background (sticks):
> Ray: total time: 15.68 sec. =3D 229.5 frames/hour. (15.68 sec. accum.)
>=20
> Surface ray (white w/ black background):
> Ray: total time: 32.67 sec. =3D 110.2 frames/hour. (48.35 sec. accum.)
>=20
> About the times I've been seeing for equivalent work I've=20
> been doing. =20
> Different system but your times don't sound too different=20
> from what I've seen on our dual-G5 2.0 GHz with an older=20
> Radeon card.  I'm running an Opteron 150
> (2.4GHz) with 1GB DDR400 ECC registered and an MSI FX5700 LE on FC4.
>=20
> On Monday 21 November 2005 13:51, Michele Fuortes wrote:
> > Hi,
> >
> > I have a 2GHz G5, 6GB RAM, running OS X 10.4.3 server.
> > I started doing some modeling after about 6 months hiatus.
> > I'm using MacPymol 0.99b29 (no flickering with this).
> > But....
> > it's slower than molasses. I get:
> >
> >   Ray: total time: 16.16 sec. =3D 222.8 frames/hour (32.15=20
> sec. accum.).
> >
> > This is simple white surface on white black background, nothing=20
> > changed from default.
> > It a fairly small molecule, 600 resi, 5400 atoms.
> >
> > My card is the stock ATI Radeon 9800 Pro.
> > Could it be I messed up something with OpenGL?
> >
> > Why is it so slooowwwww
> >
> > Thanks
> >
> > Michele
> >
> > PS: would anybody with a similar setup try 1ALK.pdb show surface in=20
> > white and tell my the time to ray?
> > Mine is:
> >
> > Ray: total time: 25.45 sec. =3D 141.4 frames/hour (57.60 sec. =
accum.).
> >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today=20
> > Register for a JBoss Training Course.  Free Certification=20
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> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
> --=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
>=20
> ____________________________________
> Stuart Endo-Streeter
> Structural Biology and Biophysics
> Dept. Biochemistry
> LSRC C266
> Duke University
> 919-681-1668
> stu...@du...
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
> 2005. For more info visit:
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> _______________________________________________
> PyMOL-users mailing list
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> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

Re: [PyMOL] Slowwwww ray

[Stuart Endo-S. <stu...@du...>]

Default view, white with black background (sticks):
Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.)

Surface ray (white w/ black background):
Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.)

About the times I've been seeing for equivalent work I've been doing.  
Different system but your times don't sound too different from what I've seen 
on our dual-G5 2.0 GHz with an older Radeon card.  I'm running an Opteron 150 
(2.4GHz) with 1GB DDR400 ECC registered and an MSI FX5700 LE on FC4.

On Monday 21 November 2005 13:51, Michele Fuortes wrote:
> Hi,
>
> I have a 2GHz G5, 6GB RAM, running OS X 10.4.3 server.
> I started doing some modeling after about 6 months hiatus.
> I'm using MacPymol 0.99b29 (no flickering with this).
> But....
> it's slower than molasses. I get:
>
>   Ray: total time: 16.16 sec. = 222.8 frames/hour (32.15 sec. accum.).
>
> This is simple white surface on white black background, nothing
> changed from default.
> It a fairly small molecule, 600 resi, 5400 atoms.
>
> My card is the stock ATI Radeon 9800 Pro.
> Could it be I messed up something with OpenGL?
>
> Why is it so slooowwwww
>
> Thanks
>
> Michele
>
> PS: would anybody with a similar setup try 1ALK.pdb show surface in
> white and tell my the time to ray?
> Mine is:
>
> Ray: total time: 25.45 sec. = 141.4 frames/hour (57.60 sec. accum.).
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
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> PyM...@li...
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-- 








____________________________________
Stuart Endo-Streeter
Structural Biology and Biophysics
Dept. Biochemistry
LSRC C266
Duke University
919-681-1668
stu...@du...

[PyMOL] Slowwwww ray

[Michele F. <mfu...@me...>]

Hi,

I have a 2GHz G5, 6GB RAM, running OS X 10.4.3 server.
I started doing some modeling after about 6 months hiatus.
I'm using MacPymol 0.99b29 (no flickering with this).
But....
it's slower than molasses. I get:

  Ray: total time: 16.16 sec. = 222.8 frames/hour (32.15 sec. accum.).

This is simple white surface on white black background, nothing  
changed from default.
It a fairly small molecule, 600 resi, 5400 atoms.

My card is the stock ATI Radeon 9800 Pro.
Could it be I messed up something with OpenGL?

Why is it so slooowwwww

Thanks

Michele

PS: would anybody with a similar setup try 1ALK.pdb show surface in  
white and tell my the time to ray?
Mine is:

Ray: total time: 25.45 sec. = 141.4 frames/hour (57.60 sec. accum.).

Re: [PyMOL] problem with amber trajectory

[Dmitry K. <dk...@bi...>]

Sorry Viktor and Warren, but I don't think your suggestions are  
applicable. I have only a single protein molecule in my trajectory,  
which I kept centered at the origin, so it never traverses the  
periodic boundary. I did strip all but 20 waters from it using ptraj  
and created the appropriate topology file for it. That topology and  
trajectory, as I mentioned, work just fine in VMD. And the problem  
begins with the first frame, so its doesn't seem like bounding box  
info is messing it up.

What I thought might be the case is that the format of that ptraj- 
generated topology might be a little different that what PyMOL  
expected, so I decided to try loading the original (fully-solvated)  
topology with the original (fully-solvated) trajectory into PyMOL.  
Well, all it did was tie up my computer for ~15 minutes and then  
crash PyMOL. The trajectory file is pretty large half a Gig) but it  
opens fine in VMD, and doesn't tie up my machine.

I'm sorry to keep harping on the VMD thing - I'd much rather render  
the trajectory in PyMOL because of its obvious graphical superiority,  
but at present I can't do it. Any ideas?
Thanks,
Dmitry



On Nov 20, 2005, at 9:34 PM, Viktor Hornak wrote:

> Dmitry,
>
> is your system a single molecule or is it composed of multiple  
> molecules (e.g. dimer)? Amber should not 'cut' your molecule into  
> pieces, imaging can only separate molecules in a dimer, trimer or  
> such.  Also, was your system solvated? Did you strip water before  
> visualizing in PyMOL? There may be an issue with your trajectory  
> containing box information which might break a correspondence of  
> trajectory coordinates and topology. To test this, see if the first  
> frame of your trajectory looks ok but all others don't. ptraj is a  
> good program to do various manipulations with your trajectory as  
> Warren suggested.
>
> Cheers,
> -Viktor
>
>
> Dmitry Kondrashov wrote:
>
>> Hi,
>>
>> I have a prloblem with viewing AMBER trajectory files,  
>> specifically,  the topology appears messed up. When I load the  
>> trajectory into the  topology object, the structure shows up  
>> dismembered into eight pieces  on the vertices of a cude. I should  
>> note that I can load an AMBER  coordinate file into the same  
>> topology with no problem, and that the  trajectory displays just  
>> fine in VMD.
>> I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in   
>> loading the trajectory, here's the last few lines:
>>
>>  ObjectMolecule: read set 757 into state 757...
>>  ObjectMolecule: read set 758 into state 758...
>>  CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
>>  CmdLoadTraj: 758 total states in the object.
>>
>> I appreciate your help,
>> Dmitry
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
>> Register for a JBoss Training Course.  Free Certification Exam
>> for All Training Attendees Through End of 2005. For more info visit:
>> http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

Re: [PyMOL] apbs problem

[J. E. S. <es...@im...>]

I have the same problem on a mac G5 dual processor with newly compiled pymol
0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.

Interestingly, the programs work fine together on my mac G4 laptop, with
single processor apbs 3.2 but an older version of the mac/x11 hybrid pymol,
using the same pdb files.


Evan Sadler

-- 
J. Evan Sadler, M.D., Ph.D.
Howard Hughes Medical Institute
Washington University
660 S. Euclid Ave., Box 8022
St. Louis, MO   63110
Tel: 314-362-9067
FAX: 314-454-3012
email: es...@im...




On 11/21/05 10:36 AM, "Ashwini Mishra" <ash...@um...> wrote:

> Hi everyone,
> I am trying to  run apbs  from pymol (0.98) on window and always end up
> getting following error message.
> objectMap load DX file-error: unable to open file!
> Even after using improved  plugin apbs tools.py , same error message.I
> also tried using externally generated .PQR file as an input from PDB
> file. Same problem. Any suggestion would be appreciated.
> Thanks
> Ashwini
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] apbs problem

[Ashwini M. <ash...@um...>]

Hi everyone,
I am trying to  run apbs  from pymol (0.98) on window and always end up 
getting following error message.
objectMap load DX file-error: unable to open file!
Even after using improved  plugin apbs tools.py , same error message.I 
also tried using externally generated .PQR file as an input from PDB  
file. Same problem. Any suggestion would be appreciated.
Thanks
Ashwini

Re: [PyMOL] APBS

[Martin M. <mg...@mr...>]

Hi Brian,

Try this, the info is from the mailing list archive (http:// 
sourceforge.net/mailarchive/forum.php?forum_id=60)it just takes a bit  
of finding....


load x.pdb

load whatever.dx, e_pot

ramp_new e_lvl, e_pot, [-15, 0, 15], [ [1,0,0], [1,1,1] , [0,0,1] ] #  
this sets the scale and colours for the e_potential scale.

show surface, x.pdb

set surface_color, e_lvl, x.pdb



# load whatever.dx, e_pot - this loads the .dx map and calls it e_pot  
(this might not load via command line. If not, use the open command  
from the file menu then rename as desired)
# ramp_new e_lvl sets the scale and colors
# [-15, 0, 15] sets the potential scale
# [1,0,0] is red, [1,1,1] is white, [0,0,1] is blue so -15 is red, 0  
is white and +15 is blue




hope it helps


MGM



On 19 Nov 2005, at 19:53, Brian J Goodfellow wrote:

> Dear Users,
>
> I was wondering does anyone know how to get nice APBS generated  
> electrostatic surfaces in MacPyMOL. I know the APBS plugin can't/ 
> won't work in MacPyMOL so I guess it's a question of what do I do  
> with the output from APBS (I assume it's the dx file) to get a  
> surface in MacPyMOL.
>
> Till now I've been generating the surfaces in PyMOLX11Hybrid with  
> the plugin and saving a pse file and then reading it into MacPyMOL,  
> which is not the end of the world I guess, but it's just a bit of a  
> pain......
>
> Cheers,
>
> Brian
>



Martin Montgomery
Director's Group
MRC Dunn Human Nutrition Unit
Hills Road
Cambridge
CB2 2XY

[PyMOL] RE: NOTICE: mail delivery status

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

Now this has got to be the funniest bounce I've received to date as
administrator of the PyMOL users list:

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> pos...@na...
> Sent: Sunday, November 20, 2005 7:40 PM
> To: pym...@li...
> Subject: NOTICE: mail delivery status
>=20
> Mail Delivery Failure
>=20
> A message sent to <name-deleted-to-protect-the-innocent> was not=20
> delivered for the following reason:
>=20
> Language in the message triggered the following rule(s):
> Violence (English)

What?  Violence on the PyMOL Mailing List?  Hmm, let's see...

What about cutting? =20

> multiple molecules (e.g. dimer)? Amber should not 'cut' your=20
> molecule into pieces, imaging can only separate molecules in=20

Check.  Stripping? =20

> a dimer, trimer or such.  Also, was your system solvated? Did=20
> you strip water before visualizing in PyMOL? There may be an=20

Gotcha.  Breaking? =20

> There may be an=20
> issue with your trajectory containing box information which=20
> might break a correspondence of trajectory coordinates and=20
> topology.=20

No doubt.  Messing things up?

> > I have a problem with viewing AMBER trajectory files,=20
> specifically, =20
> > the topology appears messed up.

Right on.  Dismembering?

> > When I load the trajectory into the =20
> > topology object, the structure shows up dismembered into=20
> eight pieces =20
> > on the vertices of a cube.=20
 =20
Excellent. =20

Congratulations Victor and Dmitry, you have won the Abdul Alhazred award
for 2005. Who needs a Necronomicon, when you've got the PyMOL mailing
list?  Lovecraft would be proud. =20

PyMOL-users email censored due to violence!  What a laugh.

Cheers,
Warren

> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Viktor Hornak
> Sent: Sunday, November 20, 2005 7:40 PM
> To: pym...@li...
> Subject: Re: [PyMOL] problem with amber trajectory]
>=20
> Dmitry,
>=20
> is your system a single molecule or is it composed of=20
> multiple molecules (e.g. dimer)? Amber should not 'cut' your=20
> molecule into pieces, imaging can only separate molecules in=20
> a dimer, trimer or such.  Also, was your system solvated? Did=20
> you strip water before visualizing in PyMOL? There may be an=20
> issue with your trajectory containing box information which=20
> might break a correspondence of trajectory coordinates and=20
> topology. To test this, see if the first frame of your=20
> trajectory looks ok but all others don't. ptraj is a good=20
> program to do various manipulations with your trajectory as=20
> Warren suggested.
>=20
> Cheers,
> -Viktor
>=20
>=20
> Dmitry Kondrashov wrote:
>=20
> > Hi,
> >
> > I have a prloblem with viewing AMBER trajectory files,=20
> specifically, =20
> > the topology appears messed up. When I load the trajectory=20
> into the =20
> > topology object, the structure shows up dismembered into=20
> eight pieces =20
> > on the vertices of a cude. I should note that I can load an AMBER =20
> > coordinate file into the same topology with no problem, and=20
> that the =20
> > trajectory displays just fine in VMD.
> > I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in =20
> > loading the trajectory, here's the last few lines:
> >
> >  ObjectMolecule: read set 757 into state 757...
> >  ObjectMolecule: read set 758 into state 758...
> >  CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
> >  CmdLoadTraj: 758 total states in the object.
> >
> > I appreciate your help,
> > Dmitry

Re: [PyMOL] problem with amber trajectory]

[Viktor H. <ho...@cs...>]

Dmitry,

is your system a single molecule or is it composed of multiple molecules 
(e.g. dimer)? Amber should not 'cut' your molecule into pieces, imaging 
can only separate molecules in a dimer, trimer or such.  Also, was your 
system solvated? Did you strip water before visualizing in PyMOL? There 
may be an issue with your trajectory containing box information which 
might break a correspondence of trajectory coordinates and topology. To 
test this, see if the first frame of your trajectory looks ok but all 
others don't. ptraj is a good program to do various manipulations with 
your trajectory as Warren suggested.

Cheers,
-Viktor


Dmitry Kondrashov wrote:

> Hi,
>
> I have a prloblem with viewing AMBER trajectory files, specifically,  
> the topology appears messed up. When I load the trajectory into the  
> topology object, the structure shows up dismembered into eight pieces  
> on the vertices of a cude. I should note that I can load an AMBER  
> coordinate file into the same topology with no problem, and that the  
> trajectory displays just fine in VMD.
> I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in  
> loading the trajectory, here's the last few lines:
>
>  ObjectMolecule: read set 757 into state 757...
>  ObjectMolecule: read set 758 into state 758...
>  CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
>  CmdLoadTraj: 758 total states in the object.
>
> I appreciate your help,
> Dmitry
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] saving multiple object in one pdb file

[kosa <ko...@ge...>]

Dear users,

I had generated many symmetry mates of my structure using pymol symexp 
command. I got many objects generated. Each contains one symmetry 
related molecule. Now I want to save all objects in one pdb file. I do 
"Select all", create new object from this selection and save the object 
as pdb file. Unfortunately since the original structure was a chain A 
all symmmetry mates also are chain A. It causes problems for several 
other programs which have troubles when pdb file which has mulitple 
residues with the same name, number and chain name.

My question is: how to save multiple objects from pymol as one nice pdb 
file, for instance with each object with different chain name?

Cheers,
Jan Kosinski

[PyMOL] APBS

[Brian J G. <bri...@dq...>]

Dear Users,

I was wondering does anyone know how to get nice APBS generated =20
electrostatic surfaces in MacPyMOL. I know the APBS plugin can't/=20
won't work in MacPyMOL so I guess it's a question of what do I do =20
with the output from APBS (I assume it's the dx file) to get a =20
surface in MacPyMOL.

Till now I've been generating the surfaces in PyMOLX11Hybrid with the =20=

plugin and saving a pse file and then reading it into MacPyMOL, which =20=

is not the end of the world I guess, but it's just a bit of a pain......

Cheers,

Brian


*******************************************
Brian J Goodfellow
Departamento de Qu=CCmica
Universidade de Aveiro
3810-193 Aveiro, Portugal
Tel: +351 234 401506, Fax: +351 234 370084
http://www.dq.ua.pt/ingles/index_mem.htm
*******************************************

RE: Question about commandline -d option (was RE: [PyMOL] displaying protein with propeptide)

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

> This is awesome.  It looks like this has been a valid setting=20
> for a *long* time, but I've never seen it.  I look at a lot=20
> of MCSS-type structures, and I have some really painful=20
> scripts that get the bonds right once the structure is loaded=20
> in PyMOL.  Now, I can just stamp the CONECT records at the=20
> end of the file and load things up in connect_mode=3D1 world=20
> and everything works.  Speaking of which, I made a little=20
> bash shell script to launch PyMOL this way:
>=20
> pymol -d "cmd.set('connect_mode',1)" $@
>=20
> It took me a couple of tries to get that right.  The=20
> documentation for command-line options says
>=20
>    -d <string> Run pymol command string upon startup.
>=20
> so I first tried
>=20
> pymol -d "set connect_mode,1" $@
>=20
> but that doesn't work.  Is this a documentation typo?  I=20
> thought a PyMOL command string was anything you could type at=20
> the PyMOL command prompt.

Michael,

The issue here is that spaces in the command used to cause trouble in
the launch process.  This has now been fixed in the current
pymol.com.template, but for now substitute a percent sign for spaces in
-d command arguments:

pymol -d "set%connect_mode,1" $@

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

RE: [PyMOL] problem with amber trajectory

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

Dmitry,

VMD may have the ability to shift and recombine the molecule relative to
the periodic boundary in order to avoid this dismembered effect, whereas
currently PyMOL does not.  I believe ptraj can do this for you, though
it has been ages since I have tried using PyMOL with Amber.

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
> Dmitry Kondrashov
> Sent: Saturday, November 19, 2005 9:57 AM
> To: pym...@li...
> Subject: [PyMOL] problem with amber trajectory
>=20
> Hi,
>=20
> I have a prloblem with viewing AMBER trajectory files,=20
> specifically, the topology appears messed up. When I load the=20
> trajectory into the topology object, the structure shows up=20
> dismembered into eight pieces on the vertices of a cude. I=20
> should note that I can load an AMBER coordinate file into the=20
> same topology with no problem, and that the trajectory=20
> displays just fine in VMD.
> I'm using MacPyMol on Mac OS 10.4.3. No error messages appear=20
> in loading the trajectory, here's the last few lines:
>=20
>   ObjectMolecule: read set 757 into state 757...
>   ObjectMolecule: read set 758 into state 758...
>   CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
>   CmdLoadTraj: 758 total states in the object.
>=20
> I appreciate your help,
> Dmitry
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
> 2005. For more info visit:
> http://ads.osdn.com/?ad_id=3D7628&alloc_id=3D16845&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] problem with amber trajectory

[Dmitry K. <dk...@bi...>]

Hi,

I have a prloblem with viewing AMBER trajectory files, specifically,  
the topology appears messed up. When I load the trajectory into the  
topology object, the structure shows up dismembered into eight pieces  
on the vertices of a cude. I should note that I can load an AMBER  
coordinate file into the same topology with no problem, and that the  
trajectory displays just fine in VMD.
I'm using MacPyMol on Mac OS 10.4.3. No error messages appear in  
loading the trajectory, here's the last few lines:

  ObjectMolecule: read set 757 into state 757...
  ObjectMolecule: read set 758 into state 758...
  CmdLoadTraj: "myo_2_20w.trj" appended into object "myo_20w".
  CmdLoadTraj: 758 total states in the object.

I appreciate your help,
Dmitry

[PyMOL] Workaround for Crash on MacPyMOL Startup

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

MacPyMOL Users,

We have figured out why MacPyMOL was crashing for a select subset of =
users on start-up.  It only happens if you extract our ".tar.gz" archive =
using StuffIt Extractor instead of Mac OS X's built-in extraction.  The =
ultimate cause is rather esoteric: I had inadvertently enabled the Hide =
File Extension attribute on the splash screen PNG file, and StuffIt =
Expandor seems to have a serious bug extracting such files.

MacPyMOL should just work if you use Safari's default ".tar.gz" handling =
when downloading from http://delsci.com/beta.  With Firefox, you need to =
make sure that StuffIt Expander is not used for ".tar.gz" files.

If all else fails, simply pop up a terminal and resort to:

tar -zxvf macpymol-0_99beta29.tar.gz

Cheers,
Warren

PS. Special thanks to Prof. James Berger at UC Berkeley for lending us =
use of his laptop for a few hours to help us to figure this all out. =20

Question about commandline -d option (was RE: [PyMOL] displaying protein with propeptide)

[Michael G. L. <ml...@um...>]

This is awesome.  It looks like this has been a valid setting for a *long*=
=20
time, but I've never seen it.  I look at a lot of MCSS-type structures,=20
and I have some really painful scripts that get the bonds right once the=20
structure is loaded in PyMOL.  Now, I can just stamp the CONECT records at=
=20
the end of the file and load things up in connect_mode=3D1 world and=20
everything works.  Speaking of which, I made a little bash shell script to=
=20
launch PyMOL this way:

pymol -d "cmd.set('connect_mode',1)" $@

It took me a couple of tries to get that right.  The documentation for=20
command-line options says

   -d <string> Run pymol command string upon startup.

so I first tried

pymol -d "set connect_mode,1" $@

but that doesn't work.  Is this a documentation typo?  I thought a PyMOL=20
command string was anything you could type at the PyMOL command prompt.

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

On Thu, 17 Nov 2005, Warren DeLano wrote:

> I'm not sure how version-dependent this is, but setting connect_mode to 1=
 before loading the PDB should disable distance-based connectivity determin=
ation.
>
> set connect_mode, 1
>
> load CONECT_only_pdb.pdb
>
> --
> 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
>> Eric Zollars
>> Sent: Thursday, November 17, 2005 5:36 PM
>> To: pym...@li...
>> Subject: Re: [PyMOL] displaying protein with propeptide
>>
>> Is there a similar command to force PyMOL to use only CONECT
>> lines in the pdb file instead of generating connectivity by distance?
>>
>> Eric
>>
>> Warren DeLano wrote:
>>> A quick fix is to use the "retain_order" setting.
>>>
>>> set retain_order
>>>
>>> which will force PyMOL to honor the order of ATOMs in the
>> PDB file over the numeric ordering of residue identifiers.
>>>
>>> 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 Joel
>>>> Tyndall
>>>> Sent: Thursday, November 17, 2005 12:15 PM
>>>> To: Anne M=F8lgaard; pym...@li...
>>>> Subject: Re: [PyMOL] displaying protein with propeptide
>>>>
>>>> Hi Ann,
>>>>
>>>> I would change the chain id of the propeptide in a text
>> editor, to say
>>>> P and remove the P from after the residue numbers.
>>>>
>>>> J
>>>>
>>>> Anne M=F8lgaard wrote:
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> I am having problems displaying proteins with unusual residue
>>>>> numbering, such as proteins with propeptides. An example is
>>>>
>>>> 1cs8, which
>>>>
>>>>> starts off like
>>>>> this:
>>>>>
>>>>> ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
>>>>> N
>>>>> ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
>>>>> C
>>>>> ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
>>>>> C
>>>>> ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
>>>>> O
>>>>> ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
>>>>> C
>>>>> ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
>>>>> O
>>>>> .
>>>>> .
>>>>> .
>>>>> And later on comes the sequence corresponding to the
>> mature protein:
>>>>>
>>>>> ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
>>>>> N
>>>>> ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
>>>>> C
>>>>> ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
>>>>> C
>>>>> ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
>>>>> O
>>>>> ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
>>>>> C
>>>>> Etc.
>>>>>
>>>>> If I open 1cs8 with PyMol, I can see everything in the "lines",
>>>>> "sticks" and "surface" representation, but in ribbon or
>> cartoon mode
>>>>> only part of the protein is shown. What do I have to do to
>>>>
>>>> show the whole sequence?
>>>>
>>>>> How do I select residues with a "P" appended to the residue
>>>>
>>>> number? If
>>>>
>>>>> I say "select resi 1P-5P" I get both 1P-5P and 1-5.
>>>>>
>>>>> Any help will be appreciated! (I am using PyMol version 0.98
>>>>
>>>> for Windows).
>>>>
>>>>> - Anne
>>>>>
>>>>> --------------------------------------------
>>>>> Anne M=F8lgaard, Ph.D.
>>>>> Center for Biological Sequence Analysis BioCentrum-DTU,
>> Building 208
>>>>> DK-2800 Lyngby
>>>>>
>>>>> Email:  an...@cb...
>>>>> Phone:  (+45)4525 2472
>>>>> --------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by the JBoss Inc.  Get
>> Certified Today
>>>>> Register for a JBoss Training Course.  Free Certification Exam for
>>>>> All Training Attendees Through End of 2005. For more info visit:
>>>>> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
>>>>> _______________________________________________
>>>>> PyMOL-users mailing list
>>>>> PyM...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> Joel Tyndall, PhD
>>>>
>>>> Lecturer
>>>> National School of Pharmacy
>>>> University of Otago
>>>> PO Box 913 Dunedin
>>>> New Zealand
>>>>
>>>> Pukenga
>>>> Te Kura Taiwhanga Putaiao
>>>> Te Whare Wananga o Otago
>>>> Pouaka Poutapeta 913 Otepoti
>>>> Aotearoa
>>>>
>>>> Ph / Waea               +64 3 4797293
>>>> Fax / Waeawhakaahua     +64 3 4797034
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by the JBoss Inc.  Get
>> Certified Today
>>>> Register for a JBoss Training Course.  Free Certification
>> Exam for All
>>>> Training Attendees Through End of 2005. For more info visit:
>>>> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> PyM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by the JBoss Inc.  Get
>> Certified Today
>>> Register for a JBoss Training Course.  Free Certification
>> Exam for All
>>> Training Attendees Through End of 2005. For more info visit:
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>>> _______________________________________________
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>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by the JBoss Inc.  Get
>> Certified Today Register for a JBoss Training Course.  Free
>> Certification Exam for All Training Attendees Through End of
>> 2005. For more info visit:
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>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
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> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>

RE: [PyMOL] displaying protein with propeptide

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

Anne,

> "select resi  1P-5P" still gives me both 1-5 and 1P-5P.
> However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20

Say you have residues 36, 37A, 37B, and 38, and you tell PyMOL you wish =
to select residues in the range 36-38.  Naturally, you'd want 37A and =
37B included in that.  It is this behavior that gives rise to the =
selection behavior you've noted above, wherein residue insertion codes =
are effectively ignored inside numerical ranges. =20

In PyMOL, ranges are defined numerically for reasons of performance.  =
Defining them based on peptide connectivity would be orders of magnitude =
slower.  Defining them based on their input file order could give okay =
performance, but the concept of input order is not always valid given =
that molecules are graphs not lists.

I agree though, that it would be nice to equip PyMOL with these =
alternate ranging concepts -- ideas for the future.

Fortunately, there is another workaround:  segment identifiers.  With =
wildcard selection in PyMOL beta builds, you can do something like this:

alter resi *B, segi=3D'SEG1'
alter not resi *B, segi=3D'SEG2'

Now you could use ranges without trouble, leaving your chain IDs =
unperturbed.

select segi SEG1 and resi 1-5

or more concisely:

select SEG1//1-5/

as distinct from

select SEG2//1-5/

> but many PDB files have insertions which are numbered with "A"s and =
"B"s after the residue number,

As for insertion codes that appear at the proper location in sequence =
(NOT the case with pathological PDB 1cs8), recent PyMOL betas handle =
such situations automatically and will draw connected cartoons.=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
> Anne M=F8lgaard
> Sent: Friday, November 18, 2005 12:47 AM
> To: pym...@li...
> Subject: RE: [PyMOL] displaying protein with propeptide
>=20
> Thanks for the comments. The "retain_order" setting solves=20
> the problem with cartoons and ribbons, but there is still a=20
> small problem with selection of these residues. "select resi=20
> 1P-5P" still gives me both 1-5 and 1P-5P.
> However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20
>=20
> I don't really want to change the chain ID in the PDB file.=20
> It makes sort of sense in the case of a propeptide (although=20
> it is covalently linked to the mature protein, so it is=20
> really only one chain), but many PDB files have insertions=20
> which are numbered with "A"s and "B"s after the residue=20
> number, and in those cases it really doesn't make sense to=20
> change the chain ID. For an example, see 1cgh below.=20
>=20
> Thanks for your help!
>=20
> - Anne
>=20
> ATOM    213  OE1 GLN A  36       8.532  36.321  21.186  0.00 25.64
> O =20
> ATOM    214  NE2 GLN A  36       7.727  36.504  19.104  0.00 25.95
> N =20
> ATOM    215  H   GLN A  36       8.523  31.138  18.943  0.00 20.00
> H =20
> ATOM    216 1HE2 GLN A  36       7.711  37.475  19.199  0.00 20.00
> H =20
> ATOM    217 2HE2 GLN A  36       7.446  36.036  18.288  0.00 20.00
> H =20
> ATOM    218  N   SER A  36A      4.622  31.686  20.477  0.00 27.20
> N =20
> ATOM    219  CA  SER A  36A      3.235  31.238  20.479  0.00 28.70
> C =20
> ATOM    220  C   SER A  36A      2.315  32.417  20.162  0.00 29.65
> C =20
> ATOM    221  O   SER A  36A      2.664  33.569  20.429  0.00 30.07
> O =20
> ATOM    222  CB  SER A  36A      2.878  30.647  21.845  0.00 28.71
> C =20
> ATOM    223  OG  SER A  36A      3.565  29.428  22.077  0.00 29.15
> O =20
> ATOM    224  H   SER A  36A      5.000  32.029  21.306  0.00 20.00
> H =20
> ATOM    225  HG  SER A  36A      4.526  29.487  22.051  0.00 20.00
> H =20
> ATOM    226  N   PRO A  36B      1.124  32.146  19.598  0.00 30.41
> N =20
> ATOM    227  CA  PRO A  36B      0.593  30.825  19.240  0.00 31.02
> C =20
> ATOM    228  C   PRO A  36B      1.323  30.182  18.061  0.00 31.62
> C =20
> ATOM    229  O   PRO A  36B      2.169  30.814  17.426  0.00 31.58
> O =20
> ATOM    230  CB  PRO A  36B     -0.867  31.125  18.914  0.00 30.83
> C =20
> ATOM    231  CG  PRO A  36B     -0.789  32.492  18.316  0.00 30.95
> C =20
> ATOM    232  CD  PRO A  36B      0.147  33.200  19.269  0.00 30.41
> C =20
> ATOM    233  N   ALA A  37       0.991  28.925  17.777  0.00 32.51
> N =20
> ATOM    234  CA  ALA A  37       1.608  28.191  16.677  0.00 33.56
> C =20
>=20
> --------------------------------------------
> Anne M=F8lgaard, Ph.D.
> Center for Biological Sequence Analysis
> BioCentrum-DTU, Building 208
> DK-2800 Lyngby
>=20
> Email:  an...@cb...
> Phone:  (+45)4525 2472
> --------------------------------------------=20
>=20
> -----Original Message-----
> From: Warren DeLano [mailto:wa...@de...]
> Sent: 18. november 2005 02:28
> To: Joel Tyndall; Anne M=F8lgaard; pym...@li...
> Subject: RE: [PyMOL] displaying protein with propeptide
>=20
> A quick fix is to use the "retain_order" setting.
>=20
> set retain_order
>=20
> which will force PyMOL to honor the order of ATOMs in the PDB=20
> file over the numeric ordering of residue identifiers.
>=20
> Cheers,
> Warren
>=20
> --
> Warren L. DeLano, Ph.D.                    =20
> Principal Scientist
>=20
> . 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
>=20
> > -----Original Message-----
> > From: pym...@li...
> > [mailto:pym...@li...] On Behalf Of Joel=20
> > Tyndall
> > Sent: Thursday, November 17, 2005 12:15 PM
> > To: Anne M=F8lgaard; pym...@li...
> > Subject: Re: [PyMOL] displaying protein with propeptide
> >=20
> > Hi Ann,
> >=20
> > I would change the chain id of the propeptide in a text=20
> editor, to say=20
> > P and remove the P from after the residue numbers.
> >=20
> > J
> >=20
> > Anne M=F8lgaard wrote:
> >=20
> > >Hi,
> > >
> > >I am having problems displaying proteins with unusual residue=20
> > >numbering, such as proteins with propeptides. An example is
> > 1cs8, which
> > >starts off like
> > >this:
> > >
> > >ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
> > >N =20
> > >ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
> > >C =20
> > >ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
> > >C =20
> > >ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
> > >O =20
> > >ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
> > >C =20
> > >ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
> > >O
> > >.
> > >.
> > >.
> > >And later on comes the sequence corresponding to the=20
> mature protein:
> > >
> > >ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
> > >N =20
> > >ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
> > >C =20
> > >ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
> > >C =20
> > >ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
> > >O =20
> > >ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
> > >C
> > >Etc.=20
> > >
> > >If I open 1cs8 with PyMol, I can see everything in the "lines",=20
> > >"sticks" and "surface" representation, but in ribbon or=20
> cartoon mode=20
> > >only part of the protein is shown. What do I have to do to
> > show the whole sequence?
> > >
> > >How do I select residues with a "P" appended to the residue
> > number? If
> > >I say "select resi 1P-5P" I get both 1P-5P and 1-5.
> > >
> > >Any help will be appreciated! (I am using PyMol version 0.98
> > for Windows).
> > >
> > >- Anne
> > >
> > >--------------------------------------------
> > >Anne M=F8lgaard, Ph.D.
> > >Center for Biological Sequence Analysis BioCentrum-DTU,=20
> Building 208=20
> > >DK-2800 Lyngby
> > >
> > >Email:  an...@cb...
> > >Phone:  (+45)4525 2472
> > >--------------------------------------------
> > >
> > >
> > >
> > >
> > >-------------------------------------------------------
> > >This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today=20
> > >Register for a JBoss Training Course.  Free Certification Exam for=20
> > >All Training Attendees Through End of 2005. For more info visit:
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> > >
> > > =20
> > >
> >=20
> > --
> > Joel Tyndall, PhD
> >=20
> > Lecturer
> > National School of Pharmacy
> > University of Otago
> > PO Box 913 Dunedin
> > New Zealand                    =20
> >=20
> > Pukenga
> > Te Kura Taiwhanga Putaiao
> > Te Whare Wananga o Otago
> > Pouaka Poutapeta 913 Otepoti
> > Aotearoa
> >=20
> > Ph / Waea               +64 3 4797293=20
> > Fax / Waeawhakaahua     +64 3 4797034
> >=20
> >=20
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today=20
> > Register for a JBoss Training Course.  Free Certification=20
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> >=20
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>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
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>=20
>=20
>=20
>=20

Re: [PyMOL] combine align and rms_cur to calculate rms for complexes

[andrea s. <and...@gm...>]

Hi Warren,
yes this is the case. My complexes are from a docking calculations with 
the same ligand.
I was just quite doubtful about the procedure... to use align and then 
rms_cur.
I compared the rms results with another software (vmd) and it seems to 
be consistents.

Thanks,
Regards,

andrea

RE: [PyMOL] displaying protein with propeptide

[<an...@cb...>]

Thanks for the comments. The "retain_order" setting solves the problem =
with
cartoons and ribbons, but there is still a small problem with selection =
of
these residues. "select resi 1P-5P" still gives me both 1-5 and 1P-5P.
However, "select resi 1P+2P+3P+4P+5P" gives me what I want. =20

I don't really want to change the chain ID in the PDB file. It makes =
sort of
sense in the case of a propeptide (although it is covalently linked to =
the
mature protein, so it is really only one chain), but many PDB files have
insertions which are numbered with "A"s and "B"s after the residue =
number,
and in those cases it really doesn't make sense to change the chain ID. =
For
an example, see 1cgh below.=20

Thanks for your help!

- Anne

ATOM    213  OE1 GLN A  36       8.532  36.321  21.186  0.00 25.64
O =20
ATOM    214  NE2 GLN A  36       7.727  36.504  19.104  0.00 25.95
N =20
ATOM    215  H   GLN A  36       8.523  31.138  18.943  0.00 20.00
H =20
ATOM    216 1HE2 GLN A  36       7.711  37.475  19.199  0.00 20.00
H =20
ATOM    217 2HE2 GLN A  36       7.446  36.036  18.288  0.00 20.00
H =20
ATOM    218  N   SER A  36A      4.622  31.686  20.477  0.00 27.20
N =20
ATOM    219  CA  SER A  36A      3.235  31.238  20.479  0.00 28.70
C =20
ATOM    220  C   SER A  36A      2.315  32.417  20.162  0.00 29.65
C =20
ATOM    221  O   SER A  36A      2.664  33.569  20.429  0.00 30.07
O =20
ATOM    222  CB  SER A  36A      2.878  30.647  21.845  0.00 28.71
C =20
ATOM    223  OG  SER A  36A      3.565  29.428  22.077  0.00 29.15
O =20
ATOM    224  H   SER A  36A      5.000  32.029  21.306  0.00 20.00
H =20
ATOM    225  HG  SER A  36A      4.526  29.487  22.051  0.00 20.00
H =20
ATOM    226  N   PRO A  36B      1.124  32.146  19.598  0.00 30.41
N =20
ATOM    227  CA  PRO A  36B      0.593  30.825  19.240  0.00 31.02
C =20
ATOM    228  C   PRO A  36B      1.323  30.182  18.061  0.00 31.62
C =20
ATOM    229  O   PRO A  36B      2.169  30.814  17.426  0.00 31.58
O =20
ATOM    230  CB  PRO A  36B     -0.867  31.125  18.914  0.00 30.83
C =20
ATOM    231  CG  PRO A  36B     -0.789  32.492  18.316  0.00 30.95
C =20
ATOM    232  CD  PRO A  36B      0.147  33.200  19.269  0.00 30.41
C =20
ATOM    233  N   ALA A  37       0.991  28.925  17.777  0.00 32.51
N =20
ATOM    234  CA  ALA A  37       1.608  28.191  16.677  0.00 33.56
C =20

--------------------------------------------
Anne M=F8lgaard, Ph.D.
Center for Biological Sequence Analysis
BioCentrum-DTU, Building 208
DK-2800 Lyngby

Email:  an...@cb...=20
Phone:  (+45)4525 2472
--------------------------------------------=20

-----Original Message-----
From: Warren DeLano [mailto:wa...@de...]=20
Sent: 18. november 2005 02:28
To: Joel Tyndall; Anne M=F8lgaard; pym...@li...
Subject: RE: [PyMOL] displaying protein with propeptide

A quick fix is to use the "retain_order" setting.

set retain_order

which will force PyMOL to honor the order of ATOMs in the PDB file over =
the
numeric ordering of residue identifiers.

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
> Joel Tyndall
> Sent: Thursday, November 17, 2005 12:15 PM
> To: Anne M=F8lgaard; pym...@li...
> Subject: Re: [PyMOL] displaying protein with propeptide
>=20
> Hi Ann,
>=20
> I would change the chain id of the propeptide in a text=20
> editor, to say P and remove the P from after the residue numbers.
>=20
> J
>=20
> Anne M=F8lgaard wrote:
>=20
> >Hi,
> >
> >I am having problems displaying proteins with unusual residue=20
> >numbering, such as proteins with propeptides. An example is=20
> 1cs8, which=20
> >starts off like
> >this:
> >
> >ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
> >N =20
> >ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
> >C =20
> >ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
> >C =20
> >ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
> >O =20
> >ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
> >C =20
> >ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
> >O
> >.
> >.
> >.
> >And later on comes the sequence corresponding to the mature protein:
> >
> >ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
> >N =20
> >ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
> >C =20
> >ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
> >C =20
> >ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
> >O =20
> >ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
> >C
> >Etc.=20
> >
> >If I open 1cs8 with PyMol, I can see everything in the "lines",=20
> >"sticks" and "surface" representation, but in ribbon or cartoon mode=20
> >only part of the protein is shown. What do I have to do to=20
> show the whole sequence?
> >
> >How do I select residues with a "P" appended to the residue=20
> number? If=20
> >I say "select resi 1P-5P" I get both 1P-5P and 1-5.
> >
> >Any help will be appreciated! (I am using PyMol version 0.98=20
> for Windows).
> >
> >- Anne
> >
> >--------------------------------------------
> >Anne M=F8lgaard, Ph.D.
> >Center for Biological Sequence Analysis BioCentrum-DTU, Building 208=20
> >DK-2800 Lyngby
> >
> >Email:  an...@cb...
> >Phone:  (+45)4525 2472
> >--------------------------------------------
> >
> >
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> >Register for a JBoss Training Course.  Free Certification Exam
> >for All Training Attendees Through End of 2005. For more info visit:
> >http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
> >_______________________________________________
> >PyMOL-users mailing list
> >PyM...@li...
> >https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
> > =20
> >
>=20
> --=20
> Joel Tyndall, PhD
>=20
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand                    =20
>=20
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa
>=20
> Ph / Waea               +64 3 4797293=20
> Fax / Waeawhakaahua     +64 3 4797034
>=20
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get Certified Today
> Register for a JBoss Training Course.  Free Certification Exam
> for All Training Attendees Through End of 2005. For more info visit:
> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] combine align and rms_cur to calculate rms for complexes

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

Andrea,

PyMOL really can't do this job generally well because you'd need to
specify an atom-by-atom correspondance between the two ligands.  Unless
the ligands are identical and have identical atom names, the numbers you
get will be misleading. =20

If that is in fact the case, then I think you're on the right track.

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
> Andrea Spitaleri
> Sent: Thursday, November 17, 2005 4:11 PM
> To: pymol-users
> Subject: [PyMOL] combine align and rms_cur to calculate rms=20
> for complexes
>=20
> Hi all,
> could someone confirm this:
> I have some complexes protein+ligand and I'd like to perform=20
> rms calculation for the position of the ligand. This what I have done:
>=20
> load reference.pdb
> select proteinreference, segi A
> select ligreference, segi B
> load compare.pdb
> select proteincomapre, segi A
> select ligcompare, segi B
> align proteinreference,proteincompare
> rms_cur ligreference,ligcompare
>=20
> is rms_cur the right command to calculate the rms for the=20
> ligand position? then, is the procedure "chemically" correct?
>=20
> thanks
>=20
> regards,
>=20
> andrea
>=20
> --
> "La conoscenza libera il genere umano dalla superstizione"
> J. Watson
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
> 2005. For more info visit:
> http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dick
> _______________________________________________
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> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] Light source questions

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

Chris,

Multiple light sources will be in the next release -- the code is
currently in CVS.  For future reference:

set light_count, 4=20

and modify the light, light2, and light3 vectors (if necessary)

light0 is fixed along Z and has no default specular component.

The Z axis light intensity is controlled via the "direct" setting.  The
"reflect" setting controls the aggregate intensity of the movable light
(now lights).

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
> Christopher Fleming
> Sent: Wednesday, November 16, 2005 5:57 PM
> To: pym...@li...
> Subject: [PyMOL] Light source questions
>=20
> Hello-
>=20
> =20
>=20
> I have a few questions about lighting in PyMol v0.98. First,=20
> is there anyway to increase the intensity of the light=20
> source? I ask because I would like to try to backlight my=20
> molecule, but whenever I do move the light to behind it, It=20
> comes up very dim. I have tried to output a file for use in=20
> POV-RAY (huge file, even after limiting the quality of=20
> cartoons and surfaces a bit) to add additional pointlights,=20
> but the file is so large It takes forever to even try to=20
> ray-trace the image. If anyone knows how to add more light=20
> sources in PyMol, that would be best but it looks like that=20
> is imposible. Any hints?
>=20
> =20
>=20
> Thanks, Chris
>=20
> =20
>=20
> Christopher D. Fleming
>=20
> Graduate Student
>=20
> Redinbo Laboratory
>=20
> Dept. of Biochemistry & Biophysics
>=20
> UNC-Chapel Hill
>=20
> w. 919-962-8270
>=20
> =20
>=20
>=20

RE: [PyMOL] Transparent background

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

Yes, in recent builds (http://delsci.com/beta).

set opaque_background, off

then

draw or ray

and then save the image.

NOTE: Some graphics cards support this in OpenGL (draw command), other =
systems can only do transparent backgrounds via the ray-tracer (ray =
command).

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
> Kerff Fr=E9d=E9ric
> Sent: Thursday, November 17, 2005 5:16 AM
> To: PyM...@li...
> Subject: [PyMOL] Transparent background
>=20
> Hi pymol users,
>=20
> I'd like to make a figure with a transparent background. Is=20
> it possible with pymol?
> Thanks for your help.
>=20
> Fred
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today Register for a JBoss Training Course.  Free=20
> Certification Exam for All Training Attendees Through End of=20
> 2005. For more info visit:
> http://ads.osdn.com/?ad_id=3D7628&alloc_id=3D16845&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] displaying protein with propeptide

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

I'm not sure how version-dependent this is, but setting connect_mode to =
1 before loading the PDB should disable distance-based connectivity =
determination.

set connect_mode, 1

load CONECT_only_pdb.pdb

--
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
> Eric Zollars
> Sent: Thursday, November 17, 2005 5:36 PM
> To: pym...@li...
> Subject: Re: [PyMOL] displaying protein with propeptide
>=20
> Is there a similar command to force PyMOL to use only CONECT=20
> lines in the pdb file instead of generating connectivity by distance?
>=20
> Eric
>=20
> Warren DeLano wrote:
> > A quick fix is to use the "retain_order" setting.
> >=20
> > set retain_order
> >=20
> > which will force PyMOL to honor the order of ATOMs in the=20
> PDB file over the numeric ordering of residue identifiers.
> >=20
> > Cheers,
> > Warren
> >=20
> > --
> > Warren L. DeLano, Ph.D.                    =20
> > Principal Scientist
> >=20
> > . 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
> >=20
> >=20
> >>-----Original Message-----
> >>From: pym...@li...
> >>[mailto:pym...@li...] On Behalf Of Joel=20
> >>Tyndall
> >>Sent: Thursday, November 17, 2005 12:15 PM
> >>To: Anne M=F8lgaard; pym...@li...
> >>Subject: Re: [PyMOL] displaying protein with propeptide
> >>
> >>Hi Ann,
> >>
> >>I would change the chain id of the propeptide in a text=20
> editor, to say=20
> >>P and remove the P from after the residue numbers.
> >>
> >>J
> >>
> >>Anne M=F8lgaard wrote:
> >>
> >>
> >>>Hi,
> >>>
> >>>I am having problems displaying proteins with unusual residue=20
> >>>numbering, such as proteins with propeptides. An example is
> >>
> >>1cs8, which
> >>
> >>>starts off like
> >>>this:
> >>>
> >>>ATOM      1  N   SER A   1P    -32.762  23.978  22.929  0.00 34.26
> >>>N =20
> >>>ATOM      2  CA  SER A   1P    -32.360  24.645  21.660  0.00 34.08
> >>>C =20
> >>>ATOM      3  C   SER A   1P    -32.303  26.162  21.821  0.00 33.91
> >>>C =20
> >>>ATOM      4  O   SER A   1P    -32.838  26.712  22.786  0.00 33.82
> >>>O =20
> >>>ATOM      5  CB  SER A   1P    -33.338  24.274  20.541  0.00 34.28
> >>>C =20
> >>>ATOM      6  OG  SER A   1P    -34.684  24.406  20.971  0.00 34.36
> >>>O
> >>>.
> >>>.
> >>>.
> >>>And later on comes the sequence corresponding to the=20
> mature protein:
> >>>
> >>>ATOM   1060  N   ALA A   1      11.470  66.852  16.148  1.00 22.69
> >>>N =20
> >>>ATOM   1061  CA  ALA A   1      11.282  65.561  15.491  1.00 20.80
> >>>C =20
> >>>ATOM   1062  C   ALA A   1      10.621  65.677  14.113  1.00 20.33
> >>>C =20
> >>>ATOM   1063  O   ALA A   1       9.920  66.649  13.835  1.00 18.43
> >>>O =20
> >>>ATOM   1064  CB  ALA A   1      10.451  64.636  16.393  1.00 19.50
> >>>C
> >>>Etc.=20
> >>>
> >>>If I open 1cs8 with PyMol, I can see everything in the "lines",=20
> >>>"sticks" and "surface" representation, but in ribbon or=20
> cartoon mode=20
> >>>only part of the protein is shown. What do I have to do to
> >>
> >>show the whole sequence?
> >>
> >>>How do I select residues with a "P" appended to the residue
> >>
> >>number? If
> >>
> >>>I say "select resi 1P-5P" I get both 1P-5P and 1-5.
> >>>
> >>>Any help will be appreciated! (I am using PyMol version 0.98
> >>
> >>for Windows).
> >>
> >>>- Anne
> >>>
> >>>--------------------------------------------
> >>>Anne M=F8lgaard, Ph.D.
> >>>Center for Biological Sequence Analysis BioCentrum-DTU,=20
> Building 208=20
> >>>DK-2800 Lyngby
> >>>
> >>>Email:  an...@cb...
> >>>Phone:  (+45)4525 2472
> >>>--------------------------------------------
> >>>
> >>>
> >>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.Net email is sponsored by the JBoss Inc.  Get=20
> Certified Today=20
> >>>Register for a JBoss Training Course.  Free Certification Exam for=20
> >>>All Training Attendees Through End of 2005. For more info visit:
> >>>http://ads.osdn.com/?ad_idv28&alloc_id=16845&op=3Dclick
> >>>_______________________________________________
> >>>PyMOL-users mailing list
> >>>PyM...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>>
> >>>=20
> >>>
> >>
> >>--
> >>Joel Tyndall, PhD
> >>
> >>Lecturer
> >>National School of Pharmacy
> >>University of Otago
> >>PO Box 913 Dunedin
> >>New Zealand                    =20
> >>
> >>Pukenga
> >>Te Kura Taiwhanga Putaiao
> >>Te Whare Wananga o Otago
> >>Pouaka Poutapeta 913 Otepoti
> >>Aotearoa
> >>
> >>Ph / Waea               +64 3 4797293=20
> >>Fax / Waeawhakaahua     +64 3 4797034
> >>
> >>
> >>
> >>
> >>
> >>-------------------------------------------------------
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