pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Displaying/defining double bonds in a ligand molecule; lighting problem

[Wulf B. <wul...@mp...>]

Warren, Mark;

thanks for these suggestions concerning "overexposed" images. We have 
dumped Warren's settings into our pymolrc file and are now getting much 
better results...

Best,


Wulf



Mark A Saper schrieb:
> Wulf et al,
>
> I've had similar results to what you report even with a session file 
> created with the latest version of PyMol.  You should first try what 
> Warren suggests.  Then, if the specular highlights still look too 
> contrasty, you can try reducing the specular_intensity to about 0.2 
> and also adjust the shininess value.
>
Wulf.

BTW: we have a little difficulty with the 0.99 version under windows:
colours have become very glary in raytracing, like an overexposed
photograph. Is this a feature, a non-optimised colour scheme or simply
my mistake?


Warren:

It may be necessary to reoptimize the lighting settings.  The new 
defaults are:

set ambient, 0.14
set gamma, 1.0
set direct, 0.45
set reflect, 0.45
set specular_intensity, 0.5
set light_count, 2
set light, [ -0.40000, -0.40000, -1.00000 ]
set spec_reflect, -1
set spec_power, -1
set shininess, 55

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

[Mark A S. <sa...@um...>]

Wulf et al,

I've had similar results to what you report even with a session file  
created with the latest version of PyMol.  You should first try what  
Warren suggests.  Then, if the specular highlights still look too  
contrasty, you can try reducing the specular_intensity to about 0.2  
and also adjust the shininess value.

-Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
930 N University Ave
Ann Arbor MI 48109-1055       U.S.A.

sa...@um...        (734) 764-3353        fax (734) 764-3323
http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

Re: [PyMOL] Arrows Too Short?

[gilleain t. <gil...@gm...>]

Hello,

This is only my opinion right...

But it seems to me that converting hbonds into secondary structure
elements (helices, strands, paperclips...) can be tricky at the
boundaries when bonds are just too short or just the other side of the
correct angle.

To illustrate this with 1m6q (which is a model, by the way, and has
some odd features, like not-quite-bonded sheets) I pick one of the
short sheets you circle (at least I think I do) : 379-383::423-427.

From the attached pictures, you can see that pymol does not consider
residue 381's oxygen to be bonded to residue 425's nitrogen. This may
well be justified, since the O->N distance is 3.69 - which is quite
long.

What I'm not sure is what can be done about this - ss assignment could
potentially have a lot of 'hacks' to deal with supposed corner cases
like this (phi-psi angles, ca-ca distances, etc) but it's a bit of a
judgement call.

gilleain torrance

On 3/3/06, oliverggmxde <oli...@us...> wrote:
> Hello all,
>
> I am using PyMOL V0.99pre06 (build from CVS repository)
>
> When viewing 1m6q.pdb (http://www.rcsb.org/pdb/files/1m6q.pdb) in
> cartoon mode, I think the arrows in beta sheet are rendered too short
> in comparison to other software (e.g. RasMOL). I posted this
> behavior already in the "bugs"-section (see comparison screenshot
> there
> https://sourceforge.net/tracker/index.php?func=3Ddetail&aid=3D1429665&gro=
up_id=3D4546&atid=3D104546).
>
> I'd like to use PyMOL of course. Is there any chance to get PyMol to
> display a larger version of these arrows?
>
> Oliver
>
>
>
>
>
>
>
>
>
>
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[PyMOL] Some VRML improvements

[Chris W. <cw...@ua...>]

Hi Warren,

I've tried sending this patch directly to your email
address a couple of times in the last month, but I never
heard back from you -- maybe your spam filter doesn't
like the attachment? (Hehe, either that or you find me
annoying.) Anyways, I'll try sending it indirectly
through the mailing list. Again, the code in the patch
should be regarded as being in the public domain.

The attached patch centers the objects in the coordinate
system, sets up three orthogonal viewpoints, reverses
non-agreeing triangle normals (needed for cartoon objects,
since the triangles tend to alternate normal direction
-- probably derived from triangle strips), and has nicer
materials under some viewers (not perfect, but I'm hoping
some other pymol users will have suggestions).

I don't currently export vertex normals, but I may need
to do that so that surfaces have smooth shading in
the VRML viewers -- something to play with for later.

One thing that I should note, exporting the surface
geometry at the triangle level might work well when
exporting to a renderer, but isn't the best way to
do export for VRML or any other scene description
format. It would be much better to export at
the object level, so that a list of vertices can
be output, then the triangles are exported as
indices into the list of vertices -- this would
lead to smaller files, and also the topology of
the surface is preserved making automatic vertex
normal interpolation possible (which is not possible
when exporting a collection of unrelated triangles).
I have no idea if it is possible to access such
information from within pymol though -- well, it is
possible to have access to this data when a surface
is first created through the RepSurface structure,
but I think that data is thrown out after the
surface is created.

Regards,
Chris

-- 
  ____________________________________________________________________
( Chris Want                                                         )
( Research Computing Support                                         )
( Academic Information and Communication Technologies (AICT)         )
( University of Alberta                                              )
( Tel: 1-780-492-9418                                                )
  --------------------------------------------------------------------

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

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

Wulf,

Unfortunately, the lighting model has changed...I am assuming that you =
are having problems with existing session files or scripts? =20

It may be necessary to reoptimize the lighting settings.  The new =
defaults are:

set ambient, 0.14
set gamma, 1.0
set direct, 0.45
set reflect, 0.45
set specular_intensity, 0.5
set light_count, 2=20
set light, [ -0.40000, -0.40000, -1.00000 ]=20
set spec_reflect, -1
set spec_power, -1
set shininess, 55

Perhaps you can simply paste those commands into your scripts?

If you want pre-0.99-like lighting model (it has an extra dot product =
that shouldn't be there).

use=20

set ray_legacy_lighting, 1

with the above settings

Cheers,
Warren

-----Original Message-----
From: Wulf Blankenfeldt [mailto:wul...@mp...]
Sent: Mon 3/6/2006 7:23 AM
To: Warren DeLano
Subject: Re: [PyMOL] Displaying/defining double bonds in a ligand =
molecule
=20
Ah, bingo!

Thanks for that, Warren.


BTW: we have a little difficulty with the 0.99 version under windows:=20
colours have become very glary in raytracing, like an overexposed=20
photograph. Is this a feature, a non-optimised colour scheme or simply=20
my mistake?


Best,



Wulf




Warren DeLano schrieb:
>
> Wulf,
>
> The easiest thing would be to convert your small molecule to an SDF,=20
> MOL, or MOL2 format before loading it into PyMOL.
>
> Short of that, you'd have to select each bond independently=20
> (ctrl-right-click while in editing mode) and use Ctrl-W to set the=20
> valences.
>

RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

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

Wulf,

The easiest thing would be to convert your small molecule to an SDF, =
MOL, or MOL2 format before loading it into PyMOL.

Short of that, you'd have to select each bond independently =
(ctrl-right-click while in editing mode) and use Ctrl-W to set the =
valences.

Cheers,
Warren


-----Original Message-----
From: pym...@li... on behalf of Wulf =
Blankenfeldt
Sent: Mon 3/6/2006 6:22 AM
To: pym...@li...
Subject: [PyMOL] Displaying/defining double bonds in a ligand molecule
=20
Hello pymolers,

I'd like to display double bonds in a small molecule ligand bound to the =

active centre of a protein. Of course, the ligand is non-standard, i.e.=20
pymol doesn't know about its chemical nature. Googling a bit, I found=20
that I can

set valence, 0.1

but this only display double bonds in the protein, which I don't want.

How do I teach pymol to display double bonds in my ligand?


Thanks for your help,




Wulf



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Re: [PyMOL] (no subject)

[gilleain t. <gil...@gm...>]

Hi,

I found out how to do ... something ... like this the other day.

From the "action" (A) menu for an object select Generate->Symmetry Mates.

This gives you the option of within 4-100 angstrom. I don't know what
it means to select different distances, all I know is that any one of
these options gives you lots more copies of that object, presumably
where they are in the crystal structure.

This came in useful when looking at the results from msdmotif at the
ebi, which was giving some ligands as binding twice to the same motif;
turns out that one of them was from a neighbour interaction.

gilleain

On 3/4/06, Blanton Tolbert <bla...@ur...> wrote:
> Hi pymol community
>
> I would like to recapitulate the crystal packing arrangement of a
> protein structure to look for neighbor interactions.  Is it possible
> to do this in pymol?  If so, please provide me some insight.
>
> Thanks,
>
>
> Blanton Tolbert
> Graduate Student
> University of Rochester
> Biophysics and Structural Biology
> 585-275-5189
> bla...@ur...
>
>
>
>
>
> -------------------------------------------------------
> 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?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=
=3D121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] gui/viewer position

[Marc B. <br...@mp...>]

hello,

is it possible to define the gui and viewer positions on startup separately?

thanks,
marc

[PyMOL] Displaying/defining double bonds in a ligand molecule

[Wulf B. <wul...@mp...>]

Hello pymolers,

I'd like to display double bonds in a small molecule ligand bound to the 
active centre of a protein. Of course, the ligand is non-standard, i.e. 
pymol doesn't know about its chemical nature. Googling a bit, I found 
that I can

set valence, 0.1

but this only display double bonds in the protein, which I don't want.

How do I teach pymol to display double bonds in my ligand?


Thanks for your help,




Wulf

[PyMOL] PDB center

[surendra n. <ne...@ya...>]

Dear User,
 Is it possible to change center of the coordinate
system in pymol to (0,0,0). I want to change center of
my PDB file to orgin.
thanks
surendra

__________________________________________________
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http://mail.yahoo.com 

RE: [PyMOL] stereo and intel macs

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

Bill,

> Does anyone know if the new intel min-macs support stereo...

Unlikely -- the new Mini's have Intel GMA950 Graphics Processor and =
there is no upgrade available.  In the PC world, Intel-based OpenGL =
systems are plagued by poor performance and compatibility problems.  It =
would surprise me if that wasn't the case with the Mac Minis too as =
well.  I've never heard of Intel supporting stereo-graphics.

As for the MacBook Pro laptops, caution is also warranted -- watch the =
discussion boards for reports from early adopters.

Though I strongly endorse Mac OS X as an operating system for scientific =
visualization, the only Mac computer systems I can recommend purchasing =
right now (based on personal experience) are: (1) the iMac Core Duo, and =
(2) the PowerMac G5 Quad with the Quadro FX 4500.=20

Cheers,
Warren

-----Original Message-----
From: pym...@li... on behalf of William Scott
Sent: Sat 3/4/2006 12:32 PM
To: pym...@li...
Subject: [PyMOL] stereo and intel macs
=20
Does anyone know if the new intel min-macs support stereo, either by =20
default or after being fitted with an appropriate video card?  The =20
idea of chucking my O2s and replacing them with mini-macs is quite =20
appealing...

Thanks.

Bill Scott


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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!
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[PyMOL] stereo and intel macs

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

Does anyone know if the new intel min-macs support stereo, either by  
default or after being fitted with an appropriate video card?  The  
idea of chucking my O2s and replacing them with mini-macs is quite  
appealing...

Thanks.

Bill Scott

RE: [PyMOL] (no subject)

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

Hi Blanton

You are probably looking for the "symexp" command. I don't remember the =
exact syntax, but there is a small help text. You can also try to search =
the mail archive.


Best wishes

Esben


-----Original Message-----
From: pym...@li... on behalf of Blanton =
Tolbert
Sent: Sat 2006-03-04 15:01
To: pym...@li...
Subject: [PyMOL] (no subject)
=20
Hi pymol community

I would like to recapitulate the crystal packing arrangement of a =20
protein structure to look for neighbor interactions.  Is it possible =20
to do this in pymol?  If so, please provide me some insight.

Thanks,


Blanton Tolbert
Graduate Student
University of Rochester
Biophysics and Structural Biology
585-275-5189
bla...@ur...





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This SF.Net email is sponsored by xPML, a groundbreaking scripting =
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and join the prime developer group breaking into this new coding =
territory!
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D=
121642
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[PyMOL] (no subject)

[Blanton T. <bla...@ur...>]

Hi pymol community

I would like to recapitulate the crystal packing arrangement of a  
protein structure to look for neighbor interactions.  Is it possible  
to do this in pymol?  If so, please provide me some insight.

Thanks,


Blanton Tolbert
Graduate Student
University of Rochester
Biophysics and Structural Biology
585-275-5189
bla...@ur...

[PyMOL] Updated PyMOL v0.99 Release Candidate

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

Folks,

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.

http://delsci.com/rel/099

Compared to the earlier 0.99 release candidates, PyMOL 0.99rc6 has up to
twice the surface calculation performance, better memory management for
large rendering jobs, and improved stability under Mac OS X. =20

Also, we restored the one-button viewing mode for laptop use (see info
below).

Cheers,
Warren

One button viewing controls (NOTE: on PC keyboards, Option is Alt).

To activate, enter "mouse one_button_viewing" or select from the Mouse
menu.

Rota: Camera rotation                 =3D click-and-drag
Move: Camera movement in XY-plane     =3D option-click-and-drag
MovZ: Camera movement along Z axis    =3D control-click-and-drag
Clip: Move clipping planes            =3D control-shift-click-and-drag

+/- : Toggle atom selections          =3D click-and-release
Cent: Center camera on an atom        =3D option-click-and-release
Menu: Context-sensitive pop-up menu   =3D control-click-and-release=20

PkAt: Pick atoms                      =3D =
control-shift-click-and-release
    =20
+Box: Select atoms using a drag box   =3D shift-click-and-drag
-Box: Deselect atoms using a drag box =3D shift-option-click-and-drag

--
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

[PyMOL] CASTpyMOL Plugin

[Binkowski, T. A. <abi...@an...>]

Greetings CASTpyMol Plugin Users:

First, thank you to all the CASTpyMol users who have been using the
plugin and have "encouraged" me to get a new version working.  Like the
PyMol project, I have been working to add improvements that to the
plugin that hopefully will be of great value to the community.

Since the demand for the plugin is so strong, I am releasing an early
version with some features still not implemented
(http://gpss.mcsg.anl.gov/GPSSpyMOL/), but which maintain the original
functionality of the plugin.  You will find that this version has many
added features including the ability to visualize ligand, metal, dna and
peptide binding surfaces.  The ability to upload your own file for
surface calculations is still being finalized, but when it is you will
be able to submit your files directly from the plugin.  Until the upload
feature is working, please feel free to contact me and I can submit the
files manually.

Also, the plugin is part of a new project, the "Global Protein Surface
Survey", which will be a single resource for all protein surface
information.  The "official" plugin release will correspond with the
launch of the GPSS webserver (http://gpss.mcsg.anl.gov), but hopefully
this one will hold everyone over until then.  So, the CASTpyMOL plugin
is now retired and the new GPSSpyMOL plugin will be actively maintained.

Thank you,

Andrew Binkowski



-----------------------------------------------------------------------
Andrew Binkowski, PhD
Structural Biology Center & Midwest Center for Structural Genomics
Biosciences Division
Argonne National Laboratory
9700 S. Cass Av. Argonne, IL 60439

abi...@an...=20
http://gpss.mcsg.anl.gov




-----Original Message-----
From: Warren DeLano [mailto:wa...@de...]=20
Sent: Thursday, March 02, 2006 5:51 PM
To: zzj; pym...@li...
Cc: Binkowski, Thomas Andrew
Subject: RE: [PyMOL] problem with CASTp pymol plugin

Regarding CASTpyMOL:

We (Delsci LLC) do not have any direct or privileged access to the CASTp
project or the CASTpyMOL plugin.  Thus, people should not expect new
versions of PyMOL to necessarily work with the CASTpyMOL plugin until
its developer(s) have had time to address any compatibility issues that
may have come up. =20

Given that CASTpyMOL is a free plugin, please be patient and gracious --
they are under no obligation to continue making it available, and all
who depend upon CASTpyMOL should thank them for doing so.

If you need to use CASTpyMOL immediately, then I recommmend using the
version of PyMOL that CASTpyMOL was developed for.  I suspect this would
be cross-platform versions of PyMOL 0.98, but perhaps they will be kind
enough to post some specific compatibility guidelines on their web
page(s) so that this uncertainty can be eliminated.

<http://sts.bioengr.uic.edu/castp/pymol.php>
<http://cast.engr.uic.edu/cast/oldindex.php>

Please accept my apologies for our role in creating incompatibilities
between PyMOL 0.98 and 0.99.  In addition to applying some minor tweaks
to the API, we finally migrated to Python 2.4.  Our hope is that the
official PyMOL 1.0 API will be stable and documented well enough to
prevent such problems in the future.

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 zzj
> Sent: Thursday, March 02, 2006 3:25 PM
> To: pym...@li...
> Subject: [PyMOL] problem with CASTp pymol plugin
>=20
> Hi everyone,
>    Has anyone else experience a problem of CASTp pymol plugin=20
> like this?
>  when you input PDB Id, it works fine; but when you input a=20
> job id in the case of uploading a structure, it complains=20
> there is no such structure on the sever even though you just=20
> submitted and did the calculation and saw it on the sever a=20
> couple minutes ago.
>   any hint? My system is macOSX.
> thanks,
> --joe
>=20
>=20
> --
> _________________________________________
> Joe (zhaocai) Zhou
> Department of Pathology & Laboratory Medicine University of=20
> Pennsylvania, School of Medicine
> 252 John Morgan Building
> 36th Street & Hamilton Walk
> Philadelphia, PA 19104-6082
> Tel: 215-898-2870
> Fax:215-898-2401
> Cell:781-330-2409
> -------------------------------------------------------------
>=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
> _______________________________________________
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> PyM...@li...
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>=20
>=20
>=20
>=20

[PyMOL] Arrows Too Short?

[oliverggmxde <oli...@us...>]

Hello all,

I am using PyMOL V0.99pre06 (build from CVS repository)

When viewing 1m6q.pdb (http://www.rcsb.org/pdb/files/1m6q.pdb) in
cartoon mode, I think the arrows in beta sheet are rendered too short
in comparison to other software (e.g. RasMOL). I posted this
behavior already in the "bugs"-section (see comparison screenshot
there
https://sourceforge.net/tracker/index.php?func=detail&aid=1429665&group_id=4546&atid=104546).

I'd like to use PyMOL of course. Is there any chance to get PyMol to
display a larger version of these arrows?

Oliver






  

RE: [PyMOL] setting correct bond length

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

Stefan,

As recommended, I suggest loading the structure in using a file format =
that contains explicit connectivity information (MOL/SDF or MOL2).  =
PyMOL generally does okay inferring protein connectivity from =
coordinates alone, but that is about it.

another thing you can do is unbond the atoms, either through picked =
atoms:

unbond pk1, pk2

or explicitly:

unbond atom-selection1, atom-selection2

Cheers,
Warren

-----Original Message-----
From: pym...@li... on behalf of Gerhardt, =
Stefan
Sent: Fri 3/3/2006 5:06 AM
To: pym...@li...
Subject: [PyMOL] setting correct bond length
=20
Dear all,

I am trying to display a bound azetidine ring, but pymol is drawing also =
a
bound between the C2 and C4 ring carbons.
=20
 <<...OLE_Obj...>>    bond length N-C 1.46=C5, C-C 1.54=C5 and C2-C4 =
2.03=C5 !!

See pymol picture attached. Is there a simple way of setting the bond =
length
to be drawn correctly?
 <<azetidine.gif>>=20


  Stefan Gerhardt, Dr
AstraZeneca
Protein Structure Laboratory
50S38 Mereside
Alderley Park, Macclesfield
SK10 4TG, UK

Re: [PyMOL] setting correct bond length

[Marc B. <br...@mp...>]

try converting the coordinates into mol-format.

On Friday 03 March 2006 13:05, Gerhardt, Stefan wrote:
> Dear all,
>
> I am trying to display a bound azetidine ring, but pymol is drawing als=
o a
> bound between the C2 and C4 ring carbons.
>
>  <<...OLE_Obj...>>    bond length N-C 1.46=C3=85, C-C 1.54=C3=85 and C2=
-C4 2.03=C3=85 !!
>
> See pymol picture attached. Is there a simple way of setting the bond
> length to be drawn correctly?
>  <<azetidine.gif>>
>
>
>   Stefan Gerhardt, Dr
> AstraZeneca
> Protein Structure Laboratory
> 50S38 Mereside
> Alderley Park, Macclesfield
> SK10 4TG, UK

Re: [PyMOL] (no subject)

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

Hi
try align or fit

regards

andrea

2006/3/3, Sri...@ju... <Sri...@ju...>:
> dear all
> can we superimpose structures in pymol
> Thanks & Regards
> srilatha potlapelly
> MSc Biotechnology
> Drug discovery,
> #450,4th D Main, 12th cross,
> Mahalakshmipuram - 560086
> Bangalore
> Office: +9180-23495461-64  Extn.-1029
>  -------------------------------------------------------
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--
"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 all </DIV><DIV>can we superimpose structures in pymol<BR></D=
IV><DIV>Thanks&nbsp;&amp;&nbsp;Regards<BR>srilatha&nbsp;potlapelly<BR>MSc&n=
bsp;Biotechnology<BR>Drug&nbsp;discovery,&nbsp;<BR>#450,4th&nbsp;D&nbsp;Mai=
n,&nbsp;12th&nbsp;cross,&nbsp;<BR>Mahalakshmipuram&nbsp;-&nbsp;560086&nbsp;=
<BR>Bangalore&nbsp;<BR>Office:&nbsp;+9180-23495461-64&nbsp;&nbsp;Extn.-1029=
<BR></DIV></FONT>=

[PyMOL] setting correct bond length

[Gerhardt, S. <Ste...@as...>]

Dear all,

I am trying to display a bound azetidine ring, but pymol is drawing =
also a
bound between the C2 and C4 ring carbons.
=20
 <<...OLE_Obj...>>    bond length N-C 1.46=C5, C-C 1.54=C5 and C2-C4 =
2.03=C5 !!

See pymol picture attached. Is there a simple way of setting the bond =
length
to be drawn correctly?
 <<azetidine.gif>>=20


  Stefan Gerhardt, Dr
AstraZeneca
Protein Structure Laboratory
50S38 Mereside
Alderley Park, Macclesfield
SK10 4TG, UK

RE: [PyMOL] align/fit

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

Enrico,

At the time it was written, the RMS code was tested against other tools
and confirmed to produce equivalent numbers.  Our superposition
algorithm is implemented using center of geometry translation followed
by an iterative three-way Jacobi rotation of the correlation tensor to
shrink the off-diagonals to within an adjustable tolerance within an
adjustable number of cycles.  RMS is then computed using the converged
rotation matrix.  I believe VMD has since adopted our code for this task
because of its robustness, though you'd have to check their sources to
be sure (at the time John pointed out a minor bug that has since been
fixed).
 =20
PyMOL's dynamic programming 1D/3D "align"-ment algorithm has not been
subjected to similar head-to-head testing, but the output of an adaptive
fitting routine is subjective and to some extent arbitrary.  In other
words, though the algorithm itself is definite, the decisions it makes
in terms of number of refinement cycles, and the RMS cutoff for outliers
will very based on the shape and noise in the distributions.  Other
"magic fit" algorithms will almost certainly produce slightly different
fits because they make different arbitrary decisions.=20

Ultimately, with PyMOL the proof is in what you see on the screen.  If
two proteins aren't well superimposed, that fact should be painfully
obvious.  As for publishing numbers, the safest way is to cite the
program, version, and the number and identity of atoms over which the
RMS value was generated.  =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
> Enrico Malito
> Sent: Friday, February 24, 2006 3:30 PM
> To: pym...@li...
> Subject: [PyMOL] align/fit
>=20
> Hi all,
> I'm using macPyMOL 0.99rc1 and found very useful the commands=20
> align&pair_fit to do superposition. I'm just wondering which=20
> specific algorithm they use, if somebody never used them to=20
> do superposition of Ca trace for publications, and if there=20
> is a specific reference to them.
> Thanks in advance,
> Enrico.
>=20
> --
> Enrico Malito
> Dept. of Biochemistry and Molecular Genetics University of=20
> Illinois at Chicago 900 S. Ashland Ave.
> Molecular Biology Research Building, Room 1116 Chicago, IL=20
> 60607 - U.S.A.
> Tel (312) 996-6299
> Fax (312) 355-4535
>=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

RE: [PyMOL] problem with CASTp pymol plugin

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

Regarding CASTpyMOL:

We (Delsci LLC) do not have any direct or privileged access to the CASTp
project or the CASTpyMOL plugin.  Thus, people should not expect new
versions of PyMOL to necessarily work with the CASTpyMOL plugin until
its developer(s) have had time to address any compatibility issues that
may have come up. =20

Given that CASTpyMOL is a free plugin, please be patient and gracious --
they are under no obligation to continue making it available, and all
who depend upon CASTpyMOL should thank them for doing so.

If you need to use CASTpyMOL immediately, then I recommmend using the
version of PyMOL that CASTpyMOL was developed for.  I suspect this would
be cross-platform versions of PyMOL 0.98, but perhaps they will be kind
enough to post some specific compatibility guidelines on their web
page(s) so that this uncertainty can be eliminated.

<http://sts.bioengr.uic.edu/castp/pymol.php>
<http://cast.engr.uic.edu/cast/oldindex.php>

Please accept my apologies for our role in creating incompatibilities
between PyMOL 0.98 and 0.99.  In addition to applying some minor tweaks
to the API, we finally migrated to Python 2.4.  Our hope is that the
official PyMOL 1.0 API will be stable and documented well enough to
prevent such problems in the future.

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 zzj
> Sent: Thursday, March 02, 2006 3:25 PM
> To: pym...@li...
> Subject: [PyMOL] problem with CASTp pymol plugin
>=20
> Hi everyone,
>    Has anyone else experience a problem of CASTp pymol plugin=20
> like this?
>  when you input PDB Id, it works fine; but when you input a=20
> job id in the case of uploading a structure, it complains=20
> there is no such structure on the sever even though you just=20
> submitted and did the calculation and saw it on the sever a=20
> couple minutes ago.
>   any hint? My system is macOSX.
> thanks,
> --joe
>=20
>=20
> --
> _________________________________________
> Joe (zhaocai) Zhou
> Department of Pathology & Laboratory Medicine University of=20
> Pennsylvania, School of Medicine
> 252 John Morgan Building
> 36th Street & Hamilton Walk
> Philadelphia, PA 19104-6082
> Tel: 215-898-2870
> Fax:215-898-2401
> Cell:781-330-2409
> -------------------------------------------------------------
>=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

[PyMOL] problem with CASTp pymol plugin

[zzj <zz...@gm...>]

Hi everyone,
   Has anyone else experience a problem of CASTp pymol plugin like this?
 when you input PDB Id, it works fine; but when you input a job id in
the case of uploading a structure, it complains there is no such
structure on the sever even though you just submitted and did the
calculation and saw it on the sever a couple minutes ago.
  any hint? My system is macOSX.
thanks,
--joe


--
_________________________________________
Joe (zhaocai) Zhou
Department of Pathology & Laboratory Medicine
University of Pennsylvania, School of Medicine
252 John Morgan Building
36th Street & Hamilton Walk
Philadelphia, PA 19104-6082
Tel: 215-898-2870
Fax:215-898-2401
Cell:781-330-2409
-------------------------------------------------------------