pymol-users — Collaborative support and tips for PyMOL users

RE: [PyMOL] Surface scribing in pymol?

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

Wulf,

Just "show surface" for selected atoms:

e.g.:

hide surface
show surface, resi 100 expand 5

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
> Wulf Blankenfeldt
> Sent: Tuesday, December 13, 2005 8:11 AM
> To: pym...@li...
> Subject: [PyMOL] Surface scribing in pymol?
>=20
> Dear pymolers,
>=20
> is there any simple way to scribe/cut surfaces in pymol,=20
> similar to the scribing function in grasp? I'd like to=20
> prepare a figure in which I only show a small piece of=20
> surface in a certain area of my molecule.
>=20
> Thanks for any help,
>=20
>=20
>=20
> Wulf
>=20
> --
> Dr. Wulf Blankenfeldt
> 	Max-Planck-Institute of Molecular Physiology
> 	Department III - Physical Biochemistry
> 	Otto-Hahn-Str. 11
> 	44227 Dortmund
> 	Germany
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web. =20
> DOWNLOAD SPLUNK!
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> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

[PyMOL] util.cba in a loop

[S. F. Y. <SY...@gn...>]

Hi,

I was trying a script similar to the following:

for i in ragne(1,5):
	print i
	util.cba(26,"resi 930-933)

The loop seems to be only iterated once right after the util.cba.  I
tried other commands like cmd.show and cmd.hide, which are fine.  Is it
possible to use util.cba in a loop?

Thanks,
Frank

[PyMOL] Surface scribing in pymol?

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

Dear pymolers,

is there any simple way to scribe/cut surfaces in pymol, similar to the 
scribing function in grasp? I'd like to prepare a figure in which I only 
show a small piece of surface in a certain area of my molecule.

Thanks for any help,



Wulf

-- 
Dr. Wulf Blankenfeldt
	Max-Planck-Institute of Molecular Physiology
	Department III - Physical Biochemistry
	Otto-Hahn-Str. 11
	44227 Dortmund
	Germany

RE: [PyMOL] Problem with crashing

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

Occasionally PyMOL experiences problems due to a variety of factors,
some of which are internal to the program, and others which are
environmental in nature.  If you encounter trouble, PyMOL may have a
bug, or your computer's OpenGL graphics system may be at fault. =20

To help those that seek to help you, please provide the following
information whenever you report a PyMOL malfunction.

A. Your operating system name, bits, and version number:

B. Your OpenGL-capable graphics card vendor and model:

C. Your OpenGL-capable graphics driver version number:

D. Your PyMOL version number:

E. Your description of the problem:

For example:

A. Windows XP, 32 bit, Service Pack 2:
B. nVidia, GeForce 4 Go
C. NVIDIA, 3.6.3.9, 8/15/2002
D. 0.99beta31
E. PyMOL crashes on startup

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
> bp...@mo...
> Sent: Monday, December 12, 2005 10:12 AM
> To: pym...@li...
> Subject: [PyMOL] Problem with crashing
>=20
> Dear all,
>=20
> I have been using Pymol for a while now and have not had any=20
> stability issues before. However since I have purchased a new=20
> computer i64_84 platform the wonderful pymol has been=20
> crashing like crazy every few minutes. It is an inconvenience=20
> and I would really like to resolve the issues. Do you have=20
> any suggestions? Thanks for help!
>=20
> Best wishes,
> Bojana
>=20
> --
> Dr Bojana Popovic
> Crystallography and Biocomputing Group
> Department of Biochemistry
> University of Cambridge
> 80 Tennis Court Road
> Cambridge
> CB2 1GA
>=20
> Phone: +44 (0)1223 766 028
> Email: bp...@ca...
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep=20
> through log files for problems?  Stop!  Download the new AJAX=20
> search engine that makes searching your log files as easy as=20
> surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20
>=20

RE: [PyMOL] HETATM in pdb

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

Paul,

rename object-name, force=3D1

will cause PyMOL to assign unique (though not necessarily sequential)
atom names...

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
> Paul Wilhelm Elsinghorst
> Sent: Monday, December 12, 2005 9:35 AM
> To: pym...@li...
> Subject: [PyMOL] HETATM in pdb
>=20
> Hi,
>=20
>=20
> I was wondering if I can get PyMol to add consecutive numbers=20
> to the HETATM labels of my ligand.
>=20
> So I'd like to get this:
>=20
>=20
>=20
> =09
> 	HETATM    1  N1  PWE     1       0.459  60.194  72.834 =20
> 1.00  0.00           N
> 	HETATM    2  N2  PWE     1       1.778  68.314  67.268 =20
> 1.00  0.00           N
> 	HETATM    3  N3  PWE     1       2.162  68.185  65.952 =20
> 1.00  0.00           N
> 	HETATM    4  N4  PWE     1       5.940  69.286  64.620 =20
> 1.00  0.00           N
> 	HETATM    5  C5  PWE     1      -2.914  55.019  74.878 =20
> 1.00  0.00           C
> 	HETATM    6  C6  PWE     1      -0.798  55.711  74.017 =20
> 1.00  0.00           C
> 	HETATM    7  C7  PWE     1      -1.065  57.076  73.908 =20
> 1.00  0.00           C
> 	HETATM    8  C8  PWE     1      -0.272  57.886  73.082 =20
> 1.00  0.00           C
> 	HETATM    9  C9  PWE     1       0.774  57.334  72.332 =20
> 1.00  0.00           C
> 	HETATM   10  C10 PWE     1       1.056  55.969  72.430 =20
> 1.00  0.00           C
> 	HETATM   11  C11 PWE     1       2.817  56.083  70.817 =20
> 1.00  0.00           C
>=20
>=20
>=20
> instead of this:
>=20
>=20
> =09
> 	HETATM    1  N  PWE     1       0.459  60.194  72.834 =20
> 1.00  0.00           N
> 	HETATM    2  N  PWE     1       1.778  68.314  67.268 =20
> 1.00  0.00           N
> 	HETATM    3  N  PWE     1       2.162  68.185  65.952 =20
> 1.00  0.00           N
> 	HETATM    4  N  PWE     1       5.940  69.286  64.620 =20
> 1.00  0.00           N
> 	HETATM    5  C  PWE     1      -2.914  55.019  74.878 =20
> 1.00  0.00           C
> 	HETATM    6  C  PWE     1      -0.798  55.711  74.017 =20
> 1.00  0.00           C
> 	HETATM    7  C  PWE     1      -1.065  57.076  73.908 =20
> 1.00  0.00           C
> 	HETATM    8  C  PWE     1      -0.272  57.886  73.082 =20
> 1.00  0.00           C
> 	HETATM    9  C  PWE     1       0.774  57.334  72.332 =20
> 1.00  0.00           C
> 	HETATM   10  C  PWE     1       1.056  55.969  72.430 =20
> 1.00  0.00           C
> 	HETATM   11  C  PWE     1       2.817  56.083  70.817 =20
> 1.00  0.00           C
>=20
>=20
>=20
>=20
> Any ideas?
>=20
>=20
> Paul
>=20

[PyMOL] HETATM in pdb

[Paul W. E. <pa...@un...>]

Hi,


I was wondering if I can get PyMol to add consecutive numbers to the
HETATM labels of my ligand.

So I'd like to get this:


> HETATM    1  N1  PWE     1       0.459  60.194  72.834  1.00  0.00           N
> HETATM    2  N2  PWE     1       1.778  68.314  67.268  1.00  0.00           N
> HETATM    3  N3  PWE     1       2.162  68.185  65.952  1.00  0.00           N
> HETATM    4  N4  PWE     1       5.940  69.286  64.620  1.00  0.00           N
> HETATM    5  C5  PWE     1      -2.914  55.019  74.878  1.00  0.00           C
> HETATM    6  C6  PWE     1      -0.798  55.711  74.017  1.00  0.00           C
> HETATM    7  C7  PWE     1      -1.065  57.076  73.908  1.00  0.00           C
> HETATM    8  C8  PWE     1      -0.272  57.886  73.082  1.00  0.00           C
> HETATM    9  C9  PWE     1       0.774  57.334  72.332  1.00  0.00           C
> HETATM   10  C10 PWE     1       1.056  55.969  72.430  1.00  0.00           C
> HETATM   11  C11 PWE     1       2.817  56.083  70.817  1.00  0.00           C


instead of this:


> HETATM    1  N  PWE     1       0.459  60.194  72.834  1.00  0.00           N
> HETATM    2  N  PWE     1       1.778  68.314  67.268  1.00  0.00           N
> HETATM    3  N  PWE     1       2.162  68.185  65.952  1.00  0.00           N
> HETATM    4  N  PWE     1       5.940  69.286  64.620  1.00  0.00           N
> HETATM    5  C  PWE     1      -2.914  55.019  74.878  1.00  0.00           C
> HETATM    6  C  PWE     1      -0.798  55.711  74.017  1.00  0.00           C
> HETATM    7  C  PWE     1      -1.065  57.076  73.908  1.00  0.00           C
> HETATM    8  C  PWE     1      -0.272  57.886  73.082  1.00  0.00           C
> HETATM    9  C  PWE     1       0.774  57.334  72.332  1.00  0.00           C
> HETATM   10  C  PWE     1       1.056  55.969  72.430  1.00  0.00           C
> HETATM   11  C  PWE     1       2.817  56.083  70.817  1.00  0.00           C



Any ideas?


Paul

[PyMOL] Pymol plugins and DRM systems?

[Andrew D. F. <and...@tu...>]

Has anyone looked into making pymol plugins work with any of the sundry 
distributed resource management systems (gridengine, lsf, pbs, condor, etc.)? 
I have a cluster that could make short work of a lot of computations that I 
want to visualize in pymol, but currently, that would mean installing pymol and 
all the pre-requisites on each compute node, and then running pymol on a given 
node and doing a SLOW remote display back to my desktop.  Needless to say, I 
think there ought to be a better way; hopefully someone has done something with 
this before I start puttering away and breaking my local installation.

Thanks,
	Andy

-- 
Andrew Fant           | The lion and the calf shall lie   | Disclaimer:
and...@tu... | down together, but the calf won't | Do you REALLY
TCCS/USG              | get much sleep.                   | think I can
Tufts University      |                  W. Allen         | speak for Tufts?

[PyMOL] Problem with crashing

[<bp...@mo...>]

Dear all,

I have been using Pymol for a while now and have not had any stability 
issues before. However since I have purchased a new computer i64_84 
platform the wonderful pymol has been crashing like crazy every few 
minutes. It is an inconvenience and I would really like to resolve the 
issues. Do you have any suggestions? Thanks for help!

Best wishes,
Bojana

-- 
Dr Bojana Popovic
Crystallography and Biocomputing Group
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge
CB2 1GA

Phone: +44 (0)1223 766 028
Email: bp...@ca...

[PyMOL] PyMol Wiki & Spammers

[tree <jav...@ut...>]

Dear PyMolers,

Recently, we have had a spate of spammers hitting our beloved wiki; some
30+ attackes in the last few days. 

Due to this unfortunate change, I have turned off new user registration
so that we can curb this abuse.  New users can still be added by
administrators/sysops, in the meantime.  Once I find a satisfactory
solution -- or someone else comes up with one -- I'll re-allow new
users.

I'll post something soon, for new (good) users to follow to get access.
This is peculiar for our wiki.  We must have hit some high in
popularity.  We have: 1470+ pages; 128,000+ page views; 190+ users; and,
the web usage increases daily.

Lastly, a hearty thanks to those who have helped maintain and keep the
wiki clean & useful.

Regards,

-- Jason

-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

[PyMOL] RE. how to color inner and outer surface of helix

[Andrew W. <sen...@gm...>]

try this:
set cartoon_highlight_color=3D$COLOR

where $COLOR is the color of choice

Andrew Wollacott, PhD
University of Washington


On 12/11/05, pym...@li...
<pym...@li...> wrote:
> Send PyMOL-users mailing list submissions to
>         pym...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
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>
> Today's Topics:
>
>    1. how to color inner and outer surface of helix (Mayer, Mark (NIH/NIC=
HD) [E])
>
> --__--__--
>
> Message: 1
> Date: Sun, 11 Dec 2005 11:41:52 -0500
> From: "Mayer, Mark \(NIH/NICHD\) [E]" <ma...@ma...>
> To: <pym...@li...>
> Subject: [PyMOL] how to color inner and outer surface of helix
>
> Hello,
>
> I'd like to color the inner and outer surface of a helix cartoon =3D
> differently and have
> forgotten how to do this. Wiki and list seaches came up empty.
>
> Thanks
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest
>

[PyMOL] how to color inner and outer surface of helix

[Mayer, M. \(NIH/NICHD\) [E] <ma...@ma...>]

Hello,

I'd like to color the inner and outer surface of a helix cartoon =
differently and have
forgotten how to do this. Wiki and list seaches came up empty.

Thanks

[PyMOL] RE: ATI as a substitute to nVIDIA

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

John & Alain,

I am not sure John really intended to cross-post that message, but now
that the damage is done, I'll take it one step further:  I believe the
problem is our sacred open-source cow Linux, or rather that nasty
amalgamation of diverse hardware, operating systems, and drivers
collectively known as the Linux "workstation".

Both major graphics vendors are reasonably committed to supporting
OpenGL on Linux given the limited size of this market as compared to
Windows 3D gaming.  But in practice, both are overwhelmed by the
staggering heterogenaiety that exists.  In my view, the task of
supporting so many different configurations is fundamentally
intractable, and that's why they both fail.  Linux is a multitude of
moving targets, and as a result, OpenGL on Linux often just doesn't work
right -- it may be no one's fault really, but there is simply no one
single party who could reasonably be expected to make Linux OpenGL work
well.  OpenGL is far too complex and demanding for the Linux "state of
the art" -- Linux is still too immature a platform to rely upon for
this.=20

Case in point:  My main development system is a Sun nVidia AMD 64-bit
Linux RedHat workstation that STILL, 11 months after purchase, cannot
run PyMOL and other 64-bit molecular graphics software without freezing
up periodically and exhibiting other major OpenGL glitches.  Nothing has
worked to solve this problem short of rewriting PyMOL's internal
rendering loops in order to pass data at a snail's pace.   Who can I
blame?  nVidia?  RedHat?  Sun?  Linux kernel developers?  AMD?  John or
myself?  No one is accountable, and as a company, we're out $5k USD plus
many hours of grief for a high-end workstation that just doesn't work.
Such stories are far too common with Linux OpenGL.  It just doesn't work
*every* time like it should.  Thus, people cannot expect to rely upon
Linux for visualization infrastructure without performing rigourous
validation prior to purchase and deployment, and again before all
subsequent upgrades.  Do people really want to endure such hassles?

That is precisely why I am so pumped about Macs -- modern Mac OS X
workstations have virtually all the advantages of Linux with almost none
of the drawbacks.  In my view, any cost premium for Apple is more than
made up for in terms of time saved NOT troubleshooting Linux.  Apple
does the OpenGL validation work for us, and they have a cracker-jack
team of experts standing behind their drivers (which they work closely
with ATI & nVidia to maintain & optimize).  Visualization on Mac OS X
just works, and nowadays it works even in windowed stereo 3D!  Apple is
a responsibility party, and they do care specifically about the needs of
science <http://www.apple.com/science/>.

While Linux is great for compute clusters and web servers, it just
plain-old stinks for visualization.  With Mac OS X proven, capable, and
mature, can anyone nowadays justify the risks and complications of using
Linux for visualization?  Apple already has crazy-fast high-end graphics
workstations <http://www.apple.com/powermac/graphics.html> and we all
expect them to soon release some fast Intel-based portable options as
well. =20

To avoid Linux headaches -- my brutually honest advice is to buy Macs
instead.  It's just that simple.
   =20
Cheers,
Warren

PS.  Alain, I am sorry the above comments do not help your current
situation.  For companies with ~50 deployed Linux systems, I really have
no other advice other than "good luck" -- we feel your pain. =20

John & I will continue to do our best, but the grief you are
experiencing is beyond our ability to fix.  With Linux, you just have to
keep trying different configurations one after the other until you find
one that works.  And once you find such a configuration, don't dare
change anything (driver, OS, or hardware) until you absolutely have to!
=20
--
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: John Stone [mailto:jo...@ks...]=20
> Sent: Thursday, December 08, 2005 11:42 AM
> To: ala...@no...
> Cc: vm...@ks...; in...@de...
> Subject: Re: ATI as a substitute to nVIDIA
>=20
>=20
> Alain,
>   The brutally honest truth (which I find hard to say on a=20
> public mailing list, but am willing to say in private email)=20
> is that ATI has terrible Linux drivers, and in my experience=20
> thus far, the open source ATI drivers have even more problems=20
> than the commercial ones based on the emails I've gotten from=20
> users of both driver sets.
>=20
> Both Warren and I put in a lot of effort making PyMol and VMD=20
> run well on all of the platforms we support, despite the=20
> large number of bugs in the video drivers people are using. =20
> Between ATI and NVidia, ATI is by far the worst offender in=20
> my experience.  I've now got a new VMD build that avoids 99%=20
> of the ATI problems, but it is only after having VMD disable=20
> the majority of OpenGL features that trigger problems on=20
> these ATI cards, when it finds that it is running on an ATI card.
> Warren and I both have code in PyMol and VMD to sidestep as=20
> many of these problems as we can, but there's a limit to the=20
> amount of time we can spend on this sort of thing, and so=20
> sometimes when ATI and NVidia release a new driver, they=20
> break something new and different, and it takes us a while to=20
> catch up with these workarounds.  On Linux, NVidia is still=20
> the best choice out there as far as I can tell, but they too=20
> have problems here and there.  On Windows I would actually=20
> recommend going with 3DLabs, as they have the most bug-free=20
> video drivers I've tested to date. =20
>=20
> You'll find that VMD and PyMol are both much more demanding=20
> of the video board that many other applications are.  Both=20
> programs use a large percentage of the available OpenGL=20
> functionality, much more than most games or screen savers do.=20
>  Their use of much of what OpenGL has to offer makes both=20
> programs very fast and powerful on machines with properly=20
> functioning video drivers, but it is this very same expansive=20
> use of OpenGL that makes our programs vulnerable to a larger=20
> number of bugs in the video drivers.  This is indeed the very=20
> reason that I added the OpenGL feature exclusion tests into=20
> VMD to allow the end-user to prevent VMD from using broken=20
> OpenGL features when the vendors release a buggy driver. =20
>=20
> These things go in cycles.  At present ATI and NVidia are=20
> both fairly buggy compared to the stability of the old Sun=20
> and SGI workstations.  In a few years time I hope that they=20
> will be as stable as the workstations from the commercial=20
> vendors were in years past.  If stability doesn't eventually=20
> improve, Warren and I may have to become more conservative in=20
> our use of new OpenGL features as the video driver bugs=20
> constitute a large percentage of the bug reports we both get.=20
>  That's certainly true in my case.
>=20
> Anyway, if you have ATI cards and you're still having any=20
> trouble with VMD, let me know and I can tell you how to work=20
> around the bugs in their video drivers.
>=20
>   John
>=20
>=20
> On Thu, Dec 08, 2005 at 03:47:43PM +0100,=20
> ala...@no... wrote:
> >=20
> > Dear Warren and John,
> >=20
> > We have a substantial park of Linux laptops and workstations (all=20
> > RHELWS 3.x, kernel 2.4.20's), and we are trying to identify some=20
> > alternatives to nVIDIA graphics board (to see what others=20
> are worth,=20
> > to see if some of the freeze problems we have with other=20
> applications=20
> > vanish, etc ... all in all to avoid being bound to them for=20
> the rest of our life).
> >=20
> > We have spent some time with an ATI FireGL V5100 (on an HP=20
> xw8200 box)=20
> > and we notice that
> >=20
> > ::: with driver 8.19.10 :::
> > VMD 1.8.2 or 1.8.4a22 the drawing of the scene is highly=20
> perturbed for=20
> > certain size of the main window - as if the same molecule was drawn=20
> > several times and stacked on each others at different=20
> viewing angles - . This of course once
> >      setenv VMD_EXCL_GL_EXTENSIONS GL_ARB_shader_objects is set as=20
> > recommended at :
> >      http://ati.cchtml.com/show_bug.cgi?id=3D123
> >      http://www.ks.uiuc.edu/Research/vmd/allversions/vmd_bugs.html
> > PyMOL 0.97, 0.98rc3, 0.99b27 sometimes crashes at startup=20
> but not always.
> > Once launched it is quite stable but we had to set=20
> BackingStore=3DOn in=20
> > X.org to avoid a black main window after=20
> molecular-manipulation (rot.trans.) and "ray".
> >=20
> > ::: with driver 8.18.8 :::
> > for both versions of VMD, we still need to set=20
> VMD_EXCL_GL_EXTENSIONS.
> > and the problem after main-window-resize stays.
> > PyMOL (all three versions) are quite unstable. I have never=20
> seen so many crashes.
> > especially after a "show surface", it is relatively easy,=20
> though not=20
> > reproducible at will, to crash it.
> >=20
> >=20
> > Given the fact that on our current nVIDIA FX1100, FX3000,=20
> FX3400 (we=20
> > have around fifty of them), once we got the "adequate"=20
> driver (mostly=20
> > of the 6xxx serie) VMD, PyMOL and many other applications=20
> > (Schrodinger/Maestro, Sybyl/Tripos, MOE, Moloc, Wit!P, O, Coot,=20
> > MOLMOL) are running very well and are quite stable, I am=20
> wondering a=20
> > bit about ATI. Note that left apart VMD and PyMOL those 'other=20
> > applications' are stable on the FireGL (either 8.19.10 or=20
> 8.18.8) - which comes rather as a shock to me. Hence this mail.
> >=20
> > Do you have good experience with ATI ? Could you recommend=20
> them for production ?
> > Do you think it's a dead end and shall we give up ?
> > On the PyMOL'wiki I found no mention of ATI - nVIDIA only.
> > I read that ATI driver for Linux is (almost) available in=20
> source-code=20
> > form. Which would be a good point in their favor. But after=20
> these troubles, I am wondering a bit.
> >=20
> > Any feedback is welcome and appreciated, Best, Alain Dietrich.
> >=20
>=20
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics=20
> Beckman Institute for Advanced Science and Technology=20
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: jo...@ks...                 Phone: 217-244-3349
>   WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>=20
>=20
>=20
>=20

[PyMOL] Hidden residue selection

[S. F. Y. <SY...@gn...>]

Hi,

When I select a residue that is shown as stick, the usual magenta dots
that highlight the residue seem to be hidden behind the stick rendering
and are not visible.  It is however okay when the residues are shown as
lines.  The latest beta version of PyMOL is used.

Also, just a suggestion, is it possible to only highlight the atoms that
are visible on selection in the case when the hydrogen atoms are hidden?
It really obscures the view with those extra dots.

Thanks,
Frank

Re: [PyMOL] label alternate conformations

[Seth H. <se...@gm...>]

Hi Bob,
Good to hear from you.

I didn't know about "alt" as a selection, so in the end that gave the
answer... Your example, which I find quite clever, didn't exactly match my
goal, though, so just to clarify:  Rather than distinguishing residues with
alternate conformations from those "normal" ones without, I wanted to have
the labels distinguish alternate conformer A from B and so on within a give=
n
residue. Since there was this backtick A or B at the end of the atom name i=
n
the right-click drop down menu I expected it would be somehow accessible vi=
a
command line in the label command. But "name" didn't do it. But of course,
using your "alt" selection I could do:
label alt a, "A"
label alt b, "B"
or indeed color all B conformations pink with:
color pink, alt b

And after realizing this, I just tried:

label myprotein, alt

which by its simplicity is obviously something I might have tried earlier.
Elegantly, as most residues don't have any "alt" conformation, it has the
nice side effect that labels only show up for those with alternate
conformations as well!

Thanks for the tip!
Seth

(By the way, neither the pymol help nor the wiki include "alt" as "symbols
defined in the name space" which currently includes things like "name, resn=
,
resi, b, q, segi, type, formal_charge, partial_charge, numeric_type,
text_type).  I guess that means I should learn to wiki it up.

On 12/7/05, Robert Immormino <imm...@gm...> wrote:
>
> This series of commands seems to do the job although a little sloppy.
>
> label alt a+"", "A%s-%s" % (resn, resi)
> label alt b+"", "B%s-%s" % (resn, resi)
> hide labels, alt ""
>
> Cheers,
>
> -bob
>
> On 12/7/05, Seth Harris <se...@gm...> wrote:
> >
> > Hi,
> >
> > I'm writing a small script to visit alternate conformations, stepping
> > through each as a frame in a movie with the cursor keys. I'd like to la=
bel
> > them to distinguish the alternates so I can see which I'd like to keep =
or
> > not, but:
> >
> > label alternates, name
> >
> > only displays the atom name without the pertinent `A or `B that the
> > right mouse click menu includes.
> >
> > Is there a way to show this information with the label command or other
> > means?
> >
> > Thanks,
> > Seth
> >
> > p.s. Those extra "3D" and other superfluous characters show up for me a=
s
> > well receiving the pymol list as a digest on gmail based web. I don't k=
now
> > if it's a result of the "digestion" process, but it seems like "=3D" si=
gns and
> > other non-alpha characters are associated with these burps of indigesti=
on,
> > invariably followed by 2D or 3D or such. I've kind of learned to ignore
> > them, but obviously they can cause some confusion and are at least mino=
rly
> > amusing when they reappear like some "who's on first" miscommunication =
as
> > warren's advice mention there should be no "3D" just the number "10" li=
ke
> > this, and then it proceeded to again display the 3D!! Perhaps the Diges=
t is
> > the culprit and could be treated? It also displays HTML as full text wi=
th
> > tags and all that garbage, by the way.
> >
> > >>>quote:
> > """I'm not sure where that "3D10" is coming from -- it should simply be
> > the
> > number 10:
> >
> > alter all, b=3D3D10
> > """
> > (!)
> > map_new can take a selection as its fourth argument, so you could
> >
>
>

Re: [PyMOL] label alternate conformations

[Robert I. <imm...@gm...>]

This series of commands seems to do the job although a little sloppy.

label alt a+"", "A%s-%s" % (resn, resi)
label alt b+"", "B%s-%s" % (resn, resi)
hide labels, alt ""

Cheers,

-bob

On 12/7/05, Seth Harris <se...@gm...> wrote:
>
> Hi,
>
> I'm writing a small script to visit alternate conformations, stepping
> through each as a frame in a movie with the cursor keys. I'd like to labe=
l
> them to distinguish the alternates so I can see which I'd like to keep or
> not, but:
>
> label alternates, name
>
> only displays the atom name without the pertinent `A or `B that the right
> mouse click menu includes.
>
> Is there a way to show this information with the label command or other
> means?
>
> Thanks,
> Seth
>
> p.s. Those extra "3D" and other superfluous characters show up for me as
> well receiving the pymol list as a digest on gmail based web. I don't kno=
w
> if it's a result of the "digestion" process, but it seems like "=3D" sign=
s and
> other non-alpha characters are associated with these burps of indigestion=
,
> invariably followed by 2D or 3D or such. I've kind of learned to ignore
> them, but obviously they can cause some confusion and are at least minorl=
y
> amusing when they reappear like some "who's on first" miscommunication as
> warren's advice mention there should be no "3D" just the number "10" like
> this, and then it proceeded to again display the 3D!! Perhaps the Digest =
is
> the culprit and could be treated? It also displays HTML as full text with
> tags and all that garbage, by the way.
>
> >>>quote:
> """I'm not sure where that "3D10" is coming from -- it should simply be
> the
> number 10:
>
> alter all, b=3D3D10
> """
> (!)
> map_new can take a selection as its fourth argument, so you could
>

[PyMOL] label alternate conformations

[Seth H. <se...@gm...>]

Hi,

I'm writing a small script to visit alternate conformations, stepping
through each as a frame in a movie with the cursor keys. I'd like to label
them to distinguish the alternates so I can see which I'd like to keep or
not, but:

label alternates, name

only displays the atom name without the pertinent `A or `B that the right
mouse click menu includes.

Is there a way to show this information with the label command or other
means?

Thanks,
Seth

p.s. Those extra "3D" and other superfluous characters show up for me as
well receiving the pymol list as a digest on gmail based web. I don't know
if it's a result of the "digestion" process, but it seems like "=3D" signs =
and
other non-alpha characters are associated with these burps of indigestion,
invariably followed by 2D or 3D or such. I've kind of learned to ignore
them, but obviously they can cause some confusion and are at least minorly
amusing when they reappear like some "who's on first" miscommunication as
warren's advice mention there should be no "3D" just the number "10" like
this, and then it proceeded to again display the 3D!! Perhaps the Digest is
the culprit and could be treated? It also displays HTML as full text with
tags and all that garbage, by the way.

>>>quote:
"""I'm not sure where that "3D10" is coming from -- it should simply be the
number 10:

alter all, b=3D3D10
"""
(!)
map_new can take a selection as its fourth argument, so you could

[PyMOL] .psw in Powerpoint for Mac

[David B. <dav...@ca...>]

Hi everyone,

I saw a friend give a presentation the other day and she embedded pymol into
powerpoint using a .psw file... This was a really great way of showing off
the structure and needless to say, I want to do it too... She has a PC, I'm
using a Mac. I'm having problems creating a working hyperlink to a .psw file
in mac powerpoint. I realise this is probably a powerpoint problem and _not_
a pymol one, but this seemed like the best place to post.

I'm using pymol 0.98 x11 hybrid, running under mac 10.3.9...

I create my .psw file with suitable scenes to run between, and create a
hyperlink in powerpoint, powerpoint can't figure open the file... Where am I
going wrong... 

I'm sure this is really simple.. But I can figure it out.

Cheers,

Dave

-- 
***************************************************************
Dr David Briggs                |
Structural Biology Lab (309)   | Tel : (+44)(0)20 7269 3360
Cancer Research UK             |
44 Lincoln's Inn Fields        |
Holborn                        |
London                         |
UK                             |
WC2A 3PX                       |
****************************************************************

[PyMOL] OT: quoted-printable encoding, was EMizing an xray structure

[D. J. A. <de...@ia...>]

On Thu, Dec 01, 2005 at 01:36:08PM -0800, Warren DeLano wrote:
  and before that, Sarina had noted:

> >    File "<string>", line 1
> >      b=3D10
> >          ^
> > SyntaxError: unexpected EOF while parsing
> > Alter-Error: Aborting on error. Assignment may be incomplete.
> > Alter: modified 0 atoms.
> > 

> Sarina,
> 
> I'm not sure where that "3D10" is coming from -- it should simply be the
> number 10:
> 
> alter all, b=10


Most likely a mismatch between the two mail programs--yours and
Sarina's--in the way they handle "quoted-printable" content
transfer encoding (see the headers of the email messages).

Some displays of quoted-printable content seem to use "=" as
some kind of escape character. Therefore, a literal "=" needs to
be escaped itself.  As it happens "3D" is the hexadecimal for an
ASCII "=".  So =3D is the quoted-printable representation of the
equals sign in your original.

-- 
Joe

[PyMOL] pymol beta31 segfault with nvidia

[Dmitriy <br...@ma...>]

Hello

I've tried latest 0.99beta31 from cvs. It does segmentation fault on my linux 
Mandriva 2006 with nvidia 81.74 drivers.

 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: GeForce3/AGP/SSE/3DNOW!
  GL_VERSION: 1.5.5 NVIDIA 81.74
zsh: segmentation fault 

version 0.99beta29 works fine with the same driver.
tried on Fedora Core 4 with Mesa 6.2.1, beta31 works fine.

so it seems to be a problem with nvidia driver. not sure about 7676.

  Thanks
     Dmitriy

[PyMOL] cvs version of pymol does not run

[Dmitriy <br...@ma...>]

Hello

I've downloaded a new version from cvs. It compiles, but do not run.

$ python /home/dim/tmp/pymol/lib/python2.4/site-packages/pymol/__init__.py
Traceback (most recent call last):
  File "/home/dim/tmp/pymol/lib/python2.4/site-packages/pymol/__init__.py", 
line 341, in ?
    import _cmd
ImportError: /home/dim/tmp/pymol/lib/python2.4/site-packages/pymol/_cmd.so: 
undefined symbol: TypeInit

What is this "TypeInit" ?
beta29 compiles and runs on Mandriva 2006 and Fedora Core 4.
Latest from cvs do not.

Does anyone have the same problem?
Thanks
   Dmitriy

RE: [PyMOL] moving molecules

[<gre...@un...>]

Dear Milton,

This question has been answered several times; please search the =
archives of
the PyMOL mailing list
(http://sourceforge.net/search/index.php?type_of_search=3Dmlists&group_id=
=3D4546
&forum_id=3D60) or have a look at pymolwiki
(http://www.pymolwiki.org/index.php/Category:FAQ)

Regards,

Gr=E9gori



-----Original Message-----
From: pym...@li...
[mailto:pym...@li...] On Behalf Of Milton H.
Werner, Ph.D.
Sent: vendredi, 2. d=E9cembre 2005 23:52
To: <PyM...@li...> =
<PyM...@li...>
Subject: [PyMOL] moving molecules

Can someone teach me how to move molecules with a mouse (or mac=20
trakpad) when a file has several different proteins?  i.e. I'd like to=20
move just one of them by hand in an interactive way.

Thanks,

MIlton Werner
--
Associate Professor and Head, Laboratory of Molecular Biophysics
The Rockefeller University
1230 York Avenue, Box 42
New York, NY 10021

212/327-7221
212/327-7222 FAX
917/494-0831 cell
mw...@po...
www.rockefeller.edu/labheads/werner/index.php

[PyMOL] moving molecules

[Milton H. W. Ph.D. <mw...@po...>]

Can someone teach me how to move molecules with a mouse (or mac 
trakpad) when a file has several different proteins?  i.e. I'd like to 
move just one of them by hand in an interactive way.

Thanks,

MIlton Werner
--
Associate Professor and Head, Laboratory of Molecular Biophysics
The Rockefeller University
1230 York Avenue, Box 42
New York, NY 10021

212/327-7221
212/327-7222 FAX
917/494-0831 cell
mw...@po...
www.rockefeller.edu/labheads/werner/index.php

[PyMOL] Coordinate file extensions

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

In MacPyMOL, if one executes "open file" from the file menu or by keystroke,
the open file dialog only permits loading of files such as "*.pdb". Many
files are automatically named "*.ent" and can't be opened this way.
Obviously there are workarounds but is there a way to change the behavior of
this dialog?

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...

Re: [PyMOL] Setting sphere_transparency for individual selections

[<Mat...@im...>]

pym...@li... wrote on 12/01/2005 05:46:26 PM:

>
> Is it possible to change the sphere_transparency setting for individual
atoms?
>
> Andrew Wollacott
>
>

It appears not, but you can change this setting for individual objects.
Create a new object containing only the atoms of interest and set sphere
transparency on it, like so:

PyMOL> load test.pdb
PyMOL> create foo, HETATM and name COO
PyMOL> set sphere_transparency,0.4,foo

- Matt


--
Matthew Franklin                     phone:(917)606-4116
Senior Scientist, ImClone Systems      fax:(212)645-2054
180 Varick Street, 6th floor
New York, NY 10014


Confidentiality Note:  This e-mail, and any attachment to it, contains
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is not the intended recipient, or the employee or agent responsible for
delivering it to the intended recipient, you are hereby notified that
reading it is strictly prohibited.  If you have received this e-mail in
error, please immediately return it to the sender and delete it from your
system.  Thank you.

[PyMOL] Setting sphere_transparency for individual selections

[Andrew W. <sen...@gm...>]

I've been trying to set the sphere_transparency for selections on my
protein, and I've tried the following:

PyMOL> load test.pdb
PyMOL> show spheres, HETATM

I've tried the following to change sphere_transparencies:
PyMOL> set sphere_transparency,0.4,name COO
PyMOL > cmd.set("sphere_transparency", 0.4, selection=3D"name COO")

neither of these work, as the sphere_transparency gets applied to ALL spher=
es

I know my selection is fine, because I can change the color of this
individual atom by typing:

PyMOL: color red, name COO

Is it possible to change the sphere_transparency setting for individual ato=
ms?

Andrew Wollacott