pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Possible to select the nth residue?

[Dan K. <dw...@ma...>]

Sorry the below actually won't work, you'll need something more...

nth_residue = 3
previous = -1
cur_res  = 0
nth_resi = 0
for at in cmd.get_model("molecule1 and chainA").atom:
    if (at.resi != previous):
         cur_res++

    if (cur_res == nth_residue):
         nth_resi = at.resi
         break

# Now do the selection...
cmd.select("myselection", "molecule1 and chain A and resi %s" % (nth_resi))


There might be a cleaner way, but something along these lines should work.

Sorry for the first email,
Dan

This looks better. However you'll want to put it in a script, wrap it 
with a function, etc...  I haven't test the above though.


Dan Kulp wrote:
> I just needed to do this and this was my solution
>
> NTH_RESIDUE=3
> cmd.select("myselection", "molecule1 and chain A and resi %s" % 
> (cmd.get_model("molecule1 and chain A").atom[NTH_RESIDUE]))
>
> will create a selection named myselection and contain only the 
> NTH_RESIDUE of molecule1 and chain  A.
>
> Hope this helps,
> ~Dan
>
> Alex Luso wrote:
>>   One more question.
>>
>>   Someone asked me this: is it possible in Pymol to select
>> the nth (e.g. the 3rd) residue in a molecule/chain without
>> knowing the pdb residue # itself?
>>
>>   -Alex
>>
>> __________________________________________________
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>>
>>   
>
>


-- 
   Dan Kulp
   Biophysics Graduate Student @ UPenn
   dw...@ma...
   http://dwkulp.homelinux.net/tiki/tiki-index.php
--

Re: [PyMOL] Possible to select the nth residue?

[Dan K. <dw...@ma...>]

I just needed to do this and this was my solution

NTH_RESIDUE=3
cmd.select("myselection", "molecule1 and chain A and resi %s" % 
(cmd.get_model("molecule1 and chain A").atom[NTH_RESIDUE]))

will create a selection named myselection and contain only the 
NTH_RESIDUE of molecule1 and chain  A.

Hope this helps,
~Dan

Alex Luso wrote:
>   One more question.
>
>   Someone asked me this: is it possible in Pymol to select
> the nth (e.g. the 3rd) residue in a molecule/chain without
> knowing the pdb residue # itself?
>
>   -Alex
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around 
> http://mail.yahoo.com 
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>   


-- 
   Dan Kulp
   Biophysics Graduate Student @ UPenn
   dw...@ma...
   http://dwkulp.homelinux.net/tiki/tiki-index.php
--

[PyMOL] Possible to select the nth residue?

[Alex L. <tap...@ya...>]

  One more question.

  Someone asked me this: is it possible in Pymol to select
the nth (e.g. the 3rd) residue in a molecule/chain without
knowing the pdb residue # itself?

  -Alex

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

[PyMOL] Labels throw shadows in Ray traced images - possible to turn off?

[Alex L. <tap...@ya...>]

  Hi,

  I noticed that Ray traced output of images containing
text labels will show the shadows thrown by and on these
labels. This is a nice feature but is there also an easy
way to turn this off (i.e. selectively turn off shadows
from/on text while mantaining global shadows)?

  Thanks,
  -Alex

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

RE: [PyMOL] Quadro-based 3D Mac Feedback

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

HI Tim!

Thank you for making the pro-Linux case.

> I thought the mailing list was for discussions regarding the=20
> usage of a program, not a forum for polemicism.

Indeed it is, and thank you also for that reminder -- let's all try to
stick to the real-world practical issues surrounding use of PyMOL on
each platform, and set aside the polemicism.

> Try telling your average OS X user to install coot (and don't=20

PyMOL on Mac OS X is simply drag & drop or download & double-click.  I
don't think it is fair to criticize Coot on the pymol list, so please
email Paul directly with concerns regarding his installation process.

> And for the record, setting up the nvidia drivers in linux=20
> (fedora, in my case) is three lines:
>=20
> rpm -ivh http://rpm.livna.org/livna-release4.rpm
> rpm --import http://rpm.livna.org/RPM-LIVNA-GPG-KEY
> yum install kernel-module-nvidia-$(uname -r)
>=20
> Then just restart X.

Even if it were just this simple on every common Linux variant, and even
if this worked for every common graphics card and CPU archicture -- and
it doesn't -- it still seems unreasonable to me to expect PyMOL Users to
have to muck about with "root" commands like the above just to able to
do OpenGL visualization. =20

> Aren't you just saying Apple's binary only drivers are better=20
> than NVidia's linux-based binary only driver? =20

Yes, with respect to PyMOL, the nVidia and ATI drivers in Mac OS X are
better in terms of performance and stability, and there is no end-user
driver installation requirement.

> If thats the logic, can't I=20
> say "since the NVidia drivers for windows are more stable=20
> than the NVidia drivers for linux (SLI support, HDTV=20
> decompression, etc), everyone should go out and buy windows=20
> since its gets more support from vendors."?

You can certainly make that argument up through Windows XP -- it has
been a strong reason for PyMOL Users to use Windows, and many have
(including myself, when on the road).  However, with Vista, Microsoft is
discouraging use of OpenGL by barely allowing it to run within their new
interface, so Apple now ends up being the vendor providing the best
OpenGL support.

> Its that linux users don't want to
> ***depend*** on anyone.  Not Apple, Microsoft or NVidia - I=20
> want, as they would say on the twilight zone, control over=20
> the horizontal as well as the vertical (I own the computer,=20
> after all).  From what I understand, its the whole reason=20
> linux was written in the first place.

To be consistent, PyMOL users who insist upon avoiding software
dependence most limit themselves to using open-source PyMOL with
open-source OpenGL renderers.  If one is willing to compromise one's
principles by using proprietary software drivers in the interests of
practicality, then why not simply run our precompiled PyMOL on a
proprietary Unix with well-supported OpenGL drivers? =20

> How is that not saying "Go Mac!"?

Yes, "Go Mac!" but with eyes open and with reasonable reservations.  New
releases from any vendor (or open-source project) always have some
issues, so do your research.  Try before you buy, and listen closely to
the experiences of your peers before making a heavy commitment.  Note
that while DeLano Scientific strongly favors Mac OS X as a visualization
platform, our views are currently in the minority. =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: Tim Fenn [mailto:fe...@st...]=20
> Sent: Thursday, January 19, 2006 5:06 AM
> To: Warren DeLano
> Cc: pym...@li...
> Subject: Re: [PyMOL] Quadro-based 3D Mac Feedback
>=20
> On Mon, Jan 16, 2006 at 04:34:44PM -0800, Warren DeLano wrote:
> >=20
> > Through extensive travel, contacts, and personal=20
> experiences over past=20
> > few years, I have come to understand just how poorly Linux=20
> is doing at=20
> > meeting the needs of the scientific visualization=20
> community.  Despite=20
> > my unabashed pro-open-source stance, it would be unethical=20
> for me to=20
> > continue advocating the adoption of Linux as the general=20
> solution for=20
> > UNIX OpenGL visualization when in practice it is only effective for=20
> > those having strong system administration skills.
> >=20
>=20
> Eh?  OS X is that much better in regards to system administration?
> Try telling your average OS X user to install coot (and don't=20
> tell him what subversion of OS X he's using), and feel free=20
> to post back how simple it was for him/her.
>=20
> And for the record, setting up the nvidia drivers in linux=20
> (fedora, in my case) is three lines:
>=20
> rpm -ivh http://rpm.livna.org/livna-release4.rpm
> rpm --import http://rpm.livna.org/RPM-LIVNA-GPG-KEY
> yum install kernel-module-nvidia-$(uname -r)
>=20
> Then just restart X.
>=20
> Or you could read any of the 800,000 pages that come up when=20
> googling "linux nvidia howto."
>=20
> > This is primarily due to incessant complications with proprietary=20
> > OpenGL drivers.  In my considered opinion, resolution of=20
> these issues=20
> > is beyond the reach of the open-source community, as no=20
> Linux vendor=20
> > has sufficient clout or motivation to effect the necessary and=20
> > permanent changes (i.e. shipping validated *proprietary* graphics=20
> > drivers with all common distributions of Linux).  In this case, the=20
> > open-source community is (correctly?) putting free software=20
> ideology=20
> > (free-software/open-source drivers!) ahead of users' needs=20
> to simply=20
> > get work done now.
>=20
> Its not a motivation issue.  Its that linux users don't want to
> ***depend*** on anyone.  Not Apple, Microsoft or NVidia - I=20
> want, as they would say on the twilight zone, control over=20
> the horizontal as well as the vertical (I own the computer,=20
> after all).  From what I understand, its the whole reason=20
> linux was written in the first place.
>=20
> > In time, this approach may yield the desired end-result, but=20
> > scientists, doctors, and engineers need a working solution today.
> >=20
> > Caught in the middle of all this, our obligation as a vendor is to=20
> > identify, advance, and promote solution which actually do=20
> work for our=20
> > customers today or very soon and not at some unspecified=20
> point in the=20
> > future.  We need an alternative answer to OpenGL under=20
> Linux, and we=20
> > obviously believe that answer lies with Mac OS X.
> >
> <snip>
> >
> > Apple, in contrast, is fully committed to OpenGL -- an open=20
> standard=20
> > that runs on any platform.  Furthermore, by switching to Intel=20
> > processors, Apple customers will now have even greater=20
> choice to run=20
> > one, two, or even three major operating systems on Apple hardware.
> > Simply put, Apple "gets it" when it comes to consumer=20
> choice, and over=20
> > the past several years they have made it a practice of synergizing=20
> > with Free Software and Open Source efforts (GCC, Darwin,=20
> KHTML, PyMOL,=20
> > etc).
>=20
> If the mailing list is meant as an infomercial, I'll start=20
> sending it to my spam folder.
>=20
> > Steve Jobs understands that open-source is transforming the=20
> software=20
> > industry, but he also apparently grasps the new role that=20
> proprietary=20
> > solution vendors must adopt in delivering extra value on=20
> top of what=20
> > is already both ubiquitous and free.  That, in a nutshell, is the=20
> > future of the software industry.  Proprietary and open-source=20
> > solutions will co-exist and complement one another to the=20
> benefit of=20
> > consumers and developers alike.
> >=20
>=20
> Aren't you just saying Apple's binary only drivers are better=20
> than NVidia's linux-based binary only driver?  The argument=20
> presented above is simply hyperbole based on nvidia chipset=20
> support from different vendors.  If thats the logic, can't I=20
> say "since the NVidia drivers for windows are more stable=20
> than the NVidia drivers for linux (SLI support, HDTV=20
> decompression, etc), everyone should go out and buy windows=20
> since its gets more support from vendors."?
>=20
> > > this blatant
> > > shilling contrasts jarringly with the open source context=20
> in which=20
> > > PyMOL is developed, distributed, and supported: PyMOL is=20
> attractive=20
> > > in part because it promises long-term, flexible access to=20
> the tools=20
> > > to do our work, without users falling into a vassal role with=20
> > > respect to one industry-dominant company.
> >
> > I apologize for excess enthusiasm -- it is perhaps an=20
> overreaction to=20
> > biased and premature dismissal of Mac OS X as a credible=20
> solution by=20
> > some members of the pharma/biotech IT & Informatics communities.
>=20
> I thought the mailing list was for discussions regarding the=20
> usage of a program, not a forum for polemicism.
>=20
> >=20
> > > Launching such a hyperbolic cheerleading campaign may belie the=20
> > > stability of the support one might expect from Apple for this=20
> > > technology, if one feels such campaigns are necessary to=20
> keep that=20
> > > support alive.
> >=20
> > But that is exactly my point:  If potential customers such=20
> as yourself=20
> > do not show strong interest in these systems through purchases or=20
> > communicate to Apple (directly or through us) why they may=20
> have missed=20
> > the mark, then Apple would be correct and justified in=20
> concluding that=20
> > we are uninterested in Mac OS X-based solutions for scientific=20
> > visualization.
> >=20
>=20
> or I could find a development community that *IS* its user=20
> base, and therefore doesn't require my input/money/praises in=20
> order to understand why its necessary to support poor little=20
> ol' me.  Which is linux/BSD!
>=20
> > So let me make clear:  We are not saying, "Go Mac!" blindly and=20
> > without reservations.
>=20
> But you said:
>=20
> On Thu, Dec 08, 2005 at 11:58:40PM -0800, Warren DeLano wrote:
> >
> > To avoid Linux headaches -- my brutually honest advice is=20
> to buy Macs=20
> > instead.  It's just that simple.
> >
>=20
> How is that not saying "Go Mac!"?
>=20
> Regards,
> Tim
>=20
> --
> ---------------------------------------------------------
>=20
>         Tim Fenn
>         fe...@st...
>         Stanford University, School of Medicine
>         James H. Clark Center
>         318 Campus Drive, Room E300
>         Stanford, CA  94305-5432
>         Phone:  (650) 736-1714
>         FAX:  (650) 736-1961
>=20
> ---------------------------------------------------------
>=20
>=20
> --
> ---------------------------------------------------------
>=20
>         Tim Fenn
>         fe...@st...
>         Stanford University, School of Medicine
>         James H. Clark Center
>         318 Campus Drive, Room E300
>         Stanford, CA  94305-5432
>         Phone:  (650) 736-1714
>         FAX:  (650) 736-1961
>=20
> ---------------------------------------------------------
>=20
>=20
>=20
>=20
>=20

Re: [PyMOL] selection disordered

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

pym...@li... wrote on 01/19/2006 06:55:11 AM:

> Hi there,
>
> i have the following problem: selecting all ca atoms in chain A of 1ao0
> the amino acids in the selection are disordered with respect to their
> occurrence in the protein.
>
(snip)
>
> So the 56th amino acid is BEFORE the first one. Whats going wrong?
>
>     Thanks:
>
>        Frank
>

Hi Frank -

Residue 56 in 1AO0 has occupancy 0 (in chains A and B).  I'm sure that's
causing a problem, but I don't know why it ends up at the front of the
list.  Residues 429-430 in chain B are also occupancy 0 - what do you see
if you run your script on chain B?

- Matt

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


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[PyMOL] reinitialize fails to clear PyMOL Viewer

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

Hi all,

I've run into a small glitch that I was wondering if anyone else had seen
(or knew of a way to fix).  At somewhat unpredicatable intervals, the
reinitialize command doesn't actually clear the viewer display (objects
show as deleted, but are still visible).

Any ideas?

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] selection disordered

[Frank D. <fra...@bi...>]

Hi there,

i have the following problem: selecting all ca atoms in chain A of 1ao0 
the amino acids in the selection are disordered with respect to their 
occurrence in the protein.

After loading the protein i tried the following:

    numbers=[]
    iterate (chain a)&(name ca),(numbers.append(resi))
    print numbers

And what i get is the following:

    ['56', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', 
'12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', '23', 
'24', '25', '26', '27','28', '29', '30', '31', '32', '33', '34', '35', 
'36', '37', '38', '39', '40', '41', '42', '43', '44', '45', '46', '47', 
'48', '49', '50', '51', '52', '53', '54', '55', '57', '58', '59', '60', 
'61', ...]

So the 56th amino acid is BEFORE the first one. Whats going wrong?

    Thanks:

       Frank

Re: [PyMOL] Quadro-based 3D Mac Feedback

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

On Mon, Jan 16, 2006 at 04:34:44PM -0800, Warren DeLano wrote:
> 
> Through extensive travel, contacts, and personal experiences over past
> few years, I have come to understand just how poorly Linux is doing at
> meeting the needs of the scientific visualization community.  Despite my
> unabashed pro-open-source stance, it would be unethical for me to
> continue advocating the adoption of Linux as the general solution for
> UNIX OpenGL visualization when in practice it is only effective for
> those having strong system administration skills.  
> 

Eh?  OS X is that much better in regards to system administration?
Try telling your average OS X user to install coot (and don't tell him
what subversion of OS X he's using), and feel free to post back how
simple it was for him/her.

And for the record, setting up the nvidia drivers in linux (fedora, in
my case) is three lines:

rpm -ivh http://rpm.livna.org/livna-release4.rpm
rpm --import http://rpm.livna.org/RPM-LIVNA-GPG-KEY
yum install kernel-module-nvidia-$(uname -r)

Then just restart X.

Or you could read any of the 800,000 pages that come up when googling
"linux nvidia howto."

> This is primarily due to incessant complications with proprietary OpenGL
> drivers.  In my considered opinion, resolution of these issues is beyond
> the reach of the open-source community, as no Linux vendor has
> sufficient clout or motivation to effect the necessary and permanent
> changes (i.e. shipping validated *proprietary* graphics drivers with all
> common distributions of Linux).  In this case, the open-source community
> is (correctly?) putting free software ideology
> (free-software/open-source drivers!) ahead of users' needs to simply get
> work done now.

Its not a motivation issue.  Its that linux users don't want to
***depend*** on anyone.  Not Apple, Microsoft or NVidia - I want, as
they would say on the twilight zone, control over the horizontal as
well as the vertical (I own the computer, after all).  From what I
understand, its the whole reason linux was written in the first place.

> In time, this approach may yield the desired end-result,
> but scientists, doctors, and engineers need a working solution today.
> 
> Caught in the middle of all this, our obligation as a vendor is to
> identify, advance, and promote solution which actually do work for our
> customers today or very soon and not at some unspecified point in the
> future.  We need an alternative answer to OpenGL under Linux, and we
> obviously believe that answer lies with Mac OS X.
>
<snip>
>
> Apple, in contrast, is fully committed to OpenGL -- an open standard
> that runs on any platform.  Furthermore, by switching to Intel
> processors, Apple customers will now have even greater choice to run
> one, two, or even three major operating systems on Apple hardware.
> Simply put, Apple "gets it" when it comes to consumer choice, and over
> the past several years they have made it a practice of synergizing with
> Free Software and Open Source efforts (GCC, Darwin, KHTML, PyMOL,
> etc).

If the mailing list is meant as an infomercial, I'll start sending it
to my spam folder.

> Steve Jobs understands that open-source is transforming the software
> industry, but he also apparently grasps the new role that proprietary
> solution vendors must adopt in delivering extra value on top of what is
> already both ubiquitous and free.  That, in a nutshell, is the future of
> the software industry.  Proprietary and open-source solutions will
> co-exist and complement one another to the benefit of consumers and
> developers alike.
> 

Aren't you just saying Apple's binary only drivers are better than
NVidia's linux-based binary only driver?  The argument presented above
is simply hyperbole based on nvidia chipset support from different
vendors.  If thats the logic, can't I say "since the NVidia drivers
for windows are more stable than the NVidia drivers for linux (SLI
support, HDTV decompression, etc), everyone should go out and buy
windows since its gets more support from vendors."?

> > this blatant
> > shilling contrasts jarringly with the open source context in
> > which PyMOL is developed, distributed, and supported: PyMOL
> > is attractive in part because it promises long-term, flexible
> > access to the tools to do our work, without users falling
> > into a vassal role with respect to one industry-dominant company.
>
> I apologize for excess enthusiasm -- it is perhaps an overreaction
> to biased and premature dismissal of Mac OS X as a credible solution
> by some members of the pharma/biotech IT & Informatics communities.

I thought the mailing list was for discussions regarding the usage of
a program, not a forum for polemicism.

> 
> > Launching such a hyperbolic cheerleading campaign may belie 
> > the stability of the support one might expect from Apple for 
> > this technology, if one feels such campaigns are necessary to 
> > keep that support alive.
> 
> But that is exactly my point:  If potential customers such as yourself
> do not show strong interest in these systems through purchases or
> communicate to Apple (directly or through us) why they may have missed
> the mark, then Apple would be correct and justified in concluding that
> we are uninterested in Mac OS X-based solutions for scientific
> visualization. 
> 

or I could find a development community that *IS* its user base, and
therefore doesn't require my input/money/praises in order to
understand why its necessary to support poor little ol' me.  Which is
linux/BSD!

> So let me make clear:  We are not saying, "Go Mac!" blindly and without
> reservations.

But you said:

On Thu, Dec 08, 2005 at 11:58:40PM -0800, Warren DeLano wrote:
>
> To avoid Linux headaches -- my brutually honest advice is to buy
> Macs instead.  It's just that simple.
>

How is that not saying "Go Mac!"?

Regards,
Tim

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

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

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


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

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

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

RE: [PyMOL] Super-smooth surfaces

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

Hi Stephen

I also use smooth surfaces - for visualizing results from small angle
xray scattering, which is a low resolution technique. I use:

set solvent_radius, 4  =20
alter my_protein, vdw=3D4=20
sort
show surface, my_protein

Maybe you can set solvent_radius a little bit higher, but not much, as
you will get "holes" in the surface like you see. You can adjust the
"blobbiness" by changing the vdw size.


Cheers

Esben


> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Stephen Graham
> Sent: 11. januar 2006 23:22
> To: pym...@li...
> Subject: [PyMOL] Super-smooth surfaces
>=20
>=20
> Hi there,
>=20
> I am making a figure in which I would like an extremely=20
> smooth molecular surface (I just want the protein as a blob=20
> with little to no definition of surface features).
>=20
> I tried setting the probe radius to a larger value:
>  set solvent_radius, 8
> but this gives rise to ugly artefacts on the surface=20
> ('triangles' of surface seem to be missing).  There seems to=20
> be a whole raft of different settings for fine-tuning=20
> surfaces (surface_carve_*, surface_trim_*, etc) but I am=20
> afraid I do not know what they do and have been unable to=20
> find documentation on them.
>=20
> How can I make a surface happy (fully connected) after having=20
> set the probe radius way up?
>=20
> Thanks,
>=20
> Stephen
>=20
> --
> Stephen Graham
> Crystallography Group
> School of Molecular and Microbial Biosciences
> University of Sydney
>=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!=20
> http://ads.osdn.com/?ad_idv37&alloc_id=16865> &op=3Dick
>=20
> _______________________________________________
>=20
> PyMOL-users mailing list
> PyM...@li...=20
> https://lists.sourceforge.net/lists/listinfo/p> ymol-users
>=20

[PyMOL] GUI output font size too small

[<bjo...@ka...>]

Hi,


How do I control the GUI output window font size? It is too small for my eyes on=20=
a 1600x1200 screen=2E I can change it manually to 12 points in the GUI window Set=
ting/Output size, but I can not find a=20=
command to do it for my =2Epymolrc! Preferably to more than 12 points as well=2E=2E=2E
I use 0=2E99beta33 on Linux and windows=2E


Thanks,


Bj=F6rn Kauppi

***************************************************************************
This e-mail may contain confidential information proprietary to Karo Bio AB
and is meant for the intended addressee(s) only=2E Any unauthorized review,
use, disclosure or distribution is prohibited=2E If you have received this
message in error, please advise the sender and delete the e-mail and any
attachments from your files=2E Thank you!
***************************************************************************

RE: [PyMOL] mac stereo questions

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

Hi Mark,

Unfortunately, the ESGI emitter only works with SGIs. For PCs and Macs
you'll need either an E2 emitter or you can switch over to using
NuVision 3D emitters and glasses, which are about 4X less expensive than
stereographics.

http://www.nuvision3d.com/the60gx.html

Also, once you have that emitter, you might want to try using the latest
MacPyMOL beta from http://delsci.com/beta  I'm planning on posting an
update within the next 48 hours.

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
> Dr. Mark Mayer
> Sent: Wednesday, January 18, 2006 11:56 AM
> To: pym...@li...
> Subject: [PyMOL] mac stereo questions
>=20
> Dear Warren and users,
>=20
> I'm in process of setting up a new G5 with stereographics=20
> card and cannot get PyMol (both MacPymol and the hybrid=20
> version) to work with quad buffered stereo. When I switch to=20
> stereo the display shows two objects in same pane, but there=20
> is no stereo effect. I've get setenv STEREO ON in my cshrc file.
>=20
> I'm using OS 10.4.4 and a rev M streographics ESGI emitter=20
> that I borrowed from an SGI. Noticably when I turn stereo on=20
> and off the emitter led does not light. The latest version of=20
> O does work in stereo on this system, albeit with a few=20
> oddities which might be hardware related. Do I need to do=20
> something else to get quad buffered stereo to work with=20
> PuMol? Is the SGI emitter  problem? I've contatced=20
> stereographics to ask about this but no response yet.
>=20
> Thanks
> --
> Mark Mayer Ph.D.
> LCMN NICHD NIH DHHS
> Bldg 35, Room 3B 1002 MSC 3712
> 35 Lincoln Drive
> Bethesda MD 20892 3712
> Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX=20
> 301-496-2396 Lab web site: http://mayerlab.nichd.nih.gov
>=20
> Send packages, Fedex and anything requiring a signature to:
>=20
> Bldg 35, Room 3B 1004
> 35 Lincoln Drive
> Bethesda MD 20892
>=20
>=20

[PyMOL] mac stereo questions

[Dr. M. M. <ma...@ma...>]

Dear Warren and users,

I'm in process of setting up a new G5 with stereographics card and 
cannot get PyMol (both MacPymol and the hybrid version) to work with 
quad buffered stereo. When I switch to stereo the display shows two 
objects in same pane, but there is no stereo effect. I've get setenv 
STEREO ON in my cshrc file.

I'm using OS 10.4.4 and a rev M streographics ESGI emitter that I 
borrowed from an SGI. Noticably when I turn stereo on and off the 
emitter led does not light. The latest version of O does work in 
stereo on this system, albeit with a few oddities which might be 
hardware related. Do I need to do something else to get quad buffered 
stereo to work with PuMol? Is the SGI emitter  problem? I've 
contatced stereographics to ask about this but no response yet.

Thanks
-- 
Mark Mayer Ph.D.
LCMN NICHD NIH DHHS
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://mayerlab.nichd.nih.gov

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

Re: [PyMOL] Bfactor

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

"...get at..."? "...display..."?

To access the B-factors, you can use "iterate" - as in "iterate resi 1,
print round(b, 2)". That will print out the b-factor for each atom in the
first residue.

gilleain torrance

On 1/16/06, Bingding Huang <bh...@bi...> wrote:
>
> How can I the Bfactor for each residue in pymol script?
>
> Bingding
>
>
>

RE: [PyMOL] Quadro-based 3D Mac Feedback

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

Joe,

Thank you for that candid and constructive criticism. =20

As a service-oriented company, our job is to advocate for and act in our
customer's interests.  When we encourage the adoption of one particular
solution over another, it is because we truly believe that our customers
will benefit from following our advice.

Through extensive travel, contacts, and personal experiences over past
few years, I have come to understand just how poorly Linux is doing at
meeting the needs of the scientific visualization community.  Despite my
unabashed pro-open-source stance, it would be unethical for me to
continue advocating the adoption of Linux as the general solution for
UNIX OpenGL visualization when in practice it is only effective for
those having strong system administration skills. =20

This is primarily due to incessant complications with proprietary OpenGL
drivers.  In my considered opinion, resolution of these issues is beyond
the reach of the open-source community, as no Linux vendor has
sufficient clout or motivation to effect the necessary and permanent
changes (i.e. shipping validated *proprietary* graphics drivers with all
common distributions of Linux).  In this case, the open-source community
is (correctly?) putting free software ideology
(free-software/open-source drivers!) ahead of users' needs to simply get
work done now.  In time, this approach may yield the desired end-result,
but scientists, doctors, and engineers need a working solution today.

Caught in the middle of all this, our obligation as a vendor is to
identify, advance, and promote solution which actually do work for our
customers today or very soon and not at some unspecified point in the
future.  We need an alternative answer to OpenGL under Linux, and we
obviously believe that answer lies with Mac OS X.

Up until now, another answer was Microsoft Windows.  However, Microsoft
has now made it crystal clear that Windows Vista will not support
current versions of OpenGL, and furthermore, that running older OpenGL
apps will compromise the quality of the Windows user interface
experience.  They are attempting to compel developers like us to adopt
their proprietary Direct 3D API, and trying to deny choice to users like
yourself.  This is simply outrageous and must be resisted.
<http://www.opengl.org/discussion_boards/cgi_directory/ultimatebb.cgi?ub
b=3Dget_topic;f=3D12;t=3D000001>

Apple, in contrast, is fully committed to OpenGL -- an open standard
that runs on any platform.  Furthermore, by switching to Intel
processors, Apple customers will now have even greater choice to run
one, two, or even three major operating systems on Apple hardware.
Simply put, Apple "gets it" when it comes to consumer choice, and over
the past several years they have made it a practice of synergizing with
Free Software and Open Source efforts (GCC, Darwin, KHTML, PyMOL, etc).
Steve Jobs understands that open-source is transforming the software
industry, but he also apparently grasps the new role that proprietary
solution vendors must adopt in delivering extra value on top of what is
already both ubiquitous and free.  That, in a nutshell, is the future of
the software industry.  Proprietary and open-source solutions will
co-exist and complement one another to the benefit of consumers and
developers alike.

> this blatant=20
> shilling contrasts jarringly with the open source context in=20
> which PyMOL is developed, distributed, and supported: PyMOL=20
> is attractive in part because it promises long-term, flexible=20
> access to the tools to do our work, without users falling=20
> into a vassal role with respect to one industry-dominant company.

I apologize for excess enthusiasm -- it is perhaps an overreaction to
biased and premature dismissal of Mac OS X as a credible solution by
some members of the pharma/biotech IT & Informatics communities. =20

> Launching such a hyperbolic cheerleading campaign may belie=20
> the stability of the support one might expect from Apple for=20
> this technology, if one feels such campaigns are necessary to=20
> keep that support alive.

But that is exactly my point:  If potential customers such as yourself
do not show strong interest in these systems through purchases or
communicate to Apple (directly or through us) why they may have missed
the mark, then Apple would be correct and justified in concluding that
we are uninterested in Mac OS X-based solutions for scientific
visualization.=20

In other words, if the nVidia Quadro FX 4500 is too high-end, but you
would definitely buy a $500 stereo-3D option, then you must say so.  If
you cannot see buying G5's now because of the pending Intel transition,
but would almost certainly buy an Intel-based equivalent to the Quad,
then you must make your voice is heard.  Likewise, if Mac OS X is still
missing critical software packages, then please name them.  Do not
remain silent yet unsatisfied.

> It seems premature, at best, to extrapolate from Apple's=20
> welcome, but very few and very recent, product releases to=20
> describe their support as "timely", "robust",=20
> "well-supported", "trouble-free" and=20
> "continuously-integrated".  Only with time can one make those=20
> claims fairly.  It seems they and their developer and user=20

We now have over three years of experience working directly with Apple
on PyMOL and associated systems.  They have been extremely responsive to
our concerns regarding UNIX source and X11 compatibility, Python,
Tcl/Tk, OpenGL bugs & performance, G5 and multiprocessor optimization,
and most recently Stereo 3D.  For a company with such diverse interests
as Apple to demonstrate this kind of commitment to the needs of an
supposedly niche community like scientific visualization is truly
remarkable. =20

Of course, I cannot say what they will do in the future.  All I can say
is that the people currently calling the shots with respect to
scientific computing are calling them appropriately.  That experience is
the justified basis for my strong endorsements -- Apple has earned them
well.

That being said, the core purpose of my email was to elicit feedback
from other who have not had such close and extended interactions with
Apple, and for us to understand the experience and perceptions of our
user community, especially with regard to these new visualization
workstations.  Some of the feedback already received has been quite
sobering.

So let me make clear:  We are not saying, "Go Mac!" blindly and without
reservations.  What we are saying is, "Consider Mac..." by carefully
evaluating their integrated hardware/driver/OS solutions and by sharing
with us your candid reactions to them.  If Macs are (still) unsuitable,
then please describe how they could be improved further.  However, if
they are now well suited to your needs, then please purchase them
aggressively.

I hope our position is now clarified, and offer my apologies for any
confusion, offense, or excess zeal.

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
> D. Joe Anderson
> Sent: Monday, January 16, 2006 9:34 AM
> To: pym...@li...
> Subject: Re: [PyMOL] Quadro-based 3D Mac Feedback
>=20
> On Sat, Jan 14, 2006 at 04:51:21PM -0800, Warren DeLano wrote:
> > The Quadro FX 4500-based PowerMac G5 is Steve Jobs' timely=20
> and direct=20
> > answer [...] The UNIX-based Mac has become the robust, low-cost,=20
> > well-supported, and high-performance replacement for SGI=20
> workstations=20
> > that Linux never delivered despite nearly a decade of=20
> opportunity and=20
> > effort (including our own).  Why does Linux fail with visualization?
> [...]
> > History shows that it takes an integrated hardware &=20
> operating systems=20
> > vendor like Apple (or formerly SGI, or Sun) to deliver and maintain=20
> > trouble-free OpenGL under UNIX.  Apple is the world's leading UNIX=20
> > vendor, and unlike with Linux, Mac hardware and operating=20
> systems are=20
> > continuously integrated with cutting-edge OpenGL graphics cards.
>=20
> > Has Apple in fact given us what you asked for?  If so, then=20
> have you=20
> > followed through with purchases?  If not, then what are you=20
> waiting for?
> > Is something crucial still missing?  Please share your=20
> thoughts.  We=20
> > guarantee that Apple and others will hear them.
>=20
> Despite the OpenGL workstation niche having been a yawning=20
> chasm for several years now, it took the concerted begging to=20
> get Apple to respond to that niche.  While congratulations in=20
> getting Apple to respond are still in order, this blatant=20
> shilling contrasts jarringly with the open source context in=20
> which PyMOL is developed, distributed, and supported: PyMOL=20
> is attractive in part because it promises long-term, flexible=20
> access to the tools to do our work, without users falling=20
> into a vassal role with respect to one industry-dominant company.
>=20
> Launching such a hyperbolic cheerleading campaign may belie=20
> the stability of the support one might expect from Apple for=20
> this technology, if one feels such campaigns are necessary to=20
> keep that support alive.
>=20
> It seems premature, at best, to extrapolate from Apple's=20
> welcome, but very few and very recent, product releases to=20
> describe their support as "timely", "robust",=20
> "well-supported", "trouble-free" and=20
> "continuously-integrated".  Only with time can one make those=20
> claims fairly.  It seems they and their developer and user=20
> communities will have their hands full with the upcoming=20
> hardware architecture migrations, during which support for=20
> many different niches might lag behind or fall by the=20
> wayside.  While one may hope they can pull it and keep it all=20
> together, let's not get ahead of ourselves: The list of=20
> Apple's predecessors in this niche, rather than being=20
> complimentary to Apple should serve as a sobering reminder of=20
> the difficulties Apple faces, and as a warning against=20
> hitching one's scientific productivity yet again to just one star.
>=20
> As for specifics of our own purchases, our purchase cycle had=20
> us replacing hardware early last summer, before the indicated=20
> hardware was available.  So, it doesn't seem to be a question=20
> of "what are you waiting for" so much as asking Apple "what=20
> took you so long?".  For this round, their support came too=20
> late, even though they've been trading for years on their=20
> claims of support for creative endeavors (cf publicity of the=20
> Genentech orders of the original G4 iMac).  Our next crack at=20
> it will probably come well after the migration to a=20
> Intel-based architecture is complete.
>=20
> As it is, we had to wait a year more than I'd have liked for=20
> funding, which put us in the position of having to navigate=20
> the replacement of hardware alongside a major release of the=20
> operating system (MacOS 10.4).  That brought with it=20
> additional support problems, notably a lag (or complete drop=20
> in) support for MacOS from other third-party developers,=20
> which issues we're still working through. =20
>=20
> Whatever the problems behind OpenGL support for Linux,=20
> entreaties to abandon it will not help convince Linux=20
> integrators or graphics vendors to support this niche.  In=20
> terms of choice and pricing, this will benefit neither Linux=20
> users nor Mac users.  Rather, what it does is re-animate the=20
> long dormant internecine Unix Wars of the days of old.  We've=20
> been through that, and we know how it turns out. =20
>=20
> For those who missed it the first time, it doesn't benefit=20
> Apple, nor users of any other Unix-like operating system.
>=20
> --
> D. Joe
>=20

Re: [PyMOL] Quadro-based 3D Mac Feedback

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

On Sat, Jan 14, 2006 at 04:51:21PM -0800, Warren DeLano wrote:
> The Quadro FX 4500-based PowerMac G5 is Steve Jobs' timely and direct
> answer [...]
> The UNIX-based Mac has become the robust, low-cost, well-supported, and
> high-performance replacement for SGI workstations that Linux never
> delivered despite nearly a decade of opportunity and effort (including
> our own).  Why does Linux fail with visualization?
[...]
> History shows that it takes an integrated hardware & operating systems
> vendor like Apple (or formerly SGI, or Sun) to deliver and maintain
> trouble-free OpenGL under UNIX.  Apple is the world's leading UNIX
> vendor, and unlike with Linux, Mac hardware and operating systems are
> continuously integrated with cutting-edge OpenGL graphics cards. 

> Has Apple in fact given us what you asked for?  If so, then have you
> followed through with purchases?  If not, then what are you waiting for?
> Is something crucial still missing?  Please share your thoughts.  We
> guarantee that Apple and others will hear them.

Despite the OpenGL workstation niche having been a yawning chasm
for several years now, it took the concerted begging to get
Apple to respond to that niche.  While congratulations in
getting Apple to respond are still in order, this blatant
shilling contrasts jarringly with the open source context in
which PyMOL is developed, distributed, and supported: PyMOL is
attractive in part because it promises long-term, flexible
access to the tools to do our work, without users falling into a
vassal role with respect to one industry-dominant company.

Launching such a hyperbolic cheerleading campaign may belie the
stability of the support one might expect from Apple for this
technology, if one feels such campaigns are necessary to keep
that support alive.

It seems premature, at best, to extrapolate from Apple's
welcome, but very few and very recent, product releases to
describe their support as "timely", "robust", "well-supported",
"trouble-free" and "continuously-integrated".  Only with time
can one make those claims fairly.  It seems they and their
developer and user communities will have their hands full with
the upcoming hardware architecture migrations, during which
support for many different niches might lag behind or fall by
the wayside.  While one may hope they can pull it and keep it
all together, let's not get ahead of ourselves: The list of
Apple's predecessors in this niche, rather than being
complimentary to Apple should serve as a sobering reminder of
the difficulties Apple faces, and as a warning against hitching
one's scientific productivity yet again to just one star.

As for specifics of our own purchases, our purchase cycle had us
replacing hardware early last summer, before the indicated
hardware was available.  So, it doesn't seem to be a question of
"what are you waiting for" so much as asking Apple "what took
you so long?".  For this round, their support came too late,
even though they've been trading for years on their claims of
support for creative endeavors (cf publicity of the Genentech
orders of the original G4 iMac).  Our next crack at it will
probably come well after the migration to a Intel-based
architecture is complete.

As it is, we had to wait a year more than I'd have liked for
funding, which put us in the position of having to navigate the
replacement of hardware alongside a major release of the
operating system (MacOS 10.4).  That brought with it additional
support problems, notably a lag (or complete drop in) support
for MacOS from other third-party developers, which issues we're
still working through.  

Whatever the problems behind OpenGL support for Linux,
entreaties to abandon it will not help convince Linux
integrators or graphics vendors to support this niche.  In terms
of choice and pricing, this will benefit neither Linux users nor
Mac users.  Rather, what it does is re-animate the long dormant
internecine Unix Wars of the days of old.  We've been through
that, and we know how it turns out.  

For those who missed it the first time, it doesn't benefit
Apple, nor users of any other Unix-like operating system.

-- 
D. Joe

[PyMOL] Bfactor

[Bingding H. <bh...@bi...>]

How can I the Bfactor for each residue in pymol script?

Bingding

Re: [PyMOL] Pymol Query

[Marc S. <mar...@gm...>]

> I have recently downloaded Pymol and can't get the protein structure 
> to display on the main screen, files are being uploaded and are 
> visible in the side bar and if I try to randomly alter colours on the
> protein parts of it appear though I can't be sure of what I am
> looking at as the program hasn't diplayed it. Is this a program fault
> or a simple menu preference?

Hi Vicki,

it would help if you would let us know some more details:

What type of hardware do you use (graphics-card, CPU)?
Which operation system do you use?
Which version of Pymol do you use?
What files did you want to display (non-standard PDB-files sometimes
produce errors or are displayed invisible)?
Are there any error messages in the console-window upon loading?

Pymol normaly loads and displays PDB-files with a standard-layout and
centers them on the screen (unlike some other/older programs like O,
where it is considered a feature NOT to center the display (i.e. you see
nothing after loading)).

-- 
Bye,

Marc Saric

Re: [PyMOL] display of multiple NMR structures stored in one PDB file

[Joel T. <joe...@ot...>]

Check out the list under NMR and my name (I asked the same question). Answer also pasted below

J

To see them all at once:

load my_struct.pdb
set all_states

Or if you want them separated into individual objects:

unset all_states
split_states my_struct
dele my_struct



Michael Weber wrote:

> Hello,
> I have a short question concerning the display of multiple NMR 
> structures stored in one PDB file. When loading NMR .PDB files with 
> SWISS-PDB-VIEWER, the number of NMR structures present in that file is 
> initially displayed during the loading process and one can select how 
> many and which of the structures are going to be loaded.
>  
> In pyMOL, when trying to load for example 1JOX.pdb (which contains 4 
> NMR models), only one single structure is displayed. How can I 
> visualize the remaining three?
>  
> Thanks for your help, ;-)
> Michael.


-- 
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

RE: [PyMOL] Lights in pymol 0.99beta ?

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

Wulf,

Its currently a bit of a pain keeping two simultaneous versions of PyMOL
running under windows because of interaction with the registry.  The
trick is to simply rename the existing "Program Files\DeLano
Scientific\PyMOL" folder before installing additional versions (in the
default manner).

You can then control which version is active by renaming the two
folders.  In other words:

"Program Files\Delano Scientific\PyMOL" will always the be active
version.  You can store inactive versions as "Program Files\Delano
Scientific\PyMOL-098",  "Program Files\Delano Scientific\PyMOL-099", and
so on.

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: Saturday, January 14, 2006 8:09 AM
> To: pym...@li...
> Subject: [PyMOL] Lights in pymol 0.99beta ?
>=20
> Dear pymolers,
>=20
> I have two questions concerning the new beta version=20
> (windows) of pymol.
>=20
> a.)  when I load a molecule (or an old session file) colours=20
> are very bright, like an over-exposed photograph. This=20
> doesn't change with raytracing and I haven't found the button=20
> to tame it yet....
>=20
> b.) I have installed this beta into another directory and=20
> wanted use it as an alternative to the 0.98 version, just to=20
> play with it a bit.=20
> However, when I now hit my desktop link pointing to the old=20
> directory, it fires up the new version (which I don't want to=20
> use because of the colour problem....). I found no other way=20
> than re-installing the old version. What am I doing wrong?
>=20
>=20
> Thanks,
>=20
>=20
>=20
> Wulf
>=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=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

[PyMOL] Quadro-based 3D Mac Feedback

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

3D Visualization Software Users:

Have you evaluated or purchased a 3D visualization workstation from
Apple yet?
<http://www.apple.com/powermac/graphics.html>=20

If so, then please provide us with your candid feedback.
mailto:ma...@de...

We believe that Mac OS X is now far superior to Linux for 3D and
(especially) stereo 3D visualization.  These Macs were specifically
modified for you in response to last year's "Stereo 3D Matters to Me"
email campaign, and we want to hear what you think about them!

The Quadro FX 4500-based PowerMac G5 is Steve Jobs' timely and direct
answer to your over 600 well-articulated emails communicating the
importance of 3D visualization in science, education, engineering, and
medicine.  It would now be irresponsible to go with Linux or even
Windows without first carefully considering the advantages of OpenGL on
Mac OS X.

The UNIX-based Mac has become the robust, low-cost, well-supported, and
high-performance replacement for SGI workstations that Linux never
delivered despite nearly a decade of opportunity and effort (including
our own).  Why does Linux fail with visualization?

Because OpenGL is a tough and continuously-evolving hardware challenge.
Open source developers cannot solve proprietary hardware integration
issues, and commercial Linux vendors have insufficient pull with
graphics card manufacturers to deliver seamless OpenGL solutions on an
ongoing basis.  Sometimes Linux OpenGL works and sometimes it doesn't,
despite everyone's best efforts.  With this bleak record, we can no
longer recommend Linux as a platform for OpenGL visualization.  Linux
may be ideal for compute clusters, but it is simply unreliable for
UNIX-dependent visualization (especially with 64 bits, ugh!).

History shows that it takes an integrated hardware & operating systems
vendor like Apple (or formerly SGI, or Sun) to deliver and maintain
trouble-free OpenGL under UNIX.  Apple is the world's leading UNIX
vendor, and unlike with Linux, Mac hardware and operating systems are
continuously integrated with cutting-edge OpenGL graphics cards.  Mac
OpenGL just works -- every time -- with no complex end-user
configuration.  That is great for software vendors, and it provides
welcome relief for users of 3D software under UNIX.

However, your real-world experiences are the ultimate test, and we
therefore need to hear direct and ongoing feedback from those of you who
have evaluated, purchased, and/or deployed Mac workstations to meet your
unique OpenGL and/or X11 visualization needs. =20

Has Apple in fact given us what you asked for?  If so, then have you
followed through with purchases?  If not, then what are you waiting for?
Is something crucial still missing?  Please share your thoughts.  We
guarantee that Apple and others will hear them.

Let's not lose this long-sought opportunity to meet the community's
platform needs on a grand scale.  If these Quadro-based Macs prove to be
as good for UNIX OpenGL visualization as we think they are, then
everyone should (indeed, must!) purchase them in quantity and begin the
process of migration.  That is the only way we can ensure that Apple
will remain highly motivated to serve this community.  Your vote will be
counted via the market!

Cheers,
Warren L. DeLano, Ph.D., PyMOL Developer, DeLano Scientific LLC

PS.  If the only reason you haven't bought a Quadro-based PowerMac G5 is
because you are waiting for the Intel-based equivalent, then please say
so -- such machines are expected by the end of 2006.  In the meantime,
you might look at the Intel-based dual-core MacBook Pro
<http://www.apple.com/macbookpro> for portable UNIX visualization, or a
dual-core Intel-iMac <http://www.apple.com/imac> as a low-cost UNIX
station.  Just $1299 for a complete system with more capabilities than
Linux and much less hassle!

[PyMOL] Lights in pymol 0.99beta ?

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

Dear pymolers,

I have two questions concerning the new beta version (windows) of pymol.

a.)  when I load a molecule (or an old session file) colours are very 
bright, like an over-exposed photograph. This doesn't change with 
raytracing and I haven't found the button to tame it yet....

b.) I have installed this beta into another directory and wanted use it 
as an alternative to the 0.98 version, just to play with it a bit. 
However, when I now hit my desktop link pointing to the old directory, 
it fires up the new version (which I don't want to use because of the 
colour problem....). I found no other way than re-installing the old 
version. What am I doing wrong?


Thanks,



Wulf

[PyMOL] Pymol Query

[<vf...@st...>]

Query

I have recently downloaded Pymol and can't get the protein structure to display
on the main screen, files are being uploaded and are visible in the side bar
and if I try to randomly alter colours on the protein parts of it appear though
I can't be sure of what I am looking at as the program hasn't diplayed it. Is
this a program fault or a simple menu preference?

Vicki Symigton



------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk

Re: [PyMOL] display of multiple NMR structures stored in one PDB file

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

Hi,you can either with mouse clicking on the left-down on ">" or on
the menu display all frames.
I hope this can help,

Regards

andrea

2006/1/13, Michael Weber <we...@st...>:
>
> Hello,
> I have a short question concerning the display of multiple NMR structures
> stored in one PDB file. When loading NMR .PDB files with SWISS-PDB-VIEWER=
,
> the number of NMR structures present in that file is initially displayed
> during the loading process and one can select how many and which of the
> structures are going to be loaded.
>
> In pyMOL, when trying to load for example 1JOX.pdb (which contains 4 NMR
> models), only one single structure is displayed. How can I visualize the
> remaining three?
>
> Thanks for your help, ;-)
> Michael.


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

[PyMOL] display of multiple NMR structures stored in one PDB file

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

Hello,
I have a short question concerning the display of multiple NMR =
structures stored in one PDB file. When loading NMR .PDB files with =
SWISS-PDB-VIEWER, the number of NMR structures present in that file is =
initially displayed during the loading process and one can select how =
many and which of the structures are going to be loaded.

In pyMOL, when trying to load for example 1JOX.pdb (which contains 4 NMR =
models), only one single structure is displayed. How can I visualize the =
remaining three?

Thanks for your help, ;-)
Michael.