pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Re: flicker Mac 10.4.3

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

Hi,

I can confirm that updating the ATI drivers and using the =20
antialiasing x2 option for MacPyMOL removes the flicker problem (at =20
least on my G4 iBook). The lines look much coarser though i.e. not as =20=

nice as usual - seems you win some you lose some......

Brian



On 4 Nov 2005, at 13:15, Martin Montgomery wrote:

> Thanks Jesper,
>
> That seems to work!!!
>
> MGM
>
>
> On 4 Nov 2005, at 13:06, Jesper Karlsen wrote:
>
>> Hi Mac users,
>>
>> MGM wrote:
>>
>> "Having just read Jesper's email regarding getting drivers at =20
>> ATI's  website, I had a look and there are no mac drivers =20
>> available as far  as I can see.  Only the ATI Displays software.  =20
>> After installing this  on my machine, nothing has changed.  The =20
>> molecule loads fine and the  window behaves in "default" line =20
>> representation but when I change to  cartoon (or any other) =20
>> representation, the window flickers badly."
>>
>> Wups!
>> I quess I did to many things at ones, if was the later =20
>> configuration that did the trick sorry!
>> I downloaded the ATI Display software from ati.com.
>> I configured the ATI Display (in System Prefs.) to use =20
>> antialiasing  (FSAA=3D2x) for MacPyMOL.app and the flickering stoped.
>>
>> Jesper Karlsen
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
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>> it for free - -and be entered to win a 42" plasma tv or your very own
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>
>
>
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*******************************************
Brian J Goodfellow
Departamento de Qu=CCmica
Universidade de Aveiro
3810-193 Aveiro, Portugal
Tel: +351 234 401506, Fax: +351 234 370084
http://www.dq.ua.pt/ingles/index_mem.htm
*******************************************

Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?

[Moriarty, D. <dmo...@si...>]

I've given it a quick run on a new Powerbook with the ATI Radeon 9700 w/128
MB, and I can't reproduce the flicker.  Same thing with a G5 with a 9800
with 256 MB.  My dual G4 with a Radeon 9000 (128 MB) does show the flicker,
however, and Jespers trick does the trick.  No more flicker.


Dan
--
Dr. Daniel Moriarty
Siena College
Chemistry and Biochemistry Dept.
515 Loudon Road
Loudonville, NY 12211
(518) 783-2472
fax: (518) 276-4887


> From: Martin Montgomery <mg...@mr...>
> Date: Fri, 4 Nov 2005 13:05:10 +0000
> To: pymol-users <pym...@li...>
> Subject: Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?
>=20
> Just for completeness, I've now checked a 20" G5 iMac with a 128MB
> ATI card and it is fine.  Also, I can confirm that there is not a
> problem whilst using X11 pymol on a 64MB ATI card.
>=20
> Cheers
>=20
> MGM
>=20
>=20
>=20
>=20
>=20
> Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under
> 10.4.3 however,  if I launch X11 and run PyMol under that - (version
> 0.97), then there's no problem
>=20
> Chris
>=20
>=20
>=20
>=20
> On 4 Nov 2005, at 12:26, Martin Montgomery wrote:
>=20
>> I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and
>> macpymol 99beta21/25 and it works fine with 10.4.3.  It seems the
>> problem is limited to ATI graphics cards with less than 256 RAM.
>> nVidea cards are not affected.  Will try an ATI card with 128MB RAM
>> if I can find one here.
>>=20
>> I have also used my powerbook which has an ATI card and has the
>> flicker problem to boot (via target mode firewire) a G5 iMac with
>> an nVidea card and there is no problem when the powerbook system
>> uses the iMac graphics.
>>=20
>>=20
>> Cheers
>>=20
>>=20
>> MGM
>>=20
>>=20
>>=20
>>=20
>>=20
>>=20
>>=20
>> On 4 Nov 2005, at 12:08, kh...@ce... wrote:
>>=20
>>> On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
>>>=20
>>>> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256
>>>> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on
>>>> that machine, everything is still fine.
>>>>=20
>>>> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that
>>>> still has a problem.  I then booted into my back up clone which
>>>> is at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the
>>>> 64MB ATI cards look to be dodgy under 10.4.3 whilst the better
>>>> spec ATI ones are OK.  Will try and find a nVidia 64MB equipped
>>>> mac for comparison.
>>>=20
>>> On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not
>>> noticed any change after updating to 10.4.3. I use a self-compiled
>>> PyMol 0.98.
>>>=20
>>> Konrad.
>>> --
>>> ---------------------------------------------------------------------
>>> Konrad Hinsen
>>> Laboratoire L=E9on Brillouin, CEA Saclay,
>>> 91191 Gif-sur-Yvette Cedex, France
>>> Tel.: +33-1 69 08 79 25
>>> Fax: +33-1 69 08 82 61
>>> E-Mail: kh...@ce...
>>> ---------------------------------------------------------------------
>>>=20
>>>=20
>>>=20
>>>=20
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by:
>>> Tame your development challenges with Apache's Geronimo App
>>> Server. Download
>>> it for free - -and be entered to win a 42" plasma tv or your very own
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>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>=20
>>=20
>>=20
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App Server.
>> Download
>> it for free - -and be entered to win a 42" plasma tv or your very own
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>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. Downl=
oad
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Re: [PyMOL] Re: PyMOL-users digest, Vol 1 #1050 - 7 msgs

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

Thanks Jesper,

That seems to work!!!

MGM


On 4 Nov 2005, at 13:06, Jesper Karlsen wrote:

> Hi Mac users,
>
> MGM wrote:
>
> "Having just read Jesper's email regarding getting drivers at  
> ATI's  website, I had a look and there are no mac drivers available  
> as far  as I can see.  Only the ATI Displays software.  After  
> installing this  on my machine, nothing has changed.  The molecule  
> loads fine and the  window behaves in "default" line representation  
> but when I change to  cartoon (or any other) representation, the  
> window flickers badly."
>
> Wups!
> I quess I did to many things at ones, if was the later  
> configuration that did the trick sorry!
> I downloaded the ATI Display software from ati.com.
> I configured the ATI Display (in System Prefs.) to use  
> antialiasing  (FSAA=2x) for MacPyMOL.app and the flickering stoped.
>
> Jesper Karlsen
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.  
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] Re: macpymol update

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

Warren et al.

I checked, and my Powerbook G4 12" has  nVIDIA GeForce4 MX, with 32  
Mb memory.  Always worked fine before.   Realize that there are two  
different types of flicker.  There is the usual mild flicker as one  
rotates a model (seems more than it used to be), and there is a more  
global flickering that is most noticeable in the menu area on the  
right of the screen.  Still haven't seen the major flickering problem  
with b19.

I will check b25.  -Mark

On Nov 4, 2005, at 7:27 AM, pym...@li...  
wrote:

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>
> Today's Topics:
>
>    1. OS X 10.4.3 comment (Mark A Saper)
>    2. Re: Mac OS X 10.4.3 (Brian J Goodfellow)
>    3. Re: problem with CASTp plugin (Sebastien Moretti)
>    4. Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs (Jesper Karlsen)
>    5. Re: macpymol beta 21 bug? (Martin Montgomery)
>    6. Re: Re: macpymol beta 21 bug? (kh...@ce...)
>    7. Re: Re: macpymol beta 21 bug? (Martin Montgomery)
>
> --__--__--
>
> Message: 1
> From: Mark A Saper <sa...@um...>
> Date: Thu, 3 Nov 2005 23:53:30 -0500
> To: pym...@li...
> Subject: [PyMOL] OS X 10.4.3 comment
>
> Quite a shock to read about the OS X 10.4.3 problem.  I upgraded
> without a second thought and now I have the same problem on my 12"
> powerbook.  This is with beta14 I believe.
>
> When I try the single window beta19 it seems to be less of a problem.
>
> -Mark
> _________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry
> Biophysics Research Division, University of Michigan
> Chemistry Building Room 3040
> 930 N University Ave
> Ann Arbor MI 48109-1055 U.S.A.
>
> sa...@um...        (734) 764-3353        fax (734) 764-3323
> http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
>
>
>
>
> --__--__--
>
> Message: 2
> Cc: pym...@li...
> From: Brian J Goodfellow <bri...@dq...>
> Subject: Re: [PyMOL] Mac OS X 10.4.3
> Date: Fri, 4 Nov 2005 09:00:07 +0000
> To: Warren DeLano <wa...@de...>
>
> Warren,
>
> with 0.99beta25 the problem still exists. After loading a molecule =20
> there's no flickering but if I do a ray trace then the flickering =20
> starts when I rotate. Shifting the window stops the flickering.
> By running show cartoon after loading I can also get the  
> flickering. =20
> Again, moving the window stops it.
>
> Brian
>
> On Nov 4, 2005, at 3:40 AM, Warren DeLano wrote:
>
>> Brian,
>>
>> Can you confirm that this problem exists in the very latest beta?   
>> =20
>> I can't reproduce on my iMac G5
>>
>> http://delsci.com/beta
>>
>> Is there any special trick to get it to happen?
>>
>> Cheers,
>> Warren
>>
>>
>> --
>> Warren L. DeLano, Ph.D.
>> Principal Scientist
>>
>> . DeLano Scientific LLC
>> . 400 Oyster Point Blvd., Suite 213
>> . South San Francisco, CA 94080 USA
>> . Biz:(650)-872-0942  Tech:(650)-872-0834
>> . Fax:(650)-872-0273  Cell:(650)-346-1154
>> . mailto:wa...@de...
>>
>>
>>> -----Original Message-----
>>> From: pym...@li...
>>> [mailto:pym...@li...] On Behalf Of
>>> Brian J Goodfellow
>>> Sent: Thursday, November 03, 2005 2:17 PM
>>> To: pym...@li...
>>> Subject: [PyMOL] Mac OS X 10.4.3
>>>
>>> Hi Mac users,
>>>
>>> has anyone noticed an annoying flickering appearing when
>>> rotating a molecule in PymolX11 and MacPyMOL under 10.4.3
>>> that wasn't present under 10.4.2? The problem appears on both
>>> my iBookG4 and iMacG5. If the window is moved then the
>>> flickering disappears. However, if a ray trace is then drawn
>>> the problem starts again until the window is moved again -
>>> very annoying!
>>>
>>> Brian Goodfellow
>>>
>>>
>>> *******************************************
>>> Brian J Goodfellow
>>> Departamento de Qu=CCmica
>>> Universidade de Aveiro
>>> 3810-193 Aveiro, Portugal
>>> Tel: +351 234 401506, Fax: +351 234 370084
>>> http://www.dq.ua.pt/ingles/index_mem.htm
>>> *******************************************
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> SF.Net email is sponsored by:
>>> Tame your development challenges with Apache's Geronimo App
>>> Server. Download it for free - -and be entered to win a 42"
>>> plasma tv or your very own Sony(tm)PSP.  Click here to play:
>>> http://sourceforge.net/geronimo.php
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>
>>>
>>>
>>>
>
>
>
> --__--__--
>
> Message: 3
> Date: Fri, 04 Nov 2005 10:59:11 +0100
> From: Sebastien Moretti <seb...@ig...>
> To: jer...@ne...,
> 	pymol-users <pym...@li...>
> Subject: Re: [PyMOL] problem with CASTp plugin
>
>> Hello,=20
>>    We are running Python v2.2.3 on Red Hat Enterprise 3 which is  
>> almost=
> =20
>> like Red Hat 9 and/or Fedora Core 1. Our RedHat version seems to  
>> be=20
>> choking on the pyc file. The following is the error we get.
>> =20
>> Exception in plugin 'CASTpyMOL' -- Traceback follows...
>> Traceback (most recent call last):
>> File "modules/pmg_tk/PMGApp.py", line 109, in initialize_plugins
>> ImportError: Bad magic number in=20
>> /usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/startup/ 
>> CASTpyMOL=
> .
>> pyc
>> Error: unable to initialize plugin 'CASTpyMOL'.
>> =20
>> =20
>> We have contacted the plugin authors but have been unable to solve  
>> this=
> =20
>> problem.
>> =20
>> Thanks,
>> JJ
>
> Hello,
> We use CASTpyMOL.pyc file, for Linux, on Suse. It works fine.
>
> The .pyc files are python compiled code and they should work only  
> for=20
> python and PyMOL versions they have been compiled for.
> So, CASTpyMOL.pyc file is for PyMOL 0.98 and must be moved in the=20
> PYMOL_HOME/modules/pmg_tk/startup/ directory.
>
> Try a binary version of PyMOL, it embeds its own python interpreter.
>
> Maybe this will resolve your problem.
>
> --=20
> S=E9bastien Moretti
> http://www.igs.cnrs-mrs.fr/
> CNRS - IGS
> 31 chemin Joseph Aiguier
> 13402 Marseille cedex
>
>
> --__--__--
>
> Message: 4
> Date: Fri, 04 Nov 2005 11:55:27 +0100
> From: Jesper Karlsen <je...@bi...>
> To: pym...@li...
> Subject: [PyMOL] Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs
>
> HI Mac users,
>
> Brian Goodfellow wrote:
>
>> has anyone noticed an annoying flickering appearing when rotating  
>> a =20
>> molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present  
>> =20
>> under 10.4.2? The problem appears on both my iBookG4 and iMacG5.  
>> If =20
>> the window is moved then the flickering disappears. However, if a  
>> ray =20=
>>
>>
> The 10.4.3 update included a display driver update.
> Just go to ati's homepage (http://ati.com) and download the latest
> driver for you card. After this everything should be back to normal.
>
> Jesper Karlsen
>
>
>
> --__--__--
>
> Message: 5
> Cc: pym...@li...
> From: Martin Montgomery <mg...@mr...>
> Date: Fri, 4 Nov 2005 11:38:47 +0000
> To: "Warren DeLano" <wa...@de...>
> Subject: [PyMOL] Re: macpymol beta 21 bug?
>
>
> --Apple-Mail-1-325788267
> Content-Transfer-Encoding: 7bit
> Content-Type: text/plain;
> 	charset=US-ASCII;
> 	delsp=yes;
> 	format=flowed
>
> Hi Warren,
>
> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB)
> with 10.4.2 and it works fine.  After upgrading to 10.4.3 on that
> machine, everything is still fine.
>
> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that
> still has a problem.  I then booted into my back up clone which is at
> 10.4.2 and 99beta21 and 99beta25 work just fine.  So the 64MB ATI
> cards look to be dodgy under 10.4.3 whilst the better spec ATI ones
> are OK.  Will try and find a nVidia 64MB equipped mac for comparison.
>
> Having just read Jesper's email regarding getting drivers at ATI's
> website, I had a look and there are no mac drivers available as far
> as I can see.  Only the ATI Displays software.  After installing this
> on my machine, nothing has changed.  The molecule loads fine and the
> window behaves in "default" line representation but when I change to
> cartoon (or any other) representation, the window flickers badly.
>
>
> Cheers
>
> MGM
>
>
>
> On 4 Nov 2005, at 03:48, Warren DeLano wrote:
>
>> Martin,
>>
>> 10.4.3 is one ingredient in this problem -- ATI may be  
>> another...still
>> trying to reproduce it here, but so far all our nVidia-based 10.4.3
>> machines are doing just fine.
>>
>> Cheers,
>> Warren
>>
>>
>> --
>> Warren L. DeLano, Ph.D.
>> Principal Scientist
>>
>> . DeLano Scientific LLC
>> . 400 Oyster Point Blvd., Suite 213
>> . South San Francisco, CA 94080 USA
>> . Biz:(650)-872-0942  Tech:(650)-872-0834
>> . Fax:(650)-872-0273  Cell:(650)-346-1154
>> . mailto:wa...@de...
>>
>>
>>> -----Original Message-----
>>> From: Martin Montgomery [mailto:mg...@mr...]
>>> Sent: Thursday, November 03, 2005 5:08 AM
>>> To: Warren DeLano
>>> Subject: macpymol beta 21 bug?
>>>
>>> Hi Warren,
>>>
>>> I'm having a problem with 0.99 beta 21.  I get an occasional
>>> glitch where the graphics pane and GUI flickers badly when I
>>> move/zoom the molecule.  This can be temporarily corrected by
>>> resizing the window and typing reset.  However sometimes,
>>> after a little while,  the flicker returns.  The "brushed
>>> metal" surround of the window does not flicker nor does the
>>> text pane.  One possible cause is that I have updated to
>>> 10.4.3 and am not sure whether the problem also occurred in
>>> 10.4.2 but I could boot into my backup clone and check.
>>> 10.4.3 has meant that the fans are running more often even
>>> when the computer is doing very little.
>>>
>>> I've got a Dual 2Ghz G5 with 3.5G RAM and the stock Radeon
>>> 9600 Pro 64mB RAM graphics card into a Cinema 20" display.
>>>
>>> Cheers
>>>
>>> MGM
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
>
>
> Martin Montgomery
> Director's Group
> MRC Dunn Human Nutrition Unit
> Hills Road
> Cambridge
> CB2 2XY
>
>
> --Apple-Mail-1-325788267
> Content-Transfer-Encoding: quoted-printable
> Content-Type: text/html;
> 	charset=ISO-8859-1
>
> <HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
> -khtml-line-break: after-white-space; ">Hi Warren,<DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Tested 99beta21 and =
> 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB) with 10.4.2 and it =
> works fine.=A0 After upgrading to 10.4.3 on that machine,  
> everything is =
> still fine.=A0=A0<DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Also tried 99beta25 on  
> my =
> machine (ATI 9600 Pro - 64MB) and that still has a problem.=A0 I  
> then =
> booted into my back up clone which is at 10.4.2 and 99beta21 and =
> 99beta25 work just fine.=A0 So the 64MB ATI cards look to be dodgy  
> under =
> 10.4.3 whilst the better spec ATI ones are OK.=A0 Will try and find  
> a =
> nVidia 64MB equipped mac for comparison.</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Having just read  
> Jesper's =
> email regarding getting drivers at ATI's website, I had a look and  
> there =
> are no mac drivers available as far as I can see.=A0 Only the ATI =
> Displays software.=A0 After installing this on my machine, nothing  
> has =
> changed.=A0=A0The molecule loads fine and the window behaves in =
> "default" line representation but when I change to cartoon (or any =
> other) representation, the window flickers badly.</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>Cheers</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV>MGM</DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></DIV><DIV><BR =
> class=3D"khtml-block-placeholder"></ 
> DIV><DIV><DIV><DIV><BR><DIV><DIV>On =
> 4 Nov 2005, at 03:48, Warren DeLano wrote:</DIV><BR =
> class=3D"Apple-interchange-newline"><BLOCKQUOTE type=3D"cite"><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">Martin,</DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
> 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; ">10.4.3 is one ingredient in  
> this =
> problem -- ATI may be another...still</DIV><DIV style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">trying =
> to reproduce it here, but so far all our nVidia-based 10.4.3</ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">machines are doing just fine.</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> ">Cheers,</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; ">Warren</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--</ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">Warren L. DeLano, Ph.D.<SPAN =
> class=3D"Apple-converted-space">=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0  
> =A0 =
> =A0</SPAN></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; ">Principal Scientist</ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">.  
> DeLano =
> Scientific LLC <SPAN class=3D"Apple-converted-space">=A0</SPAN></ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">. 400 Oyster Point Blvd., Suite 213<SPAN =
> class=3D"Apple-converted-space">=A0 =A0 =A0 =A0 =A0 =A0</SPAN></ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">. South San Francisco, CA 94080 USA<SPAN =
> class=3D"Apple-converted-space">=A0 =A0</SPAN></DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">. Biz:(650)-872-0942<SPAN =
> class=3D"Apple-converted-space">=A0 </SPAN>Tech:(650)-872-0834<SPAN =
> class=3D"Apple-converted-space">=A0 =A0 =A0</SPAN></DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">. Fax:(650)-872-0273<SPAN =
> class=3D"Apple-converted-space">=A0 </SPAN>Cell:(650)-346-1154</ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">. <A =
> href=3D"mailto:wa...@de...">mailto:wa...@de...</A> <SPAN =
> class=3D"Apple-converted-space">=A0 =A0 =A0</SPAN></DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> min-height: 14px; "><BR></DIV> <BLOCKQUOTE type=3D"cite"><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">-----Original Message-----</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">From: Martin Montgomery [<A =
> href=3D"mailto:mg...@mr...">mailto:mgm@mrc- 
> dunn.cam.ac.uk</A>]<=
> SPAN class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">Sent: Thursday, November 03, 2005 5:08 AM</ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">To: Warren DeLano</DIV><DIV style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">Subject: =
> macpymol beta 21 bug?</DIV><DIV style=3D"margin-top: 0px; margin- 
> right: =
> 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; =
> "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; ">Hi Warren,</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm =
> having a problem with 0.99 beta 21.<SPAN class=3D"Apple-converted- 
> space">=A0=
>  </SPAN>I get an occasional<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">glitch =
> where the graphics pane and GUI flickers badly when I<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> ">move/zoom the molecule.<SPAN class=3D"Apple-converted-space">=A0 =
> </SPAN>This can be temporarily corrected by<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">resizing =
> the window and typing reset.<SPAN class=3D"Apple-converted- 
> space">=A0 =
> </SPAN>However sometimes,<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">after a =
> little while,<SPAN class=3D"Apple-converted-space">=A0 </SPAN>the =
> flicker returns.<SPAN class=3D"Apple-converted-space">=A0 </SPAN>The =
> "brushed<SPAN class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">metal" surround of the window does not flicker  
> nor =
> does the<SPAN class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">text pane.<SPAN class=3D"Apple-converted- 
> space">=A0 =
> </SPAN>One possible cause is that I have updated to<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">10.4.3 =
> and am not sure whether the problem also occurred in<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">10.4.2 =
> but I could boot into my backup clone and check. <SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">10.4.3 =
> has meant that the fans are running more often even<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">when the =
> computer is doing very little.</DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
> 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; ">I've got a Dual 2Ghz G5 with =
> 3.5G RAM and the stock Radeon<SPAN =
> class=3D"Apple-converted-space">=A0</SPAN></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;  
> ">9600 Pro =
> 64mB RAM graphics card into a Cinema 20" display.</DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> ">Cheers</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; ">MGM</DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
> 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
> 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></ 
> DIV><DIV =
> style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
> margin-left: 0px; min-height: 14px; "><BR></DIV><DIV  
> style=3D"margin-top: =
> 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
> min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
> margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
> 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
> margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> =
> </BLOCKQUOTE></BLOCKQUOTE></DIV><BR></DIV></DIV></DIV></ 
> DIV><BR><BR><DIV> =
> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT  
> face=3D"Helvetica" =
> size=3D"3" style=3D"font: 12.0px Helvetica">Martin Montgomery</ 
> FONT></P> =
> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT  
> face=3D"Helvetica" =
> size=3D"3" style=3D"font: 12.0px Helvetica">Director's Group</ 
> FONT></P> =
> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT  
> face=3D"Helvetica" =
> size=3D"3" style=3D"font: 12.0px Helvetica">MRC Dunn Human Nutrition =
> Unit</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
> face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px Helvetica">Hills =
> Road</FONT></P> <P style=3D"margin: 0.0px 0.0px 0.0px 0.0px"><FONT =
> face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
> Helvetica">Cambridge</FONT></P> <P style=3D"margin: 0.0px 0.0px  
> 0.0px =
> 0.0px"><FONT face=3D"Helvetica" size=3D"3" style=3D"font: 12.0px =
> Helvetica">CB2 2XY</FONT></P>  </DIV><BR></BODY></HTML>=
>
> --Apple-Mail-1-325788267--
>
>
> --__--__--
>
> Message: 6
> From: kh...@ce...
> Subject: Re: [PyMOL] Re: macpymol beta 21 bug?
> Date: Fri, 4 Nov 2005 13:08:24 +0100
> To: pymol-users <pym...@li...>
>
> On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
>
>> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 =20
>> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on =20
>> that machine, everything is still fine.
>>
>> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that =20
>> still has a problem.  I then booted into my back up clone which is  
>> =20
>> at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the 64MB =20
>> ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI  
>> =20
>> ones are OK.  Will try and find a nVidia 64MB equipped mac for =20
>> comparison.
>
> On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not =20
> noticed any change after updating to 10.4.3. I use a self-compiled =20
> PyMol 0.98.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: kh...@ce...
> ---------------------------------------------------------------------
>
>
>
>
> --__--__--
>
> Message: 7
> From: Martin Montgomery <mg...@mr...>
> Subject: Re: [PyMOL] Re: macpymol beta 21 bug?
> Date: Fri, 4 Nov 2005 12:26:28 +0000
> To: pymol-users <pym...@li...>
>
> I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and =20
> macpymol 99beta21/25 and it works fine with 10.4.3.  It seems the =20
> problem is limited to ATI graphics cards with less than 256 RAM.  =20
> nVidea cards are not affected.  Will try an ATI card with 128MB RAM  
> =20
> if I can find one here.
>
> I have also used my powerbook which has an ATI card and has the =20
> flicker problem to boot (via target mode firewire) a G5 iMac with  
> an =20
> nVidea card and there is no problem when the powerbook system uses =20
> the iMac graphics.
>
>
> Cheers
>
>
> MGM
>
>
>
>
>
>
>
> On 4 Nov 2005, at 12:08, kh...@ce... wrote:
>
>> On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
>>
>>> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 =20
>>> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on =20
>>> that machine, everything is still fine.
>>>
>>> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that =20
>>> still has a problem.  I then booted into my back up clone which  
>>> is =20=
>
>>> at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the 64MB =20
>>> ATI cards look to be dodgy under 10.4.3 whilst the better spec  
>>> ATI =20=
>
>>> ones are OK.  Will try and find a nVidia 64MB equipped mac for =20
>>> comparison.
>>
>> On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not  
>> =20
>> noticed any change after updating to 10.4.3. I use a self-compiled  
>> =20
>> PyMol 0.98.
>>
>> Konrad.
>> --
>> ---------------------------------------------------------------------
>> Konrad Hinsen
>> Laboratoire L=E9on Brillouin, CEA Saclay,
>> 91191 Gif-sur-Yvette Cedex, France
>> Tel.: +33-1 69 08 79 25
>> Fax: +33-1 69 08 82 61
>> E-Mail: kh...@ce...
>> ---------------------------------------------------------------------
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App  
>> Server. =20=
>
>> Download
>> it for free - -and be entered to win a 42" plasma tv or your very own
>> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
>
> --__--__--
>
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest
>
>

_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

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

[PyMOL] Re: PyMOL-users digest, Vol 1 #1050 - 7 msgs

[Jesper K. <je...@bi...>]

Hi Mac users,

MGM wrote:

"Having just read Jesper's email regarding getting drivers at ATI's  
website, I had a look and there are no mac drivers available as far  
as I can see.  Only the ATI Displays software.  After installing this  
on my machine, nothing has changed.  The molecule loads fine and the  
window behaves in "default" line representation but when I change to  
cartoon (or any other) representation, the window flickers badly."

Wups!
I quess I did to many things at ones, if was the later configuration 
that did the trick sorry!
I downloaded the ATI Display software from ati.com.
I configured the ATI Display (in System Prefs.) to use antialiasing  
(FSAA=2x) for MacPyMOL.app and the flickering stoped.

Jesper Karlsen

Re: [PyMOL] Re: macpymol beta 21 bug in 10.4.3?

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

Just for completeness, I've now checked a 20" G5 iMac with a 128MB =20
ATI card and it is fine.  Also, I can confirm that there is not a =20
problem whilst using X11 pymol on a 64MB ATI card.

Cheers

MGM





Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under =20
10.4.3 however,  if I launch X11 and run PyMol under that - (version =20
0.97), then there's no problem

Chris




On 4 Nov 2005, at 12:26, Martin Montgomery wrote:

> I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and =20
> macpymol 99beta21/25 and it works fine with 10.4.3.  It seems the =20
> problem is limited to ATI graphics cards with less than 256 RAM.  =20
> nVidea cards are not affected.  Will try an ATI card with 128MB RAM =20=

> if I can find one here.
>
> I have also used my powerbook which has an ATI card and has the =20
> flicker problem to boot (via target mode firewire) a G5 iMac with =20
> an nVidea card and there is no problem when the powerbook system =20
> uses the iMac graphics.
>
>
> Cheers
>
>
> MGM
>
>
>
>
>
>
>
> On 4 Nov 2005, at 12:08, kh...@ce... wrote:
>
>> On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
>>
>>> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 =20
>>> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on =20
>>> that machine, everything is still fine.
>>>
>>> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that =20
>>> still has a problem.  I then booted into my back up clone which =20
>>> is at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the =20
>>> 64MB ATI cards look to be dodgy under 10.4.3 whilst the better =20
>>> spec ATI ones are OK.  Will try and find a nVidia 64MB equipped =20
>>> mac for comparison.
>>
>> On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not =20=

>> noticed any change after updating to 10.4.3. I use a self-compiled =20=

>> PyMol 0.98.
>>
>> Konrad.
>> --
>> ---------------------------------------------------------------------
>> Konrad Hinsen
>> Laboratoire L=E9on Brillouin, CEA Saclay,
>> 91191 Gif-sur-Yvette Cedex, France
>> Tel.: +33-1 69 08 79 25
>> Fax: +33-1 69 08 82 61
>> E-Mail: kh...@ce...
>> ---------------------------------------------------------------------
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App =20
>> Server. Download
>> it for free - -and be entered to win a 42" plasma tv or your very own
>> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. =20=

> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Re: macpymol beta 21 bug?

[Christopher Y. <chr...@ut...>]

Flicker problem here on a PowerBook 1.5 G4 w/ 64 MB ATI card under =20
10.4.3 however,  if I launch X11 and run PyMol under that - (version =20
0.97), then there's no problem

Chris

On Nov 4, 2005, at 7:26 AM, Martin Montgomery wrote:

> I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and =20
> macpymol 99beta21/25 and it works fine with 10.4.3.  It seems the =20
> problem is limited to ATI graphics cards with less than 256 RAM.  =20
> nVidea cards are not affected.  Will try an ATI card with 128MB RAM =20=

> if I can find one here.
>
> I have also used my powerbook which has an ATI card and has the =20
> flicker problem to boot (via target mode firewire) a G5 iMac with =20
> an nVidea card and there is no problem when the powerbook system =20
> uses the iMac graphics.
>
>
> Cheers
>
>
> MGM
>
>
>
>
>
>
>
> On 4 Nov 2005, at 12:08, kh...@ce... wrote:
>
>> On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
>>
>>> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 =20
>>> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on =20
>>> that machine, everything is still fine.
>>>
>>> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that =20
>>> still has a problem.  I then booted into my back up clone which =20
>>> is at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the =20
>>> 64MB ATI cards look to be dodgy under 10.4.3 whilst the better =20
>>> spec ATI ones are OK.  Will try and find a nVidia 64MB equipped =20
>>> mac for comparison.
>>
>> On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not =20=

>> noticed any change after updating to 10.4.3. I use a self-compiled =20=

>> PyMol 0.98.
>>
>> Konrad.
>> --
>> ---------------------------------------------------------------------
>> Konrad Hinsen
>> Laboratoire L=E9on Brillouin, CEA Saclay,
>> 91191 Gif-sur-Yvette Cedex, France
>> Tel.: +33-1 69 08 79 25
>> Fax: +33-1 69 08 82 61
>> E-Mail: kh...@ce...
>> ---------------------------------------------------------------------
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App =20
>> Server. Download
>> it for free - -and be entered to win a 42" plasma tv or your very own
>> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. =20=

> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Christopher M. Yip, Ph.D., P.Eng.
Associate Professor - Canada Research Chair in Molecular Imaging
Department of Chemical Engineering and Applied Chemistry
Department of Biochemistry
Institute of Biomaterials and Biomedical Engineering
The Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
Room 404 160 College St.
Toronto, ON, CANADA M5S 3E1
(416) 978-7853
(416) 978-4317 (fax)
chr...@ut...
http://bigten.ibme.utoronto.ca

Re: [PyMOL] Re: macpymol beta 21 bug?

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

I've just tested a G5 imac with a GeForce FX5200 with 64MB RAM and =20
macpymol 99beta21/25 and it works fine with 10.4.3.  It seems the =20
problem is limited to ATI graphics cards with less than 256 RAM.  =20
nVidea cards are not affected.  Will try an ATI card with 128MB RAM =20
if I can find one here.

I have also used my powerbook which has an ATI card and has the =20
flicker problem to boot (via target mode firewire) a G5 iMac with an =20
nVidea card and there is no problem when the powerbook system uses =20
the iMac graphics.


Cheers


MGM







On 4 Nov 2005, at 12:08, kh...@ce... wrote:

> On Nov 4, 2005, at 12:38, Martin Montgomery wrote:
>
>> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 =20
>> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on =20
>> that machine, everything is still fine.
>>
>> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that =20
>> still has a problem.  I then booted into my back up clone which is =20=

>> at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the 64MB =20
>> ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI =20=

>> ones are OK.  Will try and find a nVidia 64MB equipped mac for =20
>> comparison.
>
> On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not =20
> noticed any change after updating to 10.4.3. I use a self-compiled =20
> PyMol 0.98.
>
> Konrad.
> --
> ---------------------------------------------------------------------
> Konrad Hinsen
> Laboratoire L=E9on Brillouin, CEA Saclay,
> 91191 Gif-sur-Yvette Cedex, France
> Tel.: +33-1 69 08 79 25
> Fax: +33-1 69 08 82 61
> E-Mail: kh...@ce...
> ---------------------------------------------------------------------
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. =20=

> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

Re: [PyMOL] Re: macpymol beta 21 bug?

[<kh...@ce...>]

On Nov 4, 2005, at 12:38, Martin Montgomery wrote:

> Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 =20
> MB) with 10.4.2 and it works fine.  After upgrading to 10.4.3 on =20
> that machine, everything is still fine.
>
> Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that =20
> still has a problem.  I then booted into my back up clone which is =20
> at 10.4.2 and 99beta21 and 99beta25 work just fine.  So the 64MB =20
> ATI cards look to be dodgy under 10.4.3 whilst the better spec ATI =20
> ones are OK.  Will try and find a nVidia 64MB equipped mac for =20
> comparison.

On my iMac G4 (nVidia GeForce FX 5200 with 64 MB VRAM), I have not =20
noticed any change after updating to 10.4.3. I use a self-compiled =20
PyMol 0.98.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Laboratoire L=E9on Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: kh...@ce...
---------------------------------------------------------------------

[PyMOL] Re: macpymol beta 21 bug?

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

Hi Warren,

Tested 99beta21 and 99beta25 on a dual 2.5 with ATI 9800 XT (256 MB)  
with 10.4.2 and it works fine.  After upgrading to 10.4.3 on that  
machine, everything is still fine.

Also tried 99beta25 on my machine (ATI 9600 Pro - 64MB) and that  
still has a problem.  I then booted into my back up clone which is at  
10.4.2 and 99beta21 and 99beta25 work just fine.  So the 64MB ATI  
cards look to be dodgy under 10.4.3 whilst the better spec ATI ones  
are OK.  Will try and find a nVidia 64MB equipped mac for comparison.

Having just read Jesper's email regarding getting drivers at ATI's  
website, I had a look and there are no mac drivers available as far  
as I can see.  Only the ATI Displays software.  After installing this  
on my machine, nothing has changed.  The molecule loads fine and the  
window behaves in "default" line representation but when I change to  
cartoon (or any other) representation, the window flickers badly.


Cheers

MGM



On 4 Nov 2005, at 03:48, Warren DeLano wrote:

> Martin,
>
> 10.4.3 is one ingredient in this problem -- ATI may be another...still
> trying to reproduce it here, but so far all our nVidia-based 10.4.3
> machines are doing just fine.
>
> Cheers,
> Warren
>
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: Martin Montgomery [mailto:mg...@mr...]
>> Sent: Thursday, November 03, 2005 5:08 AM
>> To: Warren DeLano
>> Subject: macpymol beta 21 bug?
>>
>> Hi Warren,
>>
>> I'm having a problem with 0.99 beta 21.  I get an occasional
>> glitch where the graphics pane and GUI flickers badly when I
>> move/zoom the molecule.  This can be temporarily corrected by
>> resizing the window and typing reset.  However sometimes,
>> after a little while,  the flicker returns.  The "brushed
>> metal" surround of the window does not flicker nor does the
>> text pane.  One possible cause is that I have updated to
>> 10.4.3 and am not sure whether the problem also occurred in
>> 10.4.2 but I could boot into my backup clone and check.
>> 10.4.3 has meant that the fans are running more often even
>> when the computer is doing very little.
>>
>> I've got a Dual 2Ghz G5 with 3.5G RAM and the stock Radeon
>> 9600 Pro 64mB RAM graphics card into a Cinema 20" display.
>>
>> Cheers
>>
>> MGM
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>



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

[PyMOL] Re: PyMOL-users digest, Vol 1 #1049 - 6 msgs

[Jesper K. <je...@bi...>]

HI Mac users,

Brian Goodfellow wrote:

>has anyone noticed an annoying flickering appearing when rotating a =20
>molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20
>under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20
>the window is moved then the flickering disappears. However, if a ray =20=
>  
>
The 10.4.3 update included a display driver update.
Just go to ati's homepage (http://ati.com) and download the latest 
driver for you card. After this everything should be back to normal.

Jesper Karlsen
 

Re: [PyMOL] problem with CASTp plugin

[Sebastien M. <seb...@ig...>]

> Hello,=20
>    We are running Python v2.2.3 on Red Hat Enterprise 3 which is almost=
=20
> like Red Hat 9 and/or Fedora Core 1. Our RedHat version seems to be=20
> choking on the pyc file. The following is the error we get.
> =20
> Exception in plugin 'CASTpyMOL' -- Traceback follows...
> Traceback (most recent call last):
> File "modules/pmg_tk/PMGApp.py", line 109, in initialize_plugins
> ImportError: Bad magic number in=20
> /usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/startup/CASTpyMOL=
.
> pyc
> Error: unable to initialize plugin 'CASTpyMOL'.
> =20
> =20
> We have contacted the plugin authors but have been unable to solve this=
=20
> problem.
> =20
> Thanks,
> JJ

Hello,
We use CASTpyMOL.pyc file, for Linux, on Suse. It works fine.

The .pyc files are python compiled code and they should work only for=20
python and PyMOL versions they have been compiled for.
So, CASTpyMOL.pyc file is for PyMOL 0.98 and must be moved in the=20
PYMOL_HOME/modules/pmg_tk/startup/ directory.

Try a binary version of PyMOL, it embeds its own python interpreter.

Maybe this will resolve your problem.

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

[PyMOL] .xyz file loading problem from chempy module

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

Hello everyone

It seems to be a problem with loading an .xyz file as a chempy model.
For example doing

from chempy import io
m = io.xyz.fromFile("some.xyz")

gives:

chempy: reading "some.xyz".
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/home/dmitriy/pymol/lib/python2.4/site-packages/chempy/__init__.py", 
line 185, in fromFile
TypeError: fromList() takes exactly 1 argument (2 given)

If I've got the right idea whats going on, there should be  
fromList(self,list)  function in xyz.py which will hide the Storage one.
Like it's done in pdb.py (it works fine for io.pdb.fromFile)

I'm trying to establish a communication between my program and pymol in a 
simple .xyz format. Sending a list of strings, creating a chempy model and 
loading it into pymol will work. If there is some workaround or a fix for 
problem mention above.

Warren, Is it possible to implement a way of passing .xyz file as a string, 
not as a list of strings or a file? I've seen molstr, pdbstr etc. but not 
xyzstr. 
And a short description how to load pdbstr for example it in this way will be 
great.

Thanks
  Dmitriy

Re: [PyMOL] Mac OS X 10.4.3

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

Warren,

with 0.99beta25 the problem still exists. After loading a molecule =20
there's no flickering but if I do a ray trace then the flickering =20
starts when I rotate. Shifting the window stops the flickering.
By running show cartoon after loading I can also get the flickering. =20
Again, moving the window stops it.

Brian

On Nov 4, 2005, at 3:40 AM, Warren DeLano wrote:

> Brian,
>
> Can you confirm that this problem exists in the very latest beta?  =20
> I can't reproduce on my iMac G5
>
> http://delsci.com/beta
>
> Is there any special trick to get it to happen?
>
> Cheers,
> Warren
>
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:wa...@de...
>
>
>> -----Original Message-----
>> From: pym...@li...
>> [mailto:pym...@li...] On Behalf Of
>> Brian J Goodfellow
>> Sent: Thursday, November 03, 2005 2:17 PM
>> To: pym...@li...
>> Subject: [PyMOL] Mac OS X 10.4.3
>>
>> Hi Mac users,
>>
>> has anyone noticed an annoying flickering appearing when
>> rotating a molecule in PymolX11 and MacPyMOL under 10.4.3
>> that wasn't present under 10.4.2? The problem appears on both
>> my iBookG4 and iMacG5. If the window is moved then the
>> flickering disappears. However, if a ray trace is then drawn
>> the problem starts again until the window is moved again -
>> very annoying!
>>
>> Brian Goodfellow
>>
>>
>> *******************************************
>> Brian J Goodfellow
>> Departamento de Qu=CCmica
>> Universidade de Aveiro
>> 3810-193 Aveiro, Portugal
>> Tel: +351 234 401506, Fax: +351 234 370084
>> http://www.dq.ua.pt/ingles/index_mem.htm
>> *******************************************
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App
>> Server. Download it for free - -and be entered to win a 42"
>> plasma tv or your very own Sony(tm)PSP.  Click here to play:
>> http://sourceforge.net/geronimo.php
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>>
>>

[PyMOL] OS X 10.4.3 comment

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

Quite a shock to read about the OS X 10.4.3 problem.  I upgraded  
without a second thought and now I have the same problem on my 12"  
powerbook.  This is with beta14 I believe.

When I try the single window beta19 it seems to be less of a problem.

-Mark
_________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry
Biophysics Research Division, University of Michigan
Chemistry Building Room 3040
930 N University Ave
Ann Arbor MI 48109-1055 U.S.A.

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

[PyMOL] Independent Rotation axis...

[Nathaniel G. B. <ngb...@gm...>]

Hi All,

I was wondering if anyone know if there is anyway to assign independent 
rotation axis to two different proteins within Pymol.  Specifically, I 
amintersted in having two molecules rotate about individual axis in a 
movie sequence.

Thanks,

Nate Butlin

UCDavis - Chemistry
ngb...@uc...

Re: [PyMOL] Mac OS X 10.4.3

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

I don't know if it will make a difference (I don't even have a Mac) but=20
try opening it from a console using:

pymol -M


Serge Cohen wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>=20
> Got exactly the same problem on a 800MHz TiBook
> I was planning to try on a Dual G5, but had not the time today...
>=20
>=20
> Serge.
>=20
> Le 3 nov. 05 =E0 23:05, Brian J Goodfellow a =E9crit :
>=20
>> Hi Mac users,
>>
>> has anyone noticed an annoying flickering appearing when rotating a =20
>> molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20
>> under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20
>> the window is moved then the flickering disappears. However, if a  ray=
=20
>> trace is then drawn the problem starts again until the window  is=20
>> moved again - very annoying!
>>
>> Brian Goodfellow
>>
>=20
>=20
> *******************************************************************
> Dr. Serge COHEN
> GPG Key ID: 9CBB58FB
>=20
> N.K.I.
> Department of Molecular Carcinogenesis
> Plesmanlaan 121
> 1066 CX Amsterdam; NL
>=20
> E-Mail: s....@nk...
> Tel : +31 20 512 2053
> *******************************************************************
>=20
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.1 (Darwin)
>=20
> iD8DBQFDapuW5EPeG5y7WPsRAlA1AJ93hPA3eALJX10AQ/HVo7J6dA914gCeMz1E
> AJkFJDwrG820njkblBCpqeE=3D
> =3DF8UC
> -----END PGP SIGNATURE-----
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.=20
> Download
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] problem with CASTp plugin

[<jer...@ne...>]

Hello, 
   We are running Python v2.2.3 on Red Hat Enterprise 3 which is almost like Red Hat 9 and/or Fedora Core 1. Our RedHat version seems to be choking on the pyc file. The following is the error we get.
  
Exception in plugin 'CASTpyMOL' -- Traceback follows... 
Traceback (most recent call last): 
File "modules/pmg_tk/PMGApp.py", line 109, in initialize_plugins 
ImportError: Bad magic number in /usr/lib/python2.2/site-packages/pymol/modules/pmg_tk/startup/CASTpyMOL. 
pyc 
Error: unable to initialize plugin 'CASTpyMOL'. 
  
 
We have contacted the plugin authors but have been unable to solve this problem.
 
Thanks, 
JJ
 
  
__________________________________________________________________
Look What The New Netscape.com Can Do!
Now you can preview dozens of stories and have the ones you select delivered to you without ever leaving the Top Home Page. And the new Tool Box gives you one click access to local Movie times, Maps, White Pages and more.  See for yourself at http://netcenter.netscape.com/netcenter/

Re: [PyMOL] Mac OS X 10.4.3

[Serge C. <ser...@us...>]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Got exactly the same problem on a 800MHz TiBook
I was planning to try on a Dual G5, but had not the time today...


Serge.

Le 3 nov. 05 =E0 23:05, Brian J Goodfellow a =E9crit :

> Hi Mac users,
>
> has anyone noticed an annoying flickering appearing when rotating a =20=

> molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20
> under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20=

> the window is moved then the flickering disappears. However, if a =20
> ray trace is then drawn the problem starts again until the window =20
> is moved again - very annoying!
>
> Brian Goodfellow
>


*******************************************************************
Dr. Serge COHEN
GPG Key ID: 9CBB58FB

N.K.I.
Department of Molecular Carcinogenesis
Plesmanlaan 121
1066 CX Amsterdam; NL

E-Mail: s....@nk...
Tel : +31 20 512 2053
*******************************************************************

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.1 (Darwin)

iD8DBQFDapuW5EPeG5y7WPsRAlA1AJ93hPA3eALJX10AQ/HVo7J6dA914gCeMz1E
AJkFJDwrG820njkblBCpqeE=3D
=3DF8UC
-----END PGP SIGNATURE-----

Re: [PyMOL] Mac OS X 10.4.3

[James S. <jst...@sc...>]

Yes, its annoying me too (powerbook G4). Flickers even with the=20
MacPyMOL_beta version.
James

----------------------------------------
Dr. James Stevens
Asst. Prof., Dept. of Molecular Biology
The Scripps Research Institute
10550 North Torrey Pines Road-BCC206
La Jolla
CA 92037
USA
----------------------------------------
Tel. (858)-784-9878
Fax. (858)-784-2980
E-mail. jst...@sc...
----------------------------------------


On Thu, 3 Nov 2005, Brian J Goodfellow wrote:

> Hi Mac users,
>
> has anyone noticed an annoying flickering appearing when rotating a molec=
ule=20
> in PymolX11 and MacPyMOL under 10.4.3 that wasn't present under 10.4.2? T=
he=20
> problem appears on both my iBookG4 and iMacG5. If the window is moved the=
n=20
> the flickering disappears. However, if a ray trace is then drawn the prob=
lem=20
> starts again until the window is moved again - very annoying!
>
> Brian Goodfellow
>
>
> *******************************************
> Brian J Goodfellow
> Departamento de Qu=CCmica
> Universidade de Aveiro
> 3810-193 Aveiro, Portugal
> Tel: +351 234 401506, Fax: +351 234 370084
> http://www.dq.ua.pt/ingles/index_mem.htm
> *******************************************
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server. Downl=
oad
> it for free - -and be entered to win a 42" plasma tv or your very own
> Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] Mac OS X 10.4.3

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

Hi Mac users,

has anyone noticed an annoying flickering appearing when rotating a =20
molecule in PymolX11 and MacPyMOL under 10.4.3 that wasn't present =20
under 10.4.2? The problem appears on both my iBookG4 and iMacG5. If =20
the window is moved then the flickering disappears. However, if a ray =20=

trace is then drawn the problem starts again until the window is =20
moved again - very annoying!

Brian Goodfellow


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

Re: [PyMOL] Viewing cavities?

[Sebastien M. <seb...@ig...>]

> Marcus,
>     Here is one way (courtesy Kyle Lassila):
> Check out VOIDOO:
> http://xray.bmc.uu.se/usf/voidoo.html
>=20
> Then:
> Use VOIDOO to make a map of the cavity.  That gives a
> map in one of the electron density formats, .ezd.  Then use MAPMAN (als=
o=20
> found as Uppsala Software Factory) to
> convert to .ccp4 so that pymol can read it.
>=20
> Load the map with "load filename.ccp4".
> View the map with "isomesh msh1,filename,1.0"
>=20
> mapman input file:
> RE m1 cavity_1.ezd NEWEZD
> WR m1 cavity_1.ccp4 CCP4
> QU
>=20
> sample voidoo input file:
> c
> n
> voidoo_etc/cavity.lib
> design.pdb
> 0.75
> 1.2
> 20
> 1.05
> 1
> y
> 49.1 32.7 46.5
> n
> cavity.log
> y
> 10
> o
> 0.90
> 15
> 0.05
> 0.05
> n
> y
> cavity
> 0.2
> n
>=20
> Eric

Hi Marcus,
You can install the CASTp plugin for PyMOL :
http://cast.engr.uic.edu/cast/?mode=3DCASTpyMOL

CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface=20
Topography of proteins" and analyzes the "Anatomy of Protein Pockets and=20
Cavities".
So, with the plugin, you can get every cavities (pockets), CASTp has=20
predicted, automatically.

I hope this will help you.

>> Hello all,
>>
>> The surface rendering in PyMOL is quite nice, but I cannot separate=20
>> the "branches" of the surface.  That is, I would like to view a large=20
>> cavity inside of a protein independently from the outer, solvent=20
>> accessible surface.  Is anyone aware of a means to do this?
>>
>> Marcus Collins
>>
>> **********************************************************************=
*******=20
>>
>>                               Marcus D. Collins
>>      Gruner Biophysics Group, Cornell University Dept. of Physics, LAS=
SP
>>              (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
>>        "You have opened a new door, and I share this with you,
>>             for I have been where you are now."
>> **********************************************************************=
*******=20

--=20
S=E9bastien Moretti
http://www.igs.cnrs-mrs.fr/
CNRS - IGS
31 chemin Joseph Aiguier
13402 Marseille cedex

RE: [PyMOL] cmd.quit() kills pymol together with the external python launcher

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

PyMOL can't be stopped and restarted within a Python -- it terminates
the process.

However, you can hide the graphics window as needed...

cmd.window("hide")
cmd.window("show")

(in the future, pymol2 will support class-like behavior.)

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 Dmitriy
> Sent: Saturday, October 29, 2005 10:07 PM
> To: pym...@li...
> Subject: [PyMOL] cmd.quit() kills pymol together with the=20
> external python launcher
>=20
> Hello
>=20
> I have a question about cmd.quit() behavior.
> here goes simplest example:
> -----------------------------------------------------
> import __main__
> __main__.pymol_argv =3D [ 'pymol', '-qx' ]
>=20
> import pymol
> pymol.finish_launching()
>=20
> from pymol import cmd
>=20
> raw_input("type something")
> cmd.quit()
> print "finfished"
> ----------------------------------------------------
> cmd.quit() kills the whole program, not just PyMol's window.
> i.e. "finished" is never printed.
> Is it possible somehow to close only PyMol without=20
> interrupting the program?
> =20
> What I want to be able to do in general is to launch PyMol=20
> from my program, plot some data then close PyMol. Then launch=20
> PyMol again if I need to plot some things again, plot, close,=20
> and so on.  All these things related to PyMol are separated=20
> in a class. Calling cmd.quit() simply ruins the whole program.
>=20
> Pymol ver. 20beta I think (latest from CVS)
>=20
> Help is really appreciated
> Thanks
>     Dmitriy
>=20
>=20
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>=20
>=20
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Re: [PyMOL] Viewing cavities?

[Eric Z. <zo...@ca...>]

Marcus,
	Here is one way (courtesy Kyle Lassila):
Check out VOIDOO:
http://xray.bmc.uu.se/usf/voidoo.html

Then:
Use VOIDOO to make a map of the cavity.  That gives a
map in one of the electron density formats, .ezd.  Then use MAPMAN (also 
found as Uppsala Software Factory) to
convert to .ccp4 so that pymol can read it.

Load the map with "load filename.ccp4".
View the map with "isomesh msh1,filename,1.0"

mapman input file:
RE m1 cavity_1.ezd NEWEZD
WR m1 cavity_1.ccp4 CCP4
QU

sample voidoo input file:
c
n
voidoo_etc/cavity.lib
design.pdb
0.75
1.2
20
1.05
1
y
49.1 32.7 46.5
n
cavity.log
y
10
o
0.90
15
0.05
0.05
n
y
cavity
0.2
n

Eric

Marcus Collins wrote:
> Hello all,
> 
> The surface rendering in PyMOL is quite nice, but I cannot separate the 
> "branches" of the surface.  That is, I would like to view a large cavity 
> inside of a protein independently from the outer, solvent accessible 
> surface.  Is anyone aware of a means to do this?
> 
> Marcus Collins
> 
> ***************************************************************************** 
> 
>                               Marcus D. Collins
>      Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP
>              (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
>        "You have opened a new door, and I share this with you,
>             for I have been where you are now."
> ***************************************************************************** 
> 
> 
> 
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[PyMOL] (no subject)

[D. B. P. <bp...@ch...>]

To all:

I am new to PyMol, and to structure programs in general. I am trying to 
build a beta sheet from a peptide molecule in the pdb. I can't seem to 
load more than one molecule at a time, and I do not see any 
instructions related to it in the manual. I am running version 0.98 
beta 32 on a Mac G5 with the OS X (10.3.9) operating system. Any help 
would be greatly appreciated.

Many thanks,
Bryan Prince