pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] Re: [o-info] KVM purchasing advice

[Cameron M. <cm...@uc...>]

Hi Joe and other KVM users,

Not to revive too old of a thread (see emails below), but I thought you 
or some others might like to know what final KVM solution I settled upon 
for a mixture of windows and linux boxes.

I initially tried the common Belkin OmniView SOHO 4-port KVM switch 
(PS/2 connectors) and found it to work OK, except that most of the time 
the USB mouse (connected via USB/PS2 adapter) was completely 
unresponsive when switched to one of the linux boxes (I think it was the 
FC4 box).  So, based on its affordability, tech specs, and others 
people's recommendations, I then tried IOGEAR's USB-capable MiniView III 
(model # GCS1714).  It worked very well for toggling between a couple of 
Linux boxes (running FC4 and RHEL WS 4) connected to a high-res 22" CRT 
(2048x1536 @ 79 Hz refresh) and a USB keyboard and mouse -- at least in 
terms of little to no delay for mouse and keyboard responsiveness, 
playing well w/ the linux OS, etc... However, there was a serious 
problem with shadowing/ghosting of the graphics (at least at higher 
resolutions... 2048x1536 and 1920x1440).  After enduring a session w/ 
the IOGEAR tech rep., it was pretty much decided that this KVM switch 
simply "couldn't handle this size monitor at these resolutions...".  So, 
given that my earlier Belkin experience was OK in terms of graphics 
quality, I then tried a cheaper solution (<$70 from Fry's) -- Belkin's 
"2-port KVM switch with audio support and built-in cabling" (Belkin 
model # F1DL102U) -- and found that this worked perfectly... the USB 
mouse and keyboard both work fine on both Linux boxes, there are no 
aberrations of the graphics display (I didn't even have to resort to 
Belkin's "Gold Series" VGA cables for suitable image quality!), and only 
minimal lag (1-2 seconds) when toggling between machines...

The main lesson I learned from all this is (1) to avoid using USB-to-PS2 
adapters for keyboard and mice connected to KVM switches operating with 
linux and (2) don't use the IOGEAR MiniView III switch for high res 
displays.

Cam



=== D. Joe Anderson wrote (on 07/27/2005 08:48 AM): ===

>On Fri, Jul 15, 2005 at 01:15:13PM -0700, Cameron Mura wrote:
>
>  
>
>>there may be many O and PyMOL users who use stereo with a monitor 
>>connected through a KVM switch? 
>>    
>>
>
>  
>
>>>3) would be nice if the KVM, linux boxes, and USB mouse were all 
>>>interoperable.  Reason i point this out is that the logitech USB mouse 
>>>i had been using w/ the FC4 box freaked-out (at least on the FC4 box) 
>>>after being plugged-in (via USB<-->PS/2 adapter) to the PS/2 connector 
>>>of a Belkin KVM switch (the popular OmniView SOHO F1DS104T model)...
>>>      
>>>
>
>I've found that when switching amongst Linux boxes with a
>two-port Belkin OmniView PS/2-VGA KVM that I have to switch out
>of X Windows and into a virtual terminal and then back to X
>Windows before the pointer and mouse will work well again
>together.  So, in terms of specific keystrokes, that is for
>example Ctrl-Alt-F1 to switch from X to virtual terminal 1, and
>then Alt-F7 to switch back to X (though of course X is at Alt-F5
>on various live CDs like KNOPPIX).
>
>I'm in the process now of deploying KVMs more widely for general
>use, using a mix of connectors, including USB-VGA KVMs with
>Dell-Dell combinations and Dell-Mac combinations with and
>without USB-to-PS/2 and PS/2-to-USB adapters , and in one case,
>using a (rather pricey, but seems to work OK) DVI-USB KVM to
>switch between a G4 and a G5 PowerMac.  
>
>I have not run any quad-buffered stereo through any of the KVMs,
>yet, but hope to get the chance to do that (even if just in full
>screen mode, or in Linux if/when the drivers catch up) on the G5
>PowerMacs we're deploying now.  I'd also appreciate reading
>about experience with this that anyone has had.
>
>  
>

-- 
Cameron Mura
UCSD

[PyMOL] Re: Using CMYK color space

[<rg...@el...>]

On [2005-Aug-19]  Christopher Colbert <co...@ch...> wrote:
>
> Hi Pymol'rs,
>
> I have search the Wiki and Mail-list archive to find a protocul for using
> the CMYK color space, but have only found "color-safe" definitions.
>
> My Question(s):
>
> When do you define the color space during the creation of a figure to
> ensure usage of a particular color space, ie. cmyk?  Can this be done from
> a script and with which command, "space cmyk"?
>
> >From my understanding from the mail-list, I need to define the color
> space before I use any color.  Is this correct?  Can it also be done
> retroactively prior to ray tracing?
>
> Finally, once the color space is defined, do all the rgb colors get
> redefined automatically, or does this need to happen manually?  I
> found the table for the biggest culprits, but Warren pointed out there was
> internally defined colors for the atom types. Does someone have a macro
> that redefines the pymol defined colors including those for the atoms?

Chris,

CMYK is a device-dependent colour space, i.e. the colour that is chosen to
match to a particular RGB colour depends on the machine it is going to be
printed on (and hence the inks that will be used in the printing).
Therefore there is no one-to-one mapping of CMYK values to RGB values
(even with a  profile defining how the RGB values should be displayed).

Since pymol's idea of CMYK is so limited (and from a printer's point of
view probably shouldn't even exist) you are far better off getting the RGB
image out of pymol to look just the way you want it to (assuming a
calibrated display and approprate colour profile) and then use a
full-featured converter to generate the appropriate CMYK image for the
device it is going to be printed on. One suggestion for a converter is
GIMP (soon to be renamed something else) because it does know how to
use/respect ICC profiles.

Rich

[PyMOL] Using CMYK color space

[Christopher C. <co...@ch...>]

Hi Pymol'rs,

I have search the Wiki and Mail-list archive to find a protocul for using
the CMYK color space, but have only found "color-safe" definitions. 

My Question(s):

When do you define the color space during the creation of a figure to
ensure usage of a particular color space, ie. cmyk?  Can this be done from
a script and with which command, "space cmyk"?

From my understanding from the mail-list, I need to define the color
space before I use any color.  Is this correct?  Can it also be done
retroactively prior to ray tracing?

Finally, once the color space is defined, do all the rgb colors get
redefined automatically, or does this need to happen manually?  I
found the table for the biggest culprits, but Warren pointed out there was
internally defined colors for the atom types. Does someone have a macro
that redefines the pymol defined colors including those for the atoms?

Thanks for your help,

Chris

Christopher L. Colbert, Ph.D.
Research Associate                                Phone: (214) 645 5944
University of Texas Southwestern Medical Center	  FAX:   (214) 645 5945
6001 Forest Park Lane
Dallas, TX 75390

Re: [PyMOL] question on cctbx and pymol

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

> I am trying some of pymol scripts from Prof. Robert L. Campbell, which
require cctbx module. but I don't know how to put pymol and cctbx
togther.
> I download window version of cctbx/python2.4 bundle. and I download
pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I
got
> an error message that pymol can't locate python when I tried to install
pymol into site-packages directory. I don't know how to solve this
problem
> since I am new to python scripting. Could anyone give me a hand? Thanks!

There could be a couple of things.
The first thing to check is that the python path (called PYTHONHOME on
unix; not sure about windows) is set up correctly (the executable path may
need adjusting as well, maybe try running with the full path).  A
workaround for python path that should work on windows is to add few lines
to the beginning of a python script: import sys (may not be needed if sys
module has already been imported), followed by sys.path.append("full path
to the python/cctbx/pymol modules you want to install).
For python on windows, any compiled modules (which includes parts of cctbx
and pymol) have to be compiled with the same compiler (VisualC++,gcc,
etc), and possible same version, as the python interpreter was complied
with.  I'm not sure how you'd go about resolving this, other than hoping
the compiler versions happened to match, or trying to compile both with
the same compiler.
The third possible problem could be that both cctbx and pymol can come
packaged with their own python interpreters (I'm not sure how the windows
executable versions are packaged), so you'll need to make sure that both
are using the same interpreter.

For unix/linux(/os x?), this the fix would be to install everything from
source, and use environmental variables to make sure that pymol knows
about the cctbx packages, and cctbx knows which python to install itself
to.  For windows it's likely to be more difficult, if it was me I'd
install cygwin (unix emulator for windows), and just install everything
there.

Hope some of this is helpful,

Pete

Pete Meyer
Fu Lab
BMCB grad student
Cornell University

[PyMOL] Re: PyMOL-users digest, Vol 1 #981 - 12 msgs

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

Nat,

I'm working on a 'smart' alignment program, hence the rotation and
translation part is a subset of the work.  (The part that's written thus
far is the Kabsch algorithm for optimal alignment of two sets of points
of vectors).

I've uploaded the complete script, but what you want is the part towards
the end, which answers your question, summarized here.  (I'll skip the
lesson and just post the code.)

Given a 3x3 matrix, U; and, the translation vector, T2; and, a vector of
3D points, v; do:

stored.mol2 = map(lambda \
v:[T2[0]+((v[0]*U[0][0])+(v[1]*U[1][0])+(v[2]*U[2][0])),  \
   T2[1]+((v[0]*U[0][1])+(v[1]*U[1][1])+(v[2]*U[2][1])),  \
   T2[2]+((v[0]*U[0][2])+(v[1]*U[1][2])+(v[2]*U[2][2]))], \
   stored.mol2)

Or FinalPoint = TranslationVector + (3DVector * 3x3RotationMatrix).  If
I recall correctly, you need to rotate the points to origin to avoid an
affine operation.

The Kabsch algorithm in Python is at:
http://www.pymolwiki.org/index.php/Kabsch

HTH,

-- Jason

On Thu, 2005-08-18 at 18:26 -0700,
pym...@li... wrote:
> Message: 4
> Date: Wed, 17 Aug 2005 18:03:09 -0700 (PDT)
> From: Nat Echols <ec...@uc...>
> To: pym...@li...
> Subject: [PyMOL] applying matrices to objects
> 
> 
> Is there a simple tool for taking a rotation and translation matrix -
> in 
> this case, the BIOMT records from a PDB file - and applying it to an 
> object?  Doesn't necessarily have to be in PyMOL; a simple
> script/program 
> would do.
> 
> thanks,
> Nat
-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki

Re: [PyMOL] sudden flip / skip / jump while rotating stereo

[Indraneel M. <ind...@sm...>]

Thanks a lot. Robert told me the same thing at noon, so I actually did
this for the past few hours, and it never jumped.

One more question, will it be possible to select residues at the
sequence view on the top of the screen without having to drag the
slider, in future builds? (ie. if one have to select more residues than
are displayed, currently one has to select, then drag the slider until
unselected residues come into view, then select and so on. How about the
unselected residues come into view and are selected when the mouse goes
off the view to the left or right?)

Thanks,
Indraneel

On Thu, Aug 18, 2005 at 06:29:19PM -0700, Warren DeLano wrote:
> Indraneel,
> 
> When you're in walleye or crosseye stereo mode, try to keep the mouse on
> either the right-hand or left-hand side of the screen.  If you cross
> over the center or edge of the window, then you'll get that annoying
> jump.
> 
> Fortunately, the problem is eliminated in future builds.
> 
> 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 
> > Indraneel Majumdar
> > Sent: Thursday, August 18, 2005 12:32 PM
> > To: pym...@li...
> > Subject: [PyMOL] sudden flip / skip / jump while rotating stereo
> > 
> > Hi,
> > 
> > I could not find anything on this in the archives or google. 
> > While rotating a stereo image using the mouse, the molecule 
> > suddenly flips back by about 90 degrees. Seems like I get to 
> > see only one side of a molecule if rotated on one axis. I can 
> > get to see the other side if the molecule is made to do 
> > somersaults on all axes, and then I forget what I was looking 
> > at. Everything else is normal, but this does hurt an already 
> > bulging eyeball. AFAIR this has always been the case (~ last
> > 4 yrs) but I've never had to look at so many structures as 
> > I'm doing now... This happens with all types of graphics 
> > cards on a i32 debian box.
> > 
> > It will really help if someone can let me know what setting 
> > to tweak, or even which lines to code to patch.
> > 
> > TIA,
> > Indraneel
> > 
> > --
> > http://prodata.swmed.edu
> > 
> > 
> > -------------------------------------------------------
> > SF.Net email is Sponsored by the Better Software Conference & EXPO
> > September 19-22, 2005 * San Francisco, CA * Development 
> > Lifecycle Practices
> > Agile & Plan-Driven Development * Managing Projects & Teams * 
> > Testing & QA
> > Security * Process Improvement & Measurement * 
> > http://www.sqe.com/bsce5sf
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
> > https://lists.sourceforge.net/lists/listinfo/pymol-users
> > 
> > 
> > 

-- 
http://prodata.swmed.edu

RE: [PyMOL] sudden flip / skip / jump while rotating stereo

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

Indraneel,

When you're in walleye or crosseye stereo mode, try to keep the mouse on
either the right-hand or left-hand side of the screen.  If you cross
over the center or edge of the window, then you'll get that annoying
jump.

Fortunately, the problem is eliminated in future builds.

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
> Indraneel Majumdar
> Sent: Thursday, August 18, 2005 12:32 PM
> To: pym...@li...
> Subject: [PyMOL] sudden flip / skip / jump while rotating stereo
>=20
> Hi,
>=20
> I could not find anything on this in the archives or google.=20
> While rotating a stereo image using the mouse, the molecule=20
> suddenly flips back by about 90 degrees. Seems like I get to=20
> see only one side of a molecule if rotated on one axis. I can=20
> get to see the other side if the molecule is made to do=20
> somersaults on all axes, and then I forget what I was looking=20
> at. Everything else is normal, but this does hurt an already=20
> bulging eyeball. AFAIR this has always been the case (~ last
> 4 yrs) but I've never had to look at so many structures as=20
> I'm doing now... This happens with all types of graphics=20
> cards on a i32 debian box.
>=20
> It will really help if someone can let me know what setting=20
> to tweak, or even which lines to code to patch.
>=20
> TIA,
> Indraneel
>=20
> --
> http://prodata.swmed.edu
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development=20
> Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams *=20
> Testing & QA
> Security * Process Improvement & Measurement *=20
> http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>=20
>=20
>=20

Re: [PyMOL] question on cctbx and pymol

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

Actually I was wondering the same thing, except how to set it up in 
linux. I was able to compile the cctbx but I'm not sure how to get it to 
show up as a python module so that Pymol scripts (e.g. Dr. Campbell's 
draw_cell.py) can work. Any help would be greatly appreciated.

Yi Zhang wrote:
> Dear all,
> 
> I am trying some of pymol scripts from Prof. Robert L. Campbell, which 
> require cctbx module. but I don't know how to put pymol and cctbx 
> togther. 
> 
> Sincerely,
> 
> Yi Zhang

Re: [PyMOL] mouse middle button

[Bronwyn C. <bro...@st...>]

Thank-you, that worked beautifully.  Before the crash the MouseWorks  
software can't have been working properly.

Bronwyn

On 18/08/2005, at 10:01 AM, Xavier Deupi wrote:

> Hi Bronwyn,
>
> I had the same problem (using a Logitech MX310 under OS X 10.4.2).  
> As somebody previously suggested, I just uninstalled the Logitech  
> software, so the os treats the mouse as 'generic'. And now the  
> middle button behaves as expected.
>
> hope this helps,
>
> Xavier
>
> Bronwyn Carlisle wrote:
>
>
>> Hi, A couple of things:
>>
>> a) I've just installed the latest MacPymol (after having a major   
>> crash and having to re-install EVERYTHING), and my middle mouse   
>> button doesn't seem to work. I can't move things around on the   
>> screen.  The other buttons work fine, and the middle one scrolls  
>> OK,  so I can slab - but I want to move things!!  I have played  
>> with the  MouseWorks thing in System Prefs, and can change the  
>> middle button  clicking to do what any of the other button clicks  
>> do, but there is  no option for "middle button".  Is there a key  
>> combination I can put  in that will let it move things?
>>
>> b)I'm trying to make a surface and a cartoon of a CA-only  
>> structure.   A search of my email archive tells me that by now  
>> Pymol should be  able to create at least a ribbon from this sort  
>> of file, but I can't  figure out how to do it.  Can someone please  
>> instruct me?
>>
>> Ta
>>
>> Bronwyn
>>
>>
>>
>> Bronwyn Carlisle
>> Biochemistry Department
>> University of Otago
>> PO Box 56
>> 710 Cumberland St
>> Dunedin
>>
>> email: bro...@st...
>> tel: +64 (0)3 4797704
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle  
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
> -- 
> Xavier Deupi, Ph.D.
> Department of Molecular and Cellular Physiology
> Beckman Center for Molecular and Genetic Medicine (B161)
> 279 Campus Drive, Stanford University School of Medicine
> Stanford, CA 94305 (USA)
>
> E-mail: Xav...@st...
> Phone: +1 (650) 725-6497
> Fax : +1 (650) 725-8021
>
>


Bronwyn Carlisle
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bro...@st...
tel: +64 (0)3 4797704

[PyMOL] RE: [ccp4bb]: SUMMARY - nVidia Quadro FX 1400, FX 3400 and FX 4400

[Wang C. H. <che...@im...>]

>>>*** ABOUT RivaTuner (suggested by Wang Chern Hoe): ***
I'll keep that trick for my personal record and use, but we don't want =20
to use any dual boot solution in the lab (at least not yet). For a =20
whole lab solution I will agree with  Cameron (cm...@uc...) who =20
suggests to opt for a real hardware stereo card.
But for personal purposes I find interesting to turn a Geforce 6800 =20
into a Quadro and be able to run O, NOC and PyMol from the XP side, but  =

I've read:
- this will turn it into a Quadro 540 but not 4400 (COULD YOU CONFIRM =20
THIS, WANG ?)


The Geforce 6800 has 12-pixel pipelines & 4 vertex pipelines. Now =
compare that with Geforce 6800GT or 6800Ultra which has 16-pixel pipes =
and 5-vertex pipelines. Now it is known that a Geforce 6800 card with an =
AGP interface can be soft-modded via Rivatuner to unmask all its =
21-pipelines. You can also unlock its professional capabilities to =
provide you with stereo. As a further step, it will automatically =
determine a safe amount of overclocking for the GPU core and the =
graphics memory core. The end result is an improved performance. However =
if your Geforce 6800 comes with a PCI-E interface, then its GPU core =
(NV41) has only 12=3Dpixel pipelines in silico, and hardware unmasking =
will not work, although it is still possible to unlock stereo and to =
overclock it.

If I am not mistaken, the equivalent of Geforce 6800 is Quadro 1400, and =
the equivalent of Geforce 6600 is Quadro 540. In both cases, the =
performance is more than sufficient for crystallography.


>>>>- as asked Sabuj (sab...@va...) what is the magic =
=20
taht modify the pin connector for the emitter.
Wang could you tell us how physically the connection with the emitter =20
is made ?


The Geforce cards do not have a 3-pin mini-DIN stereo sync interface. So =
just buy a 60-GX-NSR from http://www.nuvision3d.com/the60gx.html to =
solve this problem


>>>>[Doug Bailley; ba...@nc...]
Our "standard" linux workstation is as follows.
Dell Precision 370/380, Pent.4-3.6, 1GB RAM 120GB SATA, DVD+-RW, Quadro  =

FX1400
NEC-Mitsubishi FP2141SB-BK 22" CRT
NuVision 60GX Wireless stereo emitter and glasses
RedHat Enterprise Linux WS.


Our set-up is similar to the one above, except that we use Centos 4.1, =
which is the free equivalent of Redhat Enterprise Linux ES 4. Download =
your copy from http://www.centos.org.

We also have a SGI Dial Box connected. It works under O on a Linux box =
after installing Joe Krahn's freeglut mod at =
http://spdbv.niehs.nih.gov/resources/




DISCLAIMER:
This email is confidential and may be privileged. If you are not the =
intended recipient, please delete it and notify us immediately. Please =
do not copy or use it for any purpose, or disclose its contents to any =
other person as it may be an offence under the Official Secrets Act. =
Thank you.

[PyMOL] sudden flip / skip / jump while rotating stereo

[Indraneel M. <ind...@sm...>]

Hi,

I could not find anything on this in the archives or google. While
rotating a stereo image using the mouse, the molecule suddenly flips
back by about 90 degrees. Seems like I get to see only one side of a
molecule if rotated on one axis. I can get to see the other side if
the molecule is made to do somersaults on all axes, and then I forget
what I was looking at. Everything else is normal, but this does hurt
an already bulging eyeball. AFAIR this has always been the case (~ last
4 yrs) but I've never had to look at so many structures as I'm doing
now... This happens with all types of graphics cards on a i32 debian
box.

It will really help if someone can let me know what setting to tweak, or
even which lines to code to patch.

TIA,
Indraneel

-- 
http://prodata.swmed.edu

[PyMOL] question on cctbx and pymol

[Yi Z. <yz...@xr...>]

Dear all,

I am trying some of pymol scripts from Prof. Robert L. Campbell, which 
require cctbx module. but I don't know how to put pymol and cctbx togther. 
I download window version of cctbx/python2.4 bundle. and I download 
pymol-0_98rc5-bin-win32-py24.zip. Installation of cctbx is fine, but I got 
an error message that pymol can't locate python when I tried to install 
pymol into site-packages directory. I don't know how to solve this problem 
since I am new to python scripting. Could anyone give me a hand? Thanks!

Sincerely,

Yi Zhang 

Re: [PyMOL] Ca-only and surfaces

[Bronwyn C. <bro...@st...>]

Yes, I know the move command, but my mouse USED to translate things  
when you clicked the scroll wheel, it just doesn't since I had to re- 
install things.  I like using it rather than the command line.

Bronwyn


On 18/08/2005, at 8:14 AM, Peter Adrian Meyer wrote:

> Hi Bronwyn,
>
>
>> a) I've just installed the latest MacPymol (after having a major
>> crash and having to re-install EVERYTHING), and my middle mouse
>> button doesn't seem to work. I can't move things around on the
>> screen.  The other buttons work fine, and the middle one scrolls OK,
>> so I can slab - but I want to move things!!  I have played with the
>> MouseWorks thing in System Prefs, and can change the middle button
>> clicking to do what any of the other button clicks do, but there is
>> no option for "middle button".  Is there a key combination I can put
>> in that will let it move things?
>>
>
> move x,5.0; should work as far as translating the model.  With a
> three-button mouse (no scroll wheel), middle mouse translates and
> shift-right mouse moves the clipping planes (on unix, at least, but it
> might be of use for getting the system preferences configured).
>
>
>>
>> b)I'm trying to make a surface and a cartoon of a CA-only structure.
>> A search of my email archive tells me that by now Pymol should be
>> able to create at least a ribbon from this sort of file, but I can't
>> figure out how to do it.  Can someone please instruct me?
>>
>
> Can't help you here...I've been wondering about how to do a ca- 
> trace for a
> while (not sure what use a surface from a CA model would be,  
> though...).
>
> Hope this helps,
>
> Pete
>
>
>>
>> Ta
>>
>> Bronwyn
>>
>>
>>
>> Bronwyn Carlisle
>> Biochemistry Department
>> University of Otago
>> PO Box 56
>> 710 Cumberland St
>> Dunedin
>>
>> email: bro...@st...
>> tel: +64 (0)3 4797704
>>
>>
>>
>>
>> -------------------------------------------------------
>> SF.Net email is Sponsored by the Better Software Conference & EXPO
>> September 19-22, 2005 * San Francisco, CA * Development Lifecycle
>> Practices
>> Agile & Plan-Driven Development * Managing Projects & Teams *  
>> Testing & QA
>> Security * Process Improvement & Measurement * http://www.sqe.com/ 
>> bsce5sf
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>


Bronwyn Carlisle
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bro...@st...
tel: +64 (0)3 4797704

Re: [PyMOL] mouse middle button

[Xavier D. <Xav...@st...>]

Hi Bronwyn,

I had the same problem (using a Logitech MX310 under OS X 10.4.2). As 
somebody previously suggested, I just uninstalled the Logitech software, 
so the os treats the mouse as 'generic'. And now the middle button 
behaves as expected.

hope this helps,

Xavier

Bronwyn Carlisle wrote:

> Hi, A couple of things:
>
> a) I've just installed the latest MacPymol (after having a major  
> crash and having to re-install EVERYTHING), and my middle mouse  
> button doesn't seem to work. I can't move things around on the  
> screen.  The other buttons work fine, and the middle one scrolls OK,  
> so I can slab - but I want to move things!!  I have played with the  
> MouseWorks thing in System Prefs, and can change the middle button  
> clicking to do what any of the other button clicks do, but there is  
> no option for "middle button".  Is there a key combination I can put  
> in that will let it move things?
>
> b)I'm trying to make a surface and a cartoon of a CA-only structure.   
> A search of my email archive tells me that by now Pymol should be  
> able to create at least a ribbon from this sort of file, but I can't  
> figure out how to do it.  Can someone please instruct me?
>
> Ta
>
> Bronwyn
>
>
>
> Bronwyn Carlisle
> Biochemistry Department
> University of Otago
> PO Box 56
> 710 Cumberland St
> Dunedin
>
> email: bro...@st...
> tel: +64 (0)3 4797704
>
>
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle 
> Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing 
> & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

-- 
Xavier Deupi, Ph.D.
Department of Molecular and Cellular Physiology
Beckman Center for Molecular and Genetic Medicine (B161)
279 Campus Drive, Stanford University School of Medicine
Stanford, CA 94305 (USA)

E-mail: Xav...@st...
Phone: +1 (650) 725-6497
Fax : +1 (650) 725-8021

[PyMOL] applying matrices to objects

[Nat E. <ec...@uc...>]

Is there a simple tool for taking a rotation and translation matrix - in 
this case, the BIOMT records from a PDB file - and applying it to an 
object?  Doesn't necessarily have to be in PyMOL; a simple script/program 
would do.

thanks,
Nat

Re: [PyMOL] Ca-only and surfaces

[<li...@ul...>]

On Wednesday 17 August 2005 05:44, Bronwyn Carlisle wrote:
> b)I'm trying to make a surface and a cartoon of a CA-only structure.
> A search of my email archive tells me that by now Pymol should be
> able to create at least a ribbon from this sort of file, but I can't
> figure out how to do it.  Can someone please instruct me?

For the ribbon representation:

set ribbon_trace_atoms,1

I don't know about the surface representation, though.

-- 
Lieven Buts
Ultrastructure Laboratory
Vrije Universiteit Brussel

[PyMOL] carbonyls in cartoon

[Jim S. C. a. M. M. <Jim...@br...>]

Dear All,

I am hoping someone can advise me on the best way to include main chain 
carbonyls in a cartoon figure.  I want to depict a metal centre and 
surroundings showing selected main chain carbonyls and side chains with 
remaining main chain as a secondary structure Ca trace.  How can I best 
connect main chain carbonyl carbons to my cartoon tube?

Thanks in advance- and apologies if this has come up before.

Jim
----------------------
Dr. James Spencer,
Lecturer
Department of Cellular and Molecular Medicine
University of Bristol School of Medical Sciences
University Walk
Bristol BS8 1TD
Jim...@br...
http://www.bris.ac.uk/pathandmicro/staff/spencer.html
********************
new contact nos.
Tel: 0117 928 8819
Fax: 0117 928 7896

Re: [PyMOL] Ca-only and surfaces

[Tsjerk W. <ts...@gm...>]

Hi Bronwyn,

Don't know about MacPymol, but with regards to the second issue, a
C-alpha trace, you can do it with:

set cartoon_trace,1
show cartoon

The surface will be tougher, you could play with setting the vanderwaals ra=
dius:

show surface
alter (all),vdw=3D4
rebuild

And you can repeat the last two commands for different values for the
vdwr to suit your needs. You could also play with setting the radius
for the solvent probe to determine the surface.

Hope it helps,

Tsjerk




On 8/17/05, Bronwyn Carlisle <bro...@st...> wrote:
> Hi, A couple of things:
>=20
> a) I've just installed the latest MacPymol (after having a major
> crash and having to re-install EVERYTHING), and my middle mouse
> button doesn't seem to work. I can't move things around on the
> screen.  The other buttons work fine, and the middle one scrolls OK,
> so I can slab - but I want to move things!!  I have played with the
> MouseWorks thing in System Prefs, and can change the middle button
> clicking to do what any of the other button clicks do, but there is
> no option for "middle button".  Is there a key combination I can put
> in that will let it move things?
>=20
> b)I'm trying to make a surface and a cartoon of a CA-only structure.
> A search of my email archive tells me that by now Pymol should be
> able to create at least a ribbon from this sort of file, but I can't
> figure out how to do it.  Can someone please instruct me?
>=20
> Ta
>=20
> Bronwyn
>=20
>=20
>=20
> Bronwyn Carlisle
> Biochemistry Department
> University of Otago
> PO Box 56
> 710 Cumberland St
> Dunedin
>=20
> email: bro...@st...
> tel: +64 (0)3 4797704
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practic=
es
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & Q=
A
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

[PyMOL] SUMMARY - nVidia Quadro FX 1400, FX 3400 and FX 4400

[Philippe B. <phi...@un...>]

Hi Folks,

Here are my conclusions about the nVidia graphic cards.

The benchmarks found on Tom's hardware web site show that the =20
performances of the AGP8x FX 1100 are about the same as the PCIe FX =20
1300. Taking that assumption I just took the average spec out of the 3 =20=

given on nVidia's web page (see LINKS below).

*** This gives the following table: ***

Graphic card		FX 4400	FX 3400	FX 1400	FX 1300	FX 1100
Bus type			PCIe		PCIe		PCIe		=
PCIe		AGP 8x
Perf(rel to 1100)	1.97		1.73		1.65		=
1		1
Price(rel to 1100)	2.95		1.8		0.8		=
0.5		1
Ratio Perf/Price	0.66		0.96		2.06		=
2		1

(FX 1100 costs about 780 Euros)

These numbers are probably not extremely accurate, but the tendency =20
shown in this table looks in pretty good agreement with the numerous =20
specs reported on hardware.fr (see LINKS below; unfortunately this =20
paper written in French, but charts and graphics are easy to catch).

They also look in agreement with the answers I got from our =20
crystallographic bulletin boards (see QUOTES below).

*** CONCLUSION: we'll go for an FX 1400 ! ***

*** ABOUT RivaTuner (suggested by Wang Chern Hoe): ***
I'll keep that trick for my personal record and use, but we don't want =20=

to use any dual boot solution in the lab (at least not yet). For a =20
whole lab solution I will agree with  Cameron (cm...@uc...) who =20
suggests to opt for a real hardware stereo card.
But for personal purposes I find interesting to turn a Geforce 6800 =20
into a Quadro and be able to run O, NOC and PyMol from the XP side, but =20=

I've read:
- this will turn it into a Quadro 540 but not 4400 (COULD YOU CONFIRM =20=

THIS, WANG ?)
- this could be done only on some graphic boards from UNIKA (without =20
any reseller in France I think)
- as asked Sabuj (sab...@va...) what is the magic =20
taht modify the pin connector for the emitter.
Wang could you tell us how physically the connection with the emitter =20=

is made ?

*** LINKS ***
BENCHMARK RESULTS:

FX 1100, ATIfireGLx2(t):
http://graphics.tomshardware.com/graphic/20040323/opengl-fx1100-x2t=20
-08.html

FX 1300, FX 3400, ATIfireGLv5100:
http://graphics.tomshardware.com/graphic/20040816/opengl-pcie-14.html

FX 1400, FX 3400, FX 4400, ATIfireGLv5100:
http://www.hardware.fr/articles/560-1/comparatif-7-cartes-3d-pro-pci-=20
express.html

AND:

nVIDIA graphic cards specs AGP8x/PCIe
http://www.nvidia.fr/object/IO_11761_fr.html

*** QUOTES ***

[J Mesters; me...@bi...]
We have two FX1100 (128 MB ram) up and running just fine under linux. =20=

The speed for openGL applications is more than satisfactory. .../... =20
Only Pymol will benefit clearly from faster cards with more memory when =20=

rendering etc..

The Iiyama HM204DT is the best (reference class) monitor around with =20
142 kHZ and 200 Hz maximum! Great stereo quality.
If that is too expensive, buy the Belinea 108035 with 125 kHz and 160 =20=

Hz maximum for half the price.
---
[Doug Bailley; ba...@nc...]
Our "standard" linux workstation is as follows.

Dell Precision 370/380, Pent.4-3.6, 1GB RAM 120GB SATA, DVD+-RW, Quadro =20=

FX1400
NEC-Mitsubishi FP2141SB-BK 22" CRT
NuVision 60GX Wireless stereo emitter and glasses
RedHat Enterprise Linux WS.

For our usage, we did not see a significant difference in performance =20=

between the FX1400 and some of the 3xxx series Quadro products we =20
tested to justify the higher cost.

The NEC-Mitsubishi FP2141SB-BK 22" CRT is an excellent monitor. Cannot =20=

comment on any others as the NEC is all that we use.
---
[Kay Diederichs; kay...@un...]
.../...
a) the nVidia FX3450 is a bit expensive (=801300); you won't notice a =20=

difference to a card of less than half the price (FX1300) in O.
.../...
---

Thanks to all and to any other contributor that I would have forgotten,
Philippe

------------------------------------------------------------------------
Philippe BENAS, Ph.D.
X-ray diffraction facility manager
Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculte de Pharmacie - Universite Paris 5
4, Avenue de l'Observatoire - Case 48
F-75270 Paris cedex 06
---
Office: +33.(0)1-5373-9831 (use ext. 9977 instead to leave a voice mail)
Fax: +33.(0)1-5373-9925
X-ray Room (rotating anode): +33.(0)1-5373-9977
X-ray Room (small molecules): +33.(0)1-5373-9679
---
Email: phi...@un...
Url: http://lcrbw.pharmacie.univ-paris5.fr/
------------------------------------------------------------------------

[PyMOL] Setting transparency for CGOs

[Mikko H. <mhu...@ab...>]

> i've just created many CGOs, which show up solid surfaces like spheres and
> ellipsoids. Is it possible to set the transparency of some CGO's to i.e. 0.5
> and leave the others solid?
> I've checked out the reference and the manual, and found something like:

The CGO support in Pymol does not quite seem to be all there; I had
CGOs appear correctly in raytracing some of the time, other times they
just would not render at all. I needed transparency, too, so I ended
up exporting everything to Povray and rendering the image there. This
requires some familiarity with Povray, because the material definition
for the transparent surfaces needs to be written manually and the CGOs
must be found in the Povray input that Pymol spews out (80 MB of text
in my case...). One way to do this is to write out the CGOs in one
Povray file and the molecules in another.

With Povray you can get shadows on CGOs and molecules inside
transparent CGOs to render correctly, which is not really possible in
2D (Photoshopping or such).

Mikko

[PyMOL] Ca-only and surfaces

[Bronwyn C. <bro...@st...>]

Hi, A couple of things:

a) I've just installed the latest MacPymol (after having a major  
crash and having to re-install EVERYTHING), and my middle mouse  
button doesn't seem to work. I can't move things around on the  
screen.  The other buttons work fine, and the middle one scrolls OK,  
so I can slab - but I want to move things!!  I have played with the  
MouseWorks thing in System Prefs, and can change the middle button  
clicking to do what any of the other button clicks do, but there is  
no option for "middle button".  Is there a key combination I can put  
in that will let it move things?

b)I'm trying to make a surface and a cartoon of a CA-only structure.   
A search of my email archive tells me that by now Pymol should be  
able to create at least a ribbon from this sort of file, but I can't  
figure out how to do it.  Can someone please instruct me?

Ta

Bronwyn



Bronwyn Carlisle
Biochemistry Department
University of Otago
PO Box 56
710 Cumberland St
Dunedin

email: bro...@st...
tel: +64 (0)3 4797704

Subject: [PyMOL] display problem (slab?)

[Michelle G. <mic...@ya...>]

Hi Marc,

I think I've come across the same problem when looking at your molecule as =
a=20
cartoon, sphere, or surface.  It seems to be related to two transparency=20
settings within pymol.  Maybe it's a bug??

Search for my name on the list.  The only two replies I have ever posted=20
pertain to this.

Also, you  should post your hardware so that if this is a bug, it can more=
=20
easily be tracked down and squashed.

Cheers,
Michelle Gill
Graduate Student
Molecular Biophysics and Biochemistry
Yale University

Content-Type=3Dmessage/rfc822
Content-Description=3Dembedded message
=46rom: Marc Vogt <mv...@es...>
To: PyM...@li...
Date: Tue, 16 Aug 2005 17:52:48 -0400 (EDT)
Subject: [PyMOL] display problem (slab?)

Hi all

=46or some reason I am now having a strange problem when I use pymol
to display molecules. =A0It acts sort of like it is in slab mode where
some of the molecule fades into nothingness. =A0However, when I spin
the molecule, the same regions remain invisible. =A0If it were a true
slab effect, the regions that I spin into the slab would become visible
and the ones out would be invisible. =A0I wouldn't worry about it and would
just restart the program to eliminate the setting, but for some reason
it seems to now be a default and happens no matter what I do. =A0
I think I'm just missing something really silly, but I can't catch it.
Any ideas on how to restore normal function?


thanks,
Marc

[PyMOL] display problem (slab?)

[Marc V. <mv...@es...>]

Hi all

For some reason I am now having a strange problem when I use pymol
to display molecules.  It acts sort of like it is in slab mode where
some of the molecule fades into nothingness.  However, when I spin
the molecule, the same regions remain invisible.  If it were a true
slab effect, the regions that I spin into the slab would become visible
and the ones out would be invisible.  I wouldn't worry about it and would
just restart the program to eliminate the setting, but for some reason
it seems to now be a default and happens no matter what I do.  
I think I'm just missing something really silly, but I can't catch it.
Any ideas on how to restore normal function?


thanks,
Marc

[PyMOL] Measuring dihedrals

[Christopher B. <cb...@st...>]

Hi All,

    I'm trying to measure the dihedral angle between 4 unrelated atoms, 
the alpha carbons from for disparate residues. Can I do this with 
Get_dihedral or is this command only good for backbone phi, psi 
measurements? If it is possible could someone send  me an example as I 
can't get the atom selections to work.

Thanks

Chris


_______________________________________
Christopher J Bond
Postdoctoral Scholar
Department of Microbiology and Immunology
Stanford University

650.498.7111

Re: [PyMOL] Setting transparency for CGOs

[<tan...@st...>]

Michael,

thanks for your reply, this works fine for me. However, I thought there is a
nicer solution on setting the transparency for cgo's after creation.

Regards,

Yusuf

--
Yusuf Tanrikulu
Bioinformatics Diploma Student
Department of Biosciences
Johann-Wolfgang-Goethe Univerity Frankfurt
Siesmayerstrasse 70
60323 Frankfurt am Main
- Germany -
tan...@bi...

Quoting Michael George Lerner <ml...@um...>:

>>> Quoting tan...@st...:
>>>
>>> # Hi everybody,
>>> #
>>> # i've just created many CGOs, which show up solid surfaces like 
>>> spheres and
>>> # ellipsoids. Is it possible to set the transparency of some CGO's to
>>> i.e. 0.5
>>> # and leave the others solid?
>>> # I've checked out the reference and the manual, and found something like:
>>> #
>>> # set transparency=0.5, object
>>> #
>>> # But this actually does not work for CGO's.
>>> # Any ideas....
>>> #
>>> # Yusuf
>
> The last time I looked at this, it seemed like the easiest (only?) 
> way to do this was to tweak the transparency at creation time.  So, I 
> typically have functions that look like this:
>
> def makeSphere(name,x,y,z,r,transparency=0,...):
>    ...
>    obj = []
>    ...
>    obj.extend([cgo.ALPHA,1-transparency])
>    obj.extend([cgo.SPHERE,x,y,z,r])
>    ...
>    cmd.load_cgo(obj,name,1)
>
> I don't know how to change it later, though.
>
> Hope that helps,
>
> -michael
>
>>> #
>>> #
>>> # --
>>> # Yusuf Tanrikulu
>>> # Bioinformatics Diploma Student
>>> # Department of Biosciences
>>> # Johann-Wolfgang-Goethe Univerity Frankfurt
>>> # Siesmayerstrasse 70
>>> # 60326 Frankfurt am Main
>>> # - Germany -
>>> # tan...@bi...
>>> #
>>> #
>
>
> -------------------------------------------------------
> SF.Net email is Sponsored by the Better Software Conference & EXPO
> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>