pymol-users Mailing List for PyMOL Molecular Graphics System

Hi,<br /><br />I encountered a weird recent behavior of the command align.<br /><br />In a script where I use the command<br />align (PO4 &amp; name OP1+OP2+P), PO4_target<br /><br />Where PO4 is a selection of O3&#39;,O5&quot;,P,OP1,OP2 atoms as well as PO4_target<br /><br />When I run the script with &quot;pymol -c&quot; I get the following<br /><br />PyMOL&gt;align (PO4 &amp; name OP1+OP2+P), PO4_target<br />&nbsp;Match: read scoring matrix.<br />&nbsp;Match: assigning 1 x 1 pairwise scores.<br />&nbsp;MatchAlign: aligning residues (1 vs 1)...<br />&nbsp;ExecutiveAlign: 2 atoms aligned.<br />&nbsp;Executive: RMS =&nbsp;&nbsp;&nbsp; 0.023 (2 to 2 atoms)<br /><br />The allignment is made only on 2 atoms. (OP1 and OP2)<br />While, it works if I introduce the command in the graphic window of pymol.<br /><br />This worked perfectly with earlier versions of pymol.<br /><br />Best,<br /><br />Pascal

Dear PyMOLers,

I can set the grid in the apbs_tools gui using the default file locations  (they are correct; I checked), but I get kernel dump when I try to run apbs.
A gui pops up with the message that MacPyMOL crashed although the PyMOL guis are still open and functional. The pop-u gui gives the following error message.

Best regards,

Blaine


Process:         MacPyMOL [7673]
Path:            /Applications/PyMOLX11Hybrid160.app/Contents/MacOS/MacPyMOL
Identifier:      MacPyMOL
Version:         ??? (???)
Code Type:       X86-64 (Native)
Parent Process:  MacPyMOL [7612]

Date/Time:       2013-08-30 09:09:52.027 -0500
OS Version:      Mac OS X 10.6.8 (10K549)
Report Version:  6

Interval Since Last Report:          149553 sec
Crashes Since Last Report:           23
Per-App Crashes Since Last Report:   8
Anonymous UUID:                      95441EA8-D0B3-46A9-8BC8-2FD7A7B627D1

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0xfffffffffffffff8
Crashed Thread:  Unknown

Backtrace not available

Unknown thread crashed with X86 Thread State (64-bit):
  rax: 0x0000000000000055  rbx: 0x0000000000000000  rcx: 0x0000000000000000  rdx: 0x0000000000000000
  rdi: 0x0000000000000000  rsi: 0x0000000000000000  rbp: 0x0000000000000000  rsp: 0x0000000000000000
   r8: 0x0000000000000000   r9: 0x0000000000000000  r10: 0x0000000000000000  r11: 0x0000000000000000
  r12: 0x0000000000000000  r13: 0x0000000000000000  r14: 0x0000000000000000  r15: 0x0000000000000000
  rip: 0x00007fff5fc01028  rfl: 0x0000000000010203  cr2: 0xfffffffffffffff8

Binary images description not available



Model: MacBookPro6,2, BootROM MBP61.0057.B0C, 2 processors, Intel Core i7, 2.66 GHz, 8 GB, SMC 1.58f17
Graphics: NVIDIA GeForce GT 330M, NVIDIA GeForce GT 330M, PCIe, 512 MB
Graphics: Intel HD Graphics, Intel HD Graphics, Built-In, 288 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x93), Broadcom BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 12 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en1
Serial ATA Device: ST9500420ASG, 465.76 GB
Serial ATA Device: MATSHITADVD-R   UJ-898
USB Device: Hub, 0x0424  (SMSC), 0x2514, 0xfa100000 / 2
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac  (Apple Inc.), 0x0236, 0xfa120000 / 6
USB Device: Hub, 0x05ac  (Apple Inc.), 0x9136, 0xfa140000 / 5
USB Device: Ext HDD 1021, 0x1058  (Western Digital Technologies, Inc.), 0x1021, 0xfa142000 / 14
USB Device: Keyboard Hub, 0x05ac  (Apple Inc.), 0x1006, 0xfa141000 / 8
USB Device: Apple Keyboard, 0x05ac  (Apple Inc.), 0x0220, 0xfa141200 / 13
USB Device: Hub, 0x05ac  (Apple Inc.), 0x9137, 0xfa144000 / 7
USB Device: Apple LED Cinema Display, 0x05ac  (Apple Inc.), 0x9236, 0xfa144300 / 12
USB Device: Display Audio, 0x05ac  (Apple Inc.), 0x2912, 0xfa144100 / 11
USB Device: Display iSight, 0x05ac  (Apple Inc.), 0x8508, 0xfa144200 / 10
USB Device: BRCM2070 Hub, 0x0a5c  (Broadcom Corp.), 0x4500, 0xfa110000 / 4
USB Device: Bluetooth USB Host Controller, 0x05ac  (Apple Inc.), 0x8218, 0xfa113000 / 9
USB Device: Internal Memory Card Reader, 0x05ac  (Apple Inc.), 0x8403, 0xfa130000 / 3
USB Device: Hub, 0x0424  (SMSC), 0x2514, 0xfd100000 / 2
USB Device: IR Receiver, 0x05ac  (Apple Inc.), 0x8242, 0xfd120000 / 5
USB Device: Built-in iSight, 0x05ac  (Apple Inc.), 0x8507, 0xfd110000 / 4
USB Device: Microsoft 3-Button Mouse with IntelliEye(TM), 0x045e  (Microsoft Corporation), 0x0040, 0xfd130000 / 3



Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  bla...@ou...<mailto:bla...@ou...>

Faculty webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

X-ray lab webpage: http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory

Small Angle Scattering webpage: http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links.html?sfvrsn=0

Hi Vaheh,

regarding psize.py: There is indeed a problem, I'm sorry. The simple
hotfix is to replace
  C:\Program Files\PyMOL\PyMOL\modules\freemol\apbs.py
with
  http://pymol.org/tmp/apbs.py

Regarding the "program stopped working" error: This doesn't happen for
me with 64bit Windows 7 or XP. Is there any additional information you
could provide, like does it happend with any file or just with
particular ones?

Cheers,
  Thomas

Oganesyan, Vaheh wrote, On 08/26/13 22:00:
> Hi PyMOLers,
> 
> It looks like v1.6.0.0 treats APBS plugin differently, at least on my
> 64 bit Windows laptop. After setting grid and  few seconds after
> clicking "Run APBS" button message appears in new window stating that
> program stopped working and needs to close the window. Also, it looks
> like I can't find anymore psize.py location, though not sure if these
> two issues are connected. Anybody else saw this behavior? If so, what
> is solution? PyMOL v1.5.0.5 was great in this respect; worked out of
> box.
> 
> Thanks for help.
> 
> Vaheh

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Dan,

The PDB 3ZLJ only has 13,233 atoms in the PDB. Recent versions of PyMOL
_should_ be able to handle that in 3D with transparent surfaces and sticks
just fine. I don't have an FX 4800, but have tested on similar hardware
with larger systems successfully.

Can anyone out there with a Quadro FX 4800 or similar comment on 3D
performance with 3ZLJ?

For what it's worth, in anaglyph 3D mode (which does double-rendering) for
3ZLJ, shown as described above, on a MacBook Pro with an NVidia GeForce
650M, I'm getting about 48 FPS.

Cheers,

-- Jason


On Mon, Aug 26, 2013 at 10:59 PM, Dan Piraner <dan...@gm...>wrote:

> Hello all,
>
> If anyone is using PyMOL with NVidia's 3D Vision, I am wondering if
> you could help me estimate performance with a prospective build. On
> the PyMOL web site, the graphics card recommendations for 3D Vision
> are as follows:
>
> 120Hz) NVidia 3D NVision with:
>    (entry) NVidia Quadro 580; entry level cards begin at approximately $99
>    (better) NVidia Quadro FX 3800/4800
>    (best) NVidia Quadro Q5000/Q6000
>
> As someone used to quantitative benchmarks, I'm not exactly sure what
> "entry", "better", and "best" actually mean. I'm thinking of pairing a
> Quadro FX 4800 with an i7 4770k. I've never used a 3D Vision setup
> before and am wondering what kind of performance to expect. Would it
> be able to render a reasonably complex structure (picking at random,
> 3ZLJ) with a transparent surface and stick representation without
> lagging?
>
> Any quantitative information or suggestions would be greatly appreciated.
>
> Best,
>
> Dan
>
>
> ------------------------------------------------------------------------------
> Introducing Performance Central, a new site from SourceForge and
> AppDynamics. Performance Central is your source for news, insights,
> analysis and resources for efficient Application Performance Management.
> Visit us today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi,

This is a fairly basic question about syntax. How does one: as surface the
protein and pseudoatoms in the short script below? Moreover, and work with
the Lysine amines rather than the alpha carbons?

# for_gnp.py

# fetch a protein and create whole phage
cmd.fetch("1ifp", type="pdb1", multiplex=1, async=0)


# make a blank list
l=[]

# iterate over all lysine's alpha carbons
cmd.iterate_state(1, "n. CA and resn lys", "l.append((x,y,z))")

# set a counter to 0 for controlling unique names
p=0

# iterate over all coordinates and create a
# pseudoatom at each lysine's alpha carbon
for ca in l:
    p+=1
    cmd.pseudoatom("pseudo%s" % (p), pos=ca, vdw=5.0)

# measure the pairwise distances across all pseudoatoms just created
cmd.distance("/pseudo*", "/pseudo*")



Many thanks,
James

Hi Michael,

this is exactly what the new arbitrary atom properties are intended for,
very nice. To answer your questions:

The context menu will list all property names which are found on the
first atom of the selection.

Selecting by those properties is not supported yet, but hopefully soon.

Cheers,
  Thomas

Mic...@wa... wrote, On 08/26/13 21:06:
> Hello PyMOL users,
> 
> I'm creating an export routine for a third party application we release
> that allows PyMOL to read results from our analyses such that data can
> be overlaid onto 3D structures rendered by PyMOL. Basically I'm creating
> a script where I'm assigning some data to arbitrary atom properties, for
> example:
> 
> alter /1LPH//A/5, properties["lispro_5min"]=0.40
> alter /1LPH//A/5, properties["insulin_5min"]=0.55
> alter /1LPH//A/6, properties["lispro_5min"]=0.42
> alter /1LPH//A/6, properties["insulin_5min"]=0.48
> 
> Now one really neat thing I noticed was if I do a None assignment for
> any given property:
> 
> alter /1LPH//A, properties["lispro_5min"]=None
> 
> I can then select these properties for coloring operations via the
> Spectrum command in the GUI. This is fantastic by the way, as it will
> allow users not familiar with the command line at least some level of
> access to the imported data. Without the Noneassignment, the properties
> aren't visible in the context menu, I suspect because the data I'm
> populating is sparse (not every residue has data)-- confirmation on this
> would be appreciated.
> 
> As I'm a novice PyMOL user, I have a few other questions:
> 
> Is assigning data to arbitrary properties "OK", or is there a preferred
> other method? I'll point out I'm working with multi-dimensional data, so
> simply replacing the b-factor data (for example) is not an option as
> I'll have several sets of data to associated with any residue.
> 
> Am I able to use these properties to form selections? For example, I'd
> like to be able to select any residues where a given property remains
> None, but I can't seem to build the proper selection expression.
> 
> Thank you all,
> Michael
> 
> Michael Eggertson, Ph.D.  
> Senior Research Chemist
> Instrument Research Group   	Waters Logo
> [T] 508 482 2596  
> [F] 508 482 3625  
> [W] www.waters.com
> [E] mic...@wa...
> Waters Corporation  
> 34 Maple Street  
> Milford  
> MA 01757  
> USA

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hello all,

If anyone is using PyMOL with NVidia's 3D Vision, I am wondering if
you could help me estimate performance with a prospective build. On
the PyMOL web site, the graphics card recommendations for 3D Vision
are as follows:

120Hz) NVidia 3D NVision with:
   (entry) NVidia Quadro 580; entry level cards begin at approximately $99
   (better) NVidia Quadro FX 3800/4800
   (best) NVidia Quadro Q5000/Q6000

As someone used to quantitative benchmarks, I'm not exactly sure what
"entry", "better", and "best" actually mean. I'm thinking of pairing a
Quadro FX 4800 with an i7 4770k. I've never used a 3D Vision setup
before and am wondering what kind of performance to expect. Would it
be able to render a reasonably complex structure (picking at random,
3ZLJ) with a transparent surface and stick representation without
lagging?

Any quantitative information or suggestions would be greatly appreciated.

Best,

Dan

Hi PyMOLers,

It looks like v1.6.0.0 treats APBS plugin differently, at least on my 64 bit Windows laptop. After setting grid and  few seconds after clicking "Run APBS" button message appears in new window stating that program stopped working and needs to close the window. Also, it looks like I can't find anymore psize.py location, though not sure if these two issues are connected. Anybody else saw this behavior? If so, what is solution? PyMOL v1.5.0.5 was great in this respect; worked out of box.

Thanks for help.

     Vaheh


To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Hi James,

> select resn LYS and n. CA
> dist (sele), (sele)
> 
> Aside: this doesn't work for me as `dist sele, sele`. Anyone know why?
> Is that a bug or a feature?

It's a feature. Both the "select" and the "distance" command actually
take as first argument the name of the object which they will create.
But they are "smart" enough to recognize when you skipped the first
argument, then they use default names (sele, dist01).

So better write this:

select lysca, resn LYS and n. CA
distance lysdist, lysca, lysca

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

James,

If the CA position is acceptable as the residue coordinate (as assumed in
Jason's answer), then you don't need to bother with pseudoatoms. Here's the
easiest way to display all the distances for a figure:

select resn LYS and n. CA
dist (sele), (sele)

Aside: this doesn't work for me as `dist sele, sele`. Anyone know why? Is
that a bug or a feature?

If you need to print the individual distances rather than display them,
this gets slightly harder :

atms=[]
iterate resn LYS and n. CA, atms.append( (model,ID,resi) )
# print residue IDs and CA-CA distance
print "\n".join([ "%s, %s, %s" % ( atms[i][2],atms[j][2],
cmd.distance("dist","%s and ID %s" % atms[i][:2], "%s and ID
%s"%atms[j][:2])) for i in xrange(1,len(atms)) for j in xrange(i)])


BTW, are you studying crosslinking?

-Spencer


On Thu, Aug 22, 2013 at 3:57 PM, Jason Vertrees <
jas...@sc...> wrote:

> Hi James,
>
> It could look something like this:
>
> # for_rutley.py
>
> # fetch a protein
> cmd.fetch("1rx1", async=0)
>
> # make a blank list
> l=[]
>
> # iterate over all lysine's alpha carbons
> cmd.iterate_state(1, "n. CA and resn lys", "l.append((x,y,z))")
>
> # set a counter to 0 for controlling unique names
> p=0
>
> # iterate over all coordinates and create a
> # pseudoatom at each lysine's alpha carbon
> for ca in l:
>     p+=1
>     cmd.pseudoatom("pseudo%s" % (p), pos=ca)
>
> # measure the pairwise distances across all pseudoatoms just created
> cmd.distance("/pseudo*", "/pseudo*")
>
> I bet someone like Thomas or Tsjerk could code this in half the number of
> lines, but this should be a starting point.
>
> Cheers,
>
> -- Jason
>
>
> On Thu, Aug 22, 2013 at 9:55 AM, James Rutley <jam...@gm...> wrote:
>
>>
>>
>> ---------- Forwarded message ----------
>> From: James Rutley <jam...@gm...>
>> Date: 22 August 2013 14:50
>> Subject: Script writing
>> To: pym...@li...
>>
>>
>> Hi,
>>
>> I am new to Pymol and programming. What's the best way to approach
>> creating a script that does the following:
>>
>> [image: Inline images 3]
>>
>> Thanks,
>>
>> James,
>> UCL
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Introducing Performance Central, a new site from SourceForge and
>> AppDynamics. Performance Central is your source for news, insights,
>> analysis and resources for efficient Application Performance Management.
>> Visit us today!
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Jason Vertrees, PhD
> Director of Core Modeling Products
> Schrödinger, Inc.
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> Introducing Performance Central, a new site from SourceForge and
> AppDynamics. Performance Central is your source for news, insights,
> analysis and resources for efficient Application Performance Management.
> Visit us today!
> http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi Feng,

is this open-source PyMOL from Ubuntu repository, compiled from SVN
source or Incentive PyMOL downloaded from pymol.org/dsc? If it's from
the Ubuntu repository, can you please compile from SVN source and check
if the problem still exists? Thanks!

Cheers,
  Thomas

郁峰 wrote, On 08/19/13 07:55:
> Hi everyone,
>  
> I found Pymol(1.6.0.0) will crash (segmentation fault) during loading
> any pse files on Ubuntu 12.10, even the pse file was output by itself.
>  
> Except this problem, other functions work fine. Additionally, this
> problem did not appear on Windows 7 and Scientific Linux 6.
>  
> I noticed the similar bug has been reported before, and was claimed it
> had been fix in version 1.6.0.0.
>  
> Are there anyone found same problem on the Ubuntu?  Was the bug not fix
> completely?
>  
> Thanks for any help!
> 
> Regards,
> 
> Feng Yu, yu...@si... <mailto:yu...@si...>
> 2013/8/18

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Robert,

this looks like a bug, none of the closed CGOs is rendered on the
inside, even with two_sided_lighting=on.

I filed a bug report: https://sourceforge.net/p/pymol/bugs/134/

Cheers,
  Thomas

Bryn Fenwick wrote, On 08/20/13 00:42:
> 
> Hi All,
> 
> I am trying to ray trace an empty cone. I can find no way to get an image of the inside of the cone. Does anyone have a work around. Example attached.
> 
> run test.py
> cone
> ray
> 
> when the ray command is issued the cone disappears from view.
> 
> robert
> 
> 
> #
> # test.py
> #
> 
> 
> from pymol import cmd
> from pymol.cgo import *
> 
> 
> def cone(name='cone'):
> 
>     o = []
> 
>     o.extend( [ CONE,
>               0.0, 0.0, 0.0,    # XYZ 1
>               0.0, 0.0, 1.5,    # XYZ 2
>               0.0,              # Radius 1        
>               0.3,              # Radius 2
>               1.0, 0.0, 0.0,    # RGB Color 1
>               0.0, 0.0, 1.0,    # RGB Color 2
>               0.0, 0.0,         # Caps 1 & 2
>             ] )
> 
> 
>     cmd.load_cgo(o, name)
> 
> cmd.extend('cone', cone)

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Alicia,

the DistancesRH script seems to do a lot of specific stuff beyond simple
distance matrix calculation. If you have scipy installed, this will give
you a distance matrix:

from pymol import cmd
from scipy.spatial.distance import cdist
coords = cmd.get_model('guide').get_coord_list()
distances = cdist(coords, coords)

Note the "guide" selection, which are all the polymer CAs.

See also:
http://pymolwiki.org/index.php/Get_Coordinates_I
http://pymolwiki.org/index.php/Single-word_Selectors
http://docs.scipy.org/doc/scipy/reference/spatial.distance.html

Cheers,
  Thomas

Hersey, Alicia wrote, On 08/21/13 00:59:
> Hi all,
> 
> I am trying to make a data matrix of pairwise distances between all
> alpha carbons of a protein. Currently I am using the script DistancesRH
> but this spits back the distances from one alpha carbon to all other
> atoms. Any way to only do CA to CA or is there another script to use? Thanks
> 
> - Alicia

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi all,

I am trying to make a data matrix of pairwise distances between all alpha
carbons of a protein. Currently I am using the script DistancesRH but this
spits back the distances from one alpha carbon to all other atoms. Any way
to only do CA to CA or is there another script to use? Thanks

- Alicia

Hi Hendrik,

the easiest is to patch the mutagenesis wizard. Check the attached
patch, it shows two different methods to activate a new amino acid. The
first method registers rotamers in the rotamer library, the second
method just adds the name. For the second method, you can also use
rotamer angles from some already known amino adic.

Cheers,
  Thomas

Hendrik Mohrmann wrote, On 08/05/13 17:32:
> Hello.
> I would like to use the mutagenesis tool for artificial amino acids,
> that are actually not in the list. I already added a pkl file to
> /usr/share/chempy/fragments
> 
> What other changes would be necessary to find the artificial aa in the
> list? Or would it be easier to write a script? Maybe there are already
> some solution which I could modify?
> 
> All help is appreciated.
> 
> Best, Hendrik

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi All,

I am trying to ray trace an empty cone. I can find no way to get an image of the inside of the cone. Does anyone have a work around. Example attached.

run test.py
cone
ray

when the ray command is issued the cone disappears from view.

robert


#
# test.py
#


from pymol import cmd
from pymol.cgo import *


def cone(name='cone'):

    o = []

    o.extend( [ CONE,
              0.0, 0.0, 0.0,    # XYZ 1
              0.0, 0.0, 1.5,    # XYZ 2
              0.0,              # Radius 1        
              0.3,              # Radius 2
              1.0, 0.0, 0.0,    # RGB Color 1
              0.0, 0.0, 1.0,    # RGB Color 2
              0.0, 0.0,         # Caps 1 & 2
            ] )


    cmd.load_cgo(o, name)

cmd.extend('cone', cone)

-- 
R. Bryn Fenwick,
Structural and Computational Biology,
The Scripps Research Institute,
10550 North Torrey Pines Rd.,
La Jolla, CA 92037, USA.
fe...@sc...

Hi everyone,

I found Pymol(1.6.0.0) will crash (segmentation fault) during loading any pse files on Ubuntu 12.10, even the pse file was output by itself.

Except this problem, other functions work fine. Additionally, this problem did not appear on Windows 7 and Scientific Linux 6.

I noticed the similar bug has been reported before, and was claimed it had been fix in version 1.6.0.0.

Are there anyone found same problem on the Ubuntu?  Was the bug not fix completely?

Thanks for any help!
Regards,
Feng Yu, yu...@si...
2013/8/18 

Founder of Tool Command Language to talk about Tcl Past, Present &
Future

Ann Arbor, MI -- August 16, 2013 -- The Tcl/Tk User Association, which
is celebrating over 20 years of innovation using the Tool Command
Language (Tcl), confirmed today that John Ousterhout will be a
Featured Speaker at the conference in New Orleans, LA from Sept 23-27,
2013.

 Ousterhout is the original developer of the Tcl and Tk programming
language, a combination of the Tool Command Language and the Tk
graphical user interface tookit (Tk).  His presentation will focus on
the evolution of Tcl/Tk from its original language format created at
the University of California Berkeley to the most robust and
easy-to-learn dynamic programming language that seamlessly powers
today's applications. He is also the author of Tcl and the Tk ToolKit
(2nd Edition).

"John started a revolution born out of frustration," says Clif Flynt,
President, Tcl Community Association and author of Tcl/Tk: A
Developer's Guide. "Before Tcl, programmers devised their own
languages that were intended to be embedded into applications. By
creating Tcl/Tk, John created a language for rapid prototyping that
works immediately."

The Tcl New and Proven user conference will feature several Tcl
experts including Jeff Hobbs, Chief Technical Officer at ActiveState,
Gerald Lester, creator of Tcl Web Services and a keynote speech by
Karl Lehenbauer of FlightAware.com.  Programmers attending the
conference will learn the best practices for using Tcl's new
object-oriented commands and widgets as well as seeing new
applications and techniques in the fields ranging from business
applications to health, aerospace and beyond.

"The Tcl New & Proven User Conference will be focusing on innovation
throughout the years," says Flynt. "We are very pleased to have two of
the people who helped create the Tcl we know today at our 20th
conference."

Interested in attending the Tcl conference? Go to
http://www.tcl.tk/community/tcl2013/ to register. Learn more about
Tcl/Tk by visiting the Tcl Developer Xchange http://www.tcl.tk/ where
you can download Tcl 8.6 and a free trial of TDK 5 (Tcl Dev Kit).

###

About Tcl/Tk  (http://www.tcl.tk/)

Celebrating over 20 years of providing rapid prototyping, Tool Command
Language (Tcl) is an open source, robust, powerful and easy-to-learn
dynamic programming language ideal for today's web and desktop
applications, networking, administration, and testing. Tk is a
graphical user interface toolkit that enables the development of
native-looking GUIs on multiple platforms such as Windows, Mac OS X
and Linux. The combination of Tcl and the Tk GUI toolkit is referred
to as Tcl/Tk..
 
The vibrant Tcl user community comes together on the Tcl Developer
Xchange website hosted by ActiveState (http://www.tcl.tk/), which
provides a variety of resources for programmers working with Tcl/Tk to
increase their productivity and share ideas. Worldwide Tcl
conferences, Tcl/Tk downloads and access to the Tcler's Wiki are all
available online at the Tcl Developer Xchange.  The latest books,
tutorials and demos are also accessible from this site along with the
Tcl core development team that steers the ongoing evolution of the
language.


Contact:
Amy Hesser
Hesser Communications Group
am...@he...
312-933-8324

Hi Chris,

good news: we are working on a multi-line label implementation right
now! Bad news: you have to wait for the next PyMOL release.

Cheers,
  Thomas

Christoffer Norn wrote, On 08/15/13 14:47:
> Hi,
> 
> A similar question exists already (29/3/2011, Andreas Spitzmüller
> <)." rel="nofollow">http://www.mail-archive.com/search?l=p...@li...&q=from:%22Andreas+Spitzm%C3%BCller%22>).
> Was 'newline' ever implemented for labels? I need it to label specific
> residues (Ca-atom only) with their PSSM score. In effect I want to label
> specific Ca-atoms with a 20-line list like:
> A 3.2
> W 5.0
> E -3.0
> ...
> Y 1.0
> 
> For this it would be most useful if I could use newline in my label
> definition. Hope you can help!
> 
> Thanks,
> Chris

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi,

A similar question exists already (29/3/2011, Andreas Spitzmüller). Was 'newline' ever implemented for labels? I need it to label specific residues (Ca-atom only) with their PSSM score. In effect I want to label specific Ca-atoms with a 20-line list like:
A 3.2
W 5.0
E -3.0
….
Y 1.0

For this it would be most useful if I could use newline in my label definition. Hope you can help!

Thanks,
Chris

see http://chemapps.stolaf.edu/jmol/docs/#atomproperties for several
suggestions.


On Tue, Aug 13, 2013 at 10:56 AM, Thomas Holder <
tho...@sc...> wrote:

> Greetings,
>
> this is a quick announcement that we added the "metals" keyword to the
> selection language (SVN code revision 4039).
>
> Since PyMOL's selection language is one of the powerful core features
> that make so many complex tasks so easy, we plan to add more useful
> keywords and operators. For example selecting by x,y,z coordinates, or
> selecting by secondary structure element. If you have a good idea for a
> new keyword or operator, please file a feature request on sourceforge.
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

20'th Annual Tcl/Tk Conference (Tcl'2013)
http://www.tcl.tk/community/tcl2013/

September 23 - 27, 2013
Bourbon Orleans Hotel
New Orleans, Louisiana, USA
http://www.bourbonorleans.com/

Hello all.

This is a general reminder that the offer of reduced rates for rooms
at the conference hotel expires on August 19, i.e. in a week.

	Book Now! (if you haven't already).

Of course registration for the Conference is still open at

	http://www.tcl.tk/community/tcl2013/reg.html

To book a room at the conference hotel at reduced rates please follow
the instructions on that page.

Our schedule can be found at

	http://www.tcl.tk/community/tcl2013/schedule.html

Conference Committee

Clif Flynt              Noumena Corp			General Chair, Website Admin
Andreas Kupries         ActiveState Software Inc.	Program Chair
Gerald Lester           KnG Consulting, LLC		Site/Facilities Chair
Arjen Markus            Deltares
Brian Griffin           Mentor Graphics
Cyndy Lilagan           Nat. Museum of Health & Medicine, Chicago
Donal Fellows           University of Manchester
Jeffrey Hobbs           ActiveState Software Inc.
Kevin Kenny             GE Global Research Center
Larry Virden
Mike Doyle              National Museum of Health & Medicine, Chicago
Ron Fox                 NSCL/FRIB Michigan State University
Steve Landers           Digital Smarties

Contact Information     tcl...@go...


Tcl'2013 would like to thank those who are sponsoring the conference:

ActiveState Software Inc.
Buonacorsi Foundation
Mentor Graphics
Noumena Corp.
SR Technology
Tcl Community Association

Greetings,

this is a quick announcement that we added the "metals" keyword to the
selection language (SVN code revision 4039).

Since PyMOL's selection language is one of the powerful core features
that make so many complex tasks so easy, we plan to add more useful
keywords and operators. For example selecting by x,y,z coordinates, or
selecting by secondary structure element. If you have a good idea for a
new keyword or operator, please file a feature request on sourceforge.

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

For a definition of TTT , see http://pymolwiki.org/index.php/Object_Matrix

You'll notice that set_object_ttt takes a 16-member list that corresponds to this matrix.

-David

On Aug 12, 2013, at 11:48 AM, Павел Томашевский <cro...@gm...> wrote:

> Thank you Thomas, translate and rotate works great, but I'm not sure what set_object_ttt function does. 
> 
> I'm also looking for a function that can set absolute coordinates of my cgo cone, not relative to current position like translate/rotate. Is there such a function?
> 
> 
> 2013/8/12 Thomas Holder <tho...@sc...>
>> Hi Pawel,
>> 
>> > Currently I'm working on some plugin for PyMOL and I need your help.
>> > I need to draw an object (CGO) and create some function that will move
>> > this object or simply change its coordinates.
>> > I've done my job with the first part, that is drawing a sphere on a
>> > screen using
>> >     cmd.load_cgo(data, 'name')
>> > function, but how can I change its coordinates?
>> 
>> You can use translate and rotate with the object argument.
>> 
>> PyMOL> translate [10,0,0], object=yourcgo
>> PyMOL> rotate x, 20, object=yourcgo
>> 
>> You can also use cmd.set_object_ttt, see the third example here:
>> http://pymolwiki.org/index.php/Axes
>> 
>> > My second question is about the meaning of a parameters for CONE CGO, in
>> > some examples (http://www.pymolwiki.org/index.php/Axes) CONE gets about
>> > 16 params, but I didn't found any description of those.
>> 
>> There is no proper documentation for those. Did you have a look at
>> pymol/examples/devel/cgo_axes.py, which has comments for all the CONE
>> parameters?
>> 
>> https://sourceforge.net/p/pymol/code/4038/tree/trunk/pymol/examples/devel/cgo_axes.py
>> 
>> Cheers,
>>   Thomas
>> 
>> --
>> Thomas Holder
>> PyMOL Developer
>> Schrödinger Contractor
>> 
>> ------------------------------------------------------------------------------
>> Get 100% visibility into Java/.NET code with AppDynamics Lite!
>> It's a free troubleshooting tool designed for production.
>> Get down to code-level detail for bottlenecks, with <2% overhead.
>> Download for free and get started troubleshooting in minutes.
>> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
> 
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead. 
> Download for free and get started troubleshooting in minutes. 
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

Thank you Thomas, translate and rotate works great, but I'm not sure what
set_object_ttt function does.

I'm also looking for a function that can set absolute coordinates of my cgo
cone, not relative to current position like translate/rotate. Is there such
a function?


2013/8/12 Thomas Holder <tho...@sc...>

> Hi Pawel,
>
> > Currently I'm working on some plugin for PyMOL and I need your help.
> > I need to draw an object (CGO) and create some function that will move
> > this object or simply change its coordinates.
> > I've done my job with the first part, that is drawing a sphere on a
> > screen using
> >     cmd.load_cgo(data, 'name')
> > function, but how can I change its coordinates?
>
> You can use translate and rotate with the object argument.
>
> PyMOL> translate [10,0,0], object=yourcgo
> PyMOL> rotate x, 20, object=yourcgo
>
> You can also use cmd.set_object_ttt, see the third example here:
> http://pymolwiki.org/index.php/Axes
>
> > My second question is about the meaning of a parameters for CONE CGO, in
> > some examples (http://www.pymolwiki.org/index.php/Axes) CONE gets about
> > 16 params, but I didn't found any description of those.
>
> There is no proper documentation for those. Did you have a look at
> pymol/examples/devel/cgo_axes.py, which has comments for all the CONE
> parameters?
>
>
> https://sourceforge.net/p/pymol/code/4038/tree/trunk/pymol/examples/devel/cgo_axes.py
>
> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
> ------------------------------------------------------------------------------
> Get 100% visibility into Java/.NET code with AppDynamics Lite!
> It's a free troubleshooting tool designed for production.
> Get down to code-level detail for bottlenecks, with <2% overhead.
> Download for free and get started troubleshooting in minutes.
> http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>