[PyMOL] Quick PyMOLWiki Update

2016-01-02 Thread Jason Vertrees
Greetings PyMOLers,

Traffic on the PyMOLWiki continues to grow. It serves far over 100k page
views/month. In 2015 we got traffic from almost every country on the
planet. Very cool.

While operating well, the site, schemas, and plugins were outdated. So, I
went through and upgraded everything (and reinstalled a few previously
omitted plugins). Because of the scope of the changes, something may go
wrong. If it does, please let me know.

Also, curiously, today my provider let me know that the PyMOLWiki was being
DDoS'd. I can imagine more productive use of one's time. If you encounter
issues, please let me know.

Happy New Year! I hope everyone enjoyed their holiday(s).

Cheers,

-- Jason
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Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-19 Thread Jason Vertrees
Greetings Shane, et. al.,

The issue with the database connection should be fixed permanently now.
Search should also be consistently better.

I've independently owned and run the wiki for almost a decade now. It's
heading toward 22 million page views. Anyhow, it's now on good hardware
(SSD, lots of RAM, and a nice network) and should be stable. Let me know if
not.

Cheers,

-- Jason

On Sun, Oct 18, 2015 at 6:35 PM Shane Caldwell <shane.caldwel...@gmail.com>
wrote:

> Hi Jason, pymol-users list,
>
> The pymolwiki seems to be down and has been for a few days now. It looks
> like the server's down?
>
> Any page returns:
>
> (Can't contact the database server: Can't connect to local MySQL server
> through socket '/var/run/mysqld/mysqld.sock' (111) (localhost))
>
> Is there a mirror anywhere that can be used?
>
> Shane Caldwell
> McGill University
>
> On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees <jason.vertr...@gmail.com>
> wrote:
>
>> Greetings,
>>
>> It's been a while, I hope this message finds everyone well.
>>
>> I'm writing to briefly let you know that I recently moved, upgraded, and
>> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast
>> and more useful. Feel free to report any bugs.
>>
>> Back to the startup-life.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
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Re: [PyMOL] PyMOLWiki: Quick Update

2015-10-18 Thread Jason Vertrees
Shane,

Try now.

Cheers

On Sun, Oct 18, 2015, 6:35 PM Shane Caldwell <shane.caldwel...@gmail.com>
wrote:

> Hi Jason, pymol-users list,
>
> The pymolwiki seems to be down and has been for a few days now. It looks
> like the server's down?
>
> Any page returns:
>
> (Can't contact the database server: Can't connect to local MySQL server
> through socket '/var/run/mysqld/mysqld.sock' (111) (localhost))
>
> Is there a mirror anywhere that can be used?
>
> Shane Caldwell
> McGill University
>
> On Wed, Sep 9, 2015 at 1:02 AM, Jason Vertrees <jason.vertr...@gmail.com>
> wrote:
>
>> Greetings,
>>
>> It's been a while, I hope this message finds everyone well.
>>
>> I'm writing to briefly let you know that I recently moved, upgraded, and
>> reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast
>> and more useful. Feel free to report any bugs.
>>
>> Back to the startup-life.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> --
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>> Get real-time metrics from all of your servers, apps and tools
>> in one place.
>> SourceForge users - Click here to start your Free Trial of Datadog now!
>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991=/4140
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>>
>
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[PyMOL] PyMOLWiki: Quick Update

2015-09-08 Thread Jason Vertrees
Greetings,

It's been a while, I hope this message finds everyone well.

I'm writing to briefly let you know that I recently moved, upgraded, and
reinstalled/fixed search on the PyMOLWiki. It should be, hopefully, fast
and more useful. Feel free to report any bugs.

Back to the startup-life.

Cheers,

-- Jason
--
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[PyMOL] PyMOLWiki Update

2014-06-20 Thread Jason Vertrees
Greetings,

It is my pleasure to let you know that Microlytic
http://www.microlytic.com/, a company that makes tools for
crystallographers, has graciously offered to host the PyMOLWiki. The wiki
has been successfully transferred and is serving. (The search and the port
: problems have been fixed. Please let me know if you find any other
problems.)

Please join me in thanking Microlytic http://Melanie Adams-Cioaba
m...@microlytic.com for helping serve the PyMOL community.

Cheers,

-- Jason

--
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Re: [PyMOL] PyMOLWiki Update

2014-06-20 Thread Jason Vertrees
Hi Suzanne,

Everything should look and act exactly like it has in the past, including
the address.

Cheers,

-- Jason

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On Fri, Jun 20, 2014 at 10:18 AM, Lapolla, Suzanne M (HSC) 
suzanne-lapo...@ouhsc.edu wrote:

  Great! Thank you Microlytic! I assume that the PyMol wiki site will
 still have the same web address?
  --
 *From:* Jason Vertrees [jason.vertr...@gmail.com]

 *Sent:* Friday, June 20, 2014 8:00 AM
 *To:* pymol-users
 *Cc:* Melanie Adams-Cioaba
 *Subject:* [PyMOL] PyMOLWiki Update

   Greetings,

  It is my pleasure to let you know that Microlytic
 https://urldefense.proofpoint.com/v1/url?u=http://www.microlytic.com/k=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0As=c5f009784fbe8b4462388f99a44f3232d828141afea37db017b8d2ba026b9f3d,
 a company that makes tools for crystallographers, has graciously offered to
 host the PyMOLWiki. The wiki has been successfully transferred and is
 serving. (The search and the port : problems have been fixed. Please
 let me know if you find any other problems.)

  Please join me in thanking Microlytic
 https://urldefense.proofpoint.com/v1/url?u=http://Melanie%2520Adams-Cioaba%2520%26lt%3Bmac%40microlytic.com%26gt%3Bk=7DHVT22D9IhC0F3WohFMBA%3D%3D%0Ar=1ciN0EuZ9XNq3lPnYtgkI5sKPXgKVaywidBN0C981SQ%3D%0Am=LCsIIUrfD4RcV5Fb7TWTnwdu4fFSpJmF7mTJQLv8%2BNI%3D%0As=b2e04adca315e082abf51a6d98450782b86b9d5347605cd10510bdb863aa2146
 for helping serve the PyMOL community.

  Cheers,

  -- Jason

  --
 Jason Vertrees, PhD
 (e) jason.vertr...@gmail.com
 (o) +1 (603) 374-7120

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[PyMOL] Farewell

2014-04-24 Thread Jason Vertrees
Greetings PyMOLers and CCP4ers worldwide,

It has been my great pleasure to serve the PyMOL community both in a 
volunteer and professional capacity for the past decade. I have recently 
been given an offer I can't 
refusehttp://www.linkedin.com/in/jasonvertrees/—to 
follow one of my dreams—helping lead technology and science at a new 
startuphttp://www.realmassive.com. 
March 30th marked my last day at Schrödinger and supporting PyMOL.

Because of my great fondness for PyMOL and its community, I will continue 
to operate the PyMOLWiki until I find it a suitable home. I started the 
PyMOLWiki in 2005 and since then it's been visited over 15,289,590 times! 
(If you would like to sponsor or host the wiki feel free to email me.) Now 
I can't imagine the PyMOL community without it.

Last, I am truly humbled to have followed in the footsteps of Warren 
DeLano. He was an amazing man whose ideas and actions have touched the 
lives of millions, whether they know it or not. He is missed.

It's been great fun. I wish you all the best.

Cheers,

-- Jason

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Re: [PyMOL] forward and backward keyboard shortcuts

2014-03-04 Thread Jason Vertrees
Thomas,

Right and left arrow keys.

Cheers,

Jason

On Tuesday, March 4, 2014, Thomas Evangelidis teva...@gmail.com wrote:


 Hi,

 Is there any keyboard shortcut to move to the next or the previous state
 of an object, namely something equivalent to forward and backward
 commands?


 --

 ==

 Thomas Evangelidis

 PhD student
 University of Athens
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 Department of Pharmaceutical Chemistry
 Panepistimioupoli-Zografou
 157 71 Athens
 GREECE

 email: 
 tev...@pharm.uoa.grjavascript:_e(%7B%7D,'cvml','tev...@pharm.uoa.gr');

   teva...@gmail.comjavascript:_e(%7B%7D,'cvml','teva...@gmail.com');


 website: 
 thomasevangelidishomepagehttps://sites.google.com/site/thomasevangelidishomepage/




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Re: [PyMOL] RNA stick depiction with filled-out rings

2014-02-11 Thread Jason Vertrees
Hi Claus,

Maybe this:

fetch 1rna, async=0

as sticks

show cartoon

set cartoon_side_chain_helper, 1

set cartoon_ring_mode, 1

Cheers,

-- Jason

On Mon, Feb 10, 2014 at 2:03 PM, Kuhn, Claus-Dieter k...@cshl.edu wrote:
 Hi Pymol users,

 I am trying to depict RNA as sticks, however with filled-out rings (bases and 
 ribose).
 I have been going about doing this by combining cartoon view for the 
 filled-out bases, using set_cartoon_radius=0 and stick view for the backbone.

 When doing this I am always left with a fine line of cartoon_tube, which I 
 would love to be invisible.

 How can I make this line invisible?

 Thanks a lot.

 Claus
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Re: [PyMOL] arbitrary distance label for atom pair

2014-02-04 Thread Jason Vertrees
Richard,

The PyMOL team was just discussing this a few days back. Sadly, there
is no way to do this using standard labels.

If you have Incentive PyMOL v1.7 you can use the new callout command
(http://pymol.org/dsc/dokuwiki/doku.php?id=command:callout). Otherwise
you can use the pseudoatom
(http://www.pymolwiki.org/index.php/Pseudoatom) as a label:

# create a single ala

frag ala

# create a labeled distance

dist 2/N, 2/O

# hide the labels

hide labels

# create a new label at the center of the selection

pseudoatom new_label, (2/N or 2/O), label=Some arbitrary label here: \316\261

orient


Cheers,

-- Jason

On Tue, Feb 4, 2014 at 10:07 AM, Richard Smith re...@cam.ac.uk wrote:
 Hi,

 Is there an easy way to change the label on a distance object to some
 arbitrary string?

 I would like a line connecting two atoms with an arbitrary label
 at the midpoint between the two atoms.

 for example:
 #make atom pair selection
 distance d, (id 3651, id 3691) # actual distance = 2.00

 #replace 2.00 with 100%  # or any other string
 label d, 100%



 Thanks.

 --
 ---
 Regards
 Richard Smith

 Research Associate
 Department of Zoology
 Smith Research Group
 University of Cambridge
 Downing Street
 Cambridge CB2 3EJ

 Tel.: +44 (0)1223 330933


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[PyMOL] PyMOL on Coursera

2014-02-04 Thread Jason Vertrees
Greetings,

I am happy to report that PyMOL will be used in a structural
biolnformatics lab of
an upcoming Coursera course, Bioinformatic Methods 2, taught by Nicholas Provart
of the University of Toronto. The enrollment for these courses can typically be
in the tens of thousands or more. If you would like to learn more
about this free
online course visit https://www.coursera.org/course/bioinfomethods2.

Cheers,

-- Jason

-- 
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Re: [PyMOL] List residues functionality ?

2014-01-31 Thread Jason Vertrees
Carsten,

What about http://www.pymolwiki.org/index.php/List_Selection and
http://www.pymolwiki.org/index.php/List_Selection2? I also made a similar
script for retrieving object names:
http://www.pymolwiki.org/index.php/GetNamesInSel.

Cheers,

-- Jason


On Fri, Jan 31, 2014 at 10:30 AM, Schubert, Carsten [JRDUS] 
cschu...@its.jnj.com wrote:

  Hi All,



 probably a question for the developers, but may not hurt to ask publicly:
 Is there a functionality in Pymol to list the residues in a given
 selection? I am looking for the equivalent to the get_chains() function. I
 have scripted something up, but the code is not 100% clean and not flexible
 enough. For large molecules the performance is not great either.





  start script

 def list_resi(obj=):

 

 DESCRIPTION



 list_resi prints and returns the unique residue IDs from the input

 object. The object must be present in the object list

 on the GUI. Selections are currently not implemented.

 Chain or Segments are also not taken into account

 USAGE



 list_resi obj



 EXAMPLES



 list_resi my_prot



 l = list_resi(my_prot)

 



 if ( obj ==  ):

 obj=(all)



 ol = cmd.get_object_list()

 if (obj in ol):

 pass

 else:

 print Error: Object (%s) not found % obj

 return



 stored.resi_list = []

 cmd.iterate(obj,stored.resi_list.append(int(resi)))

 stored.resi_list=list(set(stored.resi_list))  # make list
 unique

 stored.resi_list.sort()



 for i in range(0,len(stored.resi_list)):

 print %s, % stored.resi_list[i],

 if ((i+1) % 10 == 0):

 print 



 return stored.resi_list



 # End Script



 Thanks for any input





 Carsten


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(o) +1 (603) 374-7120
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Re: [PyMOL] Write map from list of coordinates.

2014-01-30 Thread Jason Vertrees
Hi Esben,

I have a list of coordinates on a regular grid with associated floating
 point values from a calculation that I want to visualise in PyMOL. Is it
 nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently
 load it, or can it be loaded directly into a map object via some fancy
 python code?


It depends on how you want to visualize the data. If dots/points or other
discrete representations are okay then you can use a XYZ or a modified
structure file. If you want the benefit of a field (volume, gradient,
isosurface) then I suggest the map.

If you already have the data in a well-formatted brick, check out the
asCCP4 function in http://www.pymolwiki.org/index.php/Tiff2ccp4. That
writes the CCP4 header and data (of a TIFF file, but you can modify that
for your needs).

If you want, send me a copy of your data. Or, I also have a very poorly
written script that will convert raw volumes of data to CCP4 maps, similar
to the aforementioned script. Email me personally and I can send you a copy
if you prefer (but it's really ugly code).

Cheers,

-- Jason


On Wed, Jan 29, 2014 at 8:02 AM, Esben Jannik Bjerrum 
esbenjan...@rocketmail.com wrote:

 Hi All-knowing Pymol'ers.

 I wonder if anyone had a couple of tips/ pointers / script snippets.

 I have a list of coordinates on a regular grid with associated floating
point values from a calculation that I want to visualise in PyMOL. Is it
nescessary to write this to an Xplor/CNS/CCP4 file format and subsequently
load it, or can it be loaded directly into a map object via some fancy
python code?

 Best Regards
 Esben Jannik Bjerrum


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Re: [PyMOL] Error while starting Pymol 1.7

2014-01-27 Thread Jason Vertrees
Hi Roy and Carsten,

Adding new features, like volume rendering, often requires using new
technology. We added geometry shaders to PyMOL v1.7 to support
rendering the new labels/callouts. Your video card does not appear to
support geometry shaders. Many users remedy this problem by updating
their graphics drivers. But, sometimes this doesn't help.

PyMOL works best with a dedicated graphics card. Integrated rendering
systems that share system memory, which are often found on a laptops,
are not sufficient for optimal PyMOL rendering. If PyMOL cannot
compile or execute a shader then PyMOL disables GLSL-based rendering
and falls back to the old-style fixed pipeline. In that case PyMOL
complains but should still work, offering basic functionality. This
way we can offer basic rendering for old or weak hardware while adding
new features for better graphics cards.

Last, we do not code only for NVidia cards. We stick to the OpenGL
specification. Thus those systems that run PyMOL better have video
cards and drivers that more thoroughly implement the OpenGL
specification.

Cheers,

-- Jason

On Mon, Jan 27, 2014 at 6:44 AM, Roy Eylenstein
roy.eylenst...@morphosys.com wrote:
 Dear all,



 I see following error message when starting pymol 1.7 incentive on Win 7
 enterprise SP1 32 bit (i3 M370)



 This Executable Build integrates and extends Open-Source PyMOL 1.7.0.1.

 Detected OpenGL version 2.0 or greater. Shaders available.

 CShaderPrg_New-Error: geometry shader compilation failed name='connector';
 log follows.

 infoLog=ERROR: 0:2: '' :  extension 'GL_EXT_geometry_shader4' is not
 supported

 ERROR: 0:3: '' :  extension 'GL_EXT_gpu_shader4' is not supported

 ERROR: 0:5: 'vec3' : syntax error parse error





 Any suggestions?



 Best,





 Roy


 

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 Handelsregister/Commercial Register: Amtsgericht München HRB 121023;
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Re: [PyMOL] Font problem

2014-01-21 Thread Jason Vertrees
Justin,

Yes, we put quite a bit of effort into improving the font rendering. It's
still not perfect, but should be improved over the pre-release versions.
Please let me know where you still have issues. (Just send me a PSE file as
an example.)

Cheers,

-- Jason


On Tue, Jan 21, 2014 at 5:27 AM, Justin Lecher j.lec...@fz-juelich.dewrote:

 On 22/11/13 17:44, Jason Vertrees wrote:
  Hi Justin,
 
  We'll fix that, too.
 
  Cheers,
 
  -- Jason
 
 

 Hi Jason,

 did you find time to look into that?

 Thanks
 justin

 --
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 Institute of Complex Systems
 ICS-6 Structural Biochemistry
 Research Centre Juelich
 52425 Juelich, Germany
 phone: +49 2461 61 2117





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Re: [PyMOL] PyMOL v1.7 Released

2014-01-20 Thread Jason Vertrees
Michael,

Nice catch—we'll fix it. Thanks for letting us know.

Cheers,

-- Jason


On Mon, Jan 20, 2014 at 9:11 AM, Michael Banck mba...@gmx.net wrote:

 Hi,

 On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote:
  We are happy to announce the release of PyMOL v1.7.0.0!

 Congrats!

 One thing though: the open-source splash image has not been updated for
 1.7 and still says 1.6.x.


 Michael


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Re: [PyMOL] Pymol, number and label the helices

2014-01-20 Thread Jason Vertrees
Gefei,

Please read about labels (http://www.pymolwiki.org/index.php/Label; and
http://www.pymolwiki.org/index.php/Category:Labeling) and pseudoatoms (
http://www.pymolwiki.org/index.php/Pseudoatom). These should help you label
what you need to.

Cheers,

-- Jason


On Mon, Jan 20, 2014 at 9:57 AM, Gefei Chen cgf-2...@hotmail.com wrote:


 Hi guys,
 I am now preparing some proteins structure figures, and I think Pymol is a
 good program. But now something happened to me, my protein just has  5
 helices, and I want to number and label the helices as H1, H2 …and H5 in
 the figure with using Pymol directly (not photoshop), but I am sorry I have
 no idea for finishing it, however I have read the guide of Pymol.
 could anyone tell me something about how to number and label the helices?
 That will be very helpful, and thank you very much!

 Best wishes,
 Gefei


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Re: [PyMOL] mutagenesis wizard data file loading

2014-01-20 Thread Jason Vertrees
Michael,

I think you're right. We'll make and push the changes.

Cheers,

-- Jason


On Mon, Jan 20, 2014 at 10:40 AM, Michael Banck mba...@gmx.net wrote:

 Hi,

 I noticed that the mutagenesis wizard uses PYMOL_PATH/data to locate the
 chempy sidechains, however, PYMOL_DATA would be more appropriate if the
 data is not installed alongside the pymol modules.

 The attached patch fixes this.


 Michael


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Re: [PyMOL] combining multiple objects into one multistate object

2014-01-16 Thread Jason Vertrees
Jed,

You are correct in that you should be using the create command:

# creates new_obj from old_obj1 by copying old_obj1
# in state 1 to new_obj in state 1

create new_obj, old_obj1, 1, 1

# creates new_obj from old_obj2 by copying old_obj2
# in state 1 to new_obj in state 2

create new_obj, old_obj2, 1, 2

# creates new_obj from old_obj3 by copying old_obj3
# in state 1 to new_obj in state 3

create new_obj, old_obj3, 1, 3



If you have any empty session, this will automate the process:

python

for x in cmd.get_names():

  cmd.create(combined_models, x, 1, -1)

python end

Cheers,

-- Jason



On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.edu wrote:

 I know this seems silly, but I can't figure out how to combine multiple
 separate objects into one multistate object. I have a set of Modeler
 models loaded from a single pdb file, automagically separated into
 separate objects that have been aligned, and I want to combine them into
 one object in order to run Robert Cambell's rmsf_states script (and,
 also since it's just easier to compare and manipulate).

 I've searched the manual, the sourceforge list, and the wiki. Somehow
 the command 'create' with 'target_state=-1' and 'discrete=1' seems like
 it should do this, but all the objects end up in the first state (and
 the cartoon representation is a subset of what it should be (other
 representations are fine).
 I'm using incentive v1.6.0.0 on Windows 7.

 Jed

 --
 
 Jed Goldstone, PhD
 Research Specialist
 Woods Hole Oceanographic Institution
 Redfield 3-52 MS#32
 Woods Hole, MA 02543
 http://www.whoi.edu/hpb/Site.do?id=481
 Phone: 508-289-4823



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Re: [PyMOL] combining multiple objects into one multistate object

2014-01-16 Thread Jason Vertrees
Jed,

Yes, the create command should more intelligently handle the wildcard. In
fact, I started out trying the same thing you did. I'll add this as a
feature request.

Cheers,

-- Jason


On Thu, Jan 16, 2014 at 10:06 AM, Jed Goldstone jgoldst...@whoi.edu wrote:

  Thanks! That works. I kept trying to avoid writing a script, figuring
 that it should just be an option in 'create'. That is, if the selection
 old_obj has a wild card, then
 create new_obj, old_obj*,1,-1
 should work. Clearly not; could this be a future feature?

 Jed




 On 1/16/2014 10:56 AM, Jason Vertrees wrote:

 Jed,

  You are correct in that you should be using the create command:

  # creates new_obj from old_obj1 by copying old_obj1
 # in state 1 to new_obj in state 1

  create new_obj, old_obj1, 1, 1

  # creates new_obj from old_obj2 by copying old_obj2
 # in state 1 to new_obj in state 2

  create new_obj, old_obj2, 1, 2

  # creates new_obj from old_obj3 by copying old_obj3
 # in state 1 to new_obj in state 3

  create new_obj, old_obj3, 1, 3



  If you have any empty session, this will automate the process:

  python

  for x in cmd.get_names():

cmd.create(combined_models, x, 1, -1)

  python end

  Cheers,

  -- Jason



 On Thu, Jan 16, 2014 at 9:28 AM, Jed Goldstone jgoldst...@whoi.eduwrote:

 I know this seems silly, but I can't figure out how to combine multiple
 separate objects into one multistate object. I have a set of Modeler
 models loaded from a single pdb file, automagically separated into
 separate objects that have been aligned, and I want to combine them into
 one object in order to run Robert Cambell's rmsf_states script (and,
 also since it's just easier to compare and manipulate).

 I've searched the manual, the sourceforge list, and the wiki. Somehow
 the command 'create' with 'target_state=-1' and 'discrete=1' seems like
 it should do this, but all the objects end up in the first state (and
 the cartoon representation is a subset of what it should be (other
 representations are fine).
 I'm using incentive v1.6.0.0 on Windows 7.

 Jed

 --
 
 Jed Goldstone, PhD
 Research Specialist
 Woods Hole Oceanographic Institution
 Redfield 3-52 MS#32
 Woods Hole, MA 02543
 http://www.whoi.edu/hpb/Site.do?id=481
 Phone: 508-289-4823



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 Jason Vertrees, PhD
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 Schrödinger, Inc.

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


 --
 
 Jed Goldstone, PhD
 Research Specialist
 Woods Hole Oceanographic Institution
 Redfield 3-52 MS#32
 Woods Hole, MA 02543http://www.whoi.edu/hpb/Site.do?id=481
 Phone: 508-289-4823




-- 
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Director of Core Modeling Products
Schrödinger, Inc.

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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[PyMOL] PyMOL v1.7 Released

2014-01-14 Thread Jason Vertrees
Greetings,

We are happy to announce the release of PyMOL v1.7.0.0! Official
PyMOL sponsors can download ready-to-use installers from
http://pymol.org/dsc/ip . The open-source code has been pushed to
sourceforge svn (revision 4060) and a downloadable bz2 source file is
also available from http://sf.net/p/pymol/. A few improvements include:

Incentive PyMOL (for licensed users)
 * Improved labels, with connectors, backgrounds, outlines, and multiline
text
 * Callouts for general labeling
 * 675 documented settings in the Settings  Edit All GUI
 * New Find Wizard (CTRL-F) for locating objects in the object menu panel
 * ...and more

Open Source and Incentive PyMOL
 * Added the focal_blur command
 * Added the get_renderer command to return information about the graphics
renderer
 * Fetch command now takes SID and CID codes for PubChem
 * New selection keywords: metals, backbone, and sidechain
 * Access to settings and properties from the iterate/alter commands
 * Improved the PDB Loader GUI
 * Lots of Bugs Fixes

AxPyMOL (for licensed users):
 * Built as a PowerPoint Add In
 * Option to embed data into the PowerPoint file
 * Supports PowerPoint PPTX files
 * Added support for presenting Maestro (.mae and .maegz) files
 * Added support for Windows 8, MS Office 2010 and 2013 (32- and 64-bit)
 * Support for shader-based rendering

We encourage PyMOL sponsors to check out the internal documentation:
  * -- http://pymol.org/dsc/dokuwiki/doku.php?id=media:new17

We welcome any feedback and bug reports.

Cheers,

-- Jason

-- 
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Schrödinger, Inc.

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Re: [PyMOL] Pymol and Oculus Rift

2014-01-13 Thread Jason Vertrees
Hi Matthew,

I had a chance to play with the Oculus Rift, but have not added it to PyMOL
as an input device.

While definitely a cool device, its integration would have to be
well-thought out: with PyMOL you look at a given point and rotate data
around that point whereas with the Oculus Rift, the viewer's head is the
center of rotation.

Cheers,

-- Jason


On Fri, Jan 10, 2014 at 1:45 PM, Matthew Baumgartner mp...@pitt.edu wrote:

 Hi,
 Has anyone tried to get pymol working with the Oculus Rift?
 I just got my hands on one and I think it would be awesome to use it
 with pymol?

 Thanks,

 Matthew Baumgartner


 --



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Re: [PyMOL] Selection algebra issue

2013-12-13 Thread Jason Vertrees
Hi Katherine,

PyMOL can do what you want. I've done this exact task before.

Here's the idea. If you have a PDB with multiple ligands and you use,

  select allLigands, organic and myProtein

you create the selection allLigands which contains all the ligand
atoms in myProtein. What you need to do is extract each ligand,
molecule by molecule, from the allLigands selection using selection
algebra until myLigands is empty. It's done like this:

# create a selection containing the atoms of all ligands

select allLigands, organic and myProtein

# create a selection to use later as we iterate across
# all ligands, this will hold individual ligands we extract
# from allLigands

select current_ligand, none

# enter a Python block so we can use Python while-loop
# and other Python syntax

python

# loop until allLigands is not empty

while cmd.count_atoms(myLigands)  0:

  # copy the first ligand selection, by molecule, into
  # the, current_ligand

  cmd.select(current_ligand, bm. first allLigands)

  # do something with current_ligand, like finding all ligands
  # without waters nearby

  if cmd.count_atoms(solvent within 5 of current_ligand) == 0:

print This is an interesting ligand.

  # now remove current_ligand from allLigands
  # and loop again

  cmd.select(allLigands, allLigands and not current_ligand)

python end

Good luck!

Cheers,

-- Jason


On Fri, Dec 13, 2013 at 4:58 PM, Katherine Sippel
katherine.sip...@gmail.com wrote:
 Hi Carsten,

 Thanks for the help. I've tried variants of that selection and it works
 great if there is only one ligand. Unfortunately it breaks down when there
 are multiple ligands and they don't all fit the criteria. I'm surveying
 almost half the PDB so these are all different proteins with different
 binding sites and ligands. I was hoping for a way to get pymol to recognize
 each individual ligand automatically by grouping common resids within the
 non-solvent hetatm selection. Using the %s %(resi) seems to require an
 explicit input.

 I might be able to extract an explicit chain/resi designation for each file
 from the het portion of the pdb header, though I'm not sure how to automate
 this. I suppose it's back to the script repository for me.

 Cheers,
 Katherine


 On Fri, Dec 13, 2013 at 2:50 PM, Schubert, Carsten [JRDUS]
 cschu...@its.jnj.com wrote:

 Katherine,



 not sure if that is what you are looking for but you can select for
 non-polymer residues with:



 select lig, prot and organic



 That will select any non polymer (protein and R(D)NA) residues present in
 the pdb. You then would need to break the selection further into the
 individual constituents, by either chain Id and resid.



 Hope this helps a bit.



 Carsten



 From: Katherine Sippel [mailto:katherine.sip...@gmail.com]
 Sent: Friday, December 13, 2013 10:28 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Selection algebra issue



 Hi all,

 I'm trying to write a script to data mine the pdb. I'm want to look at the
 ligands in a pdb file and fish out those that meet a certain criteria. I've
 got a script that can look at the ligands all at once but I need to assess
 each ligand individually. Since I'm looking at 40,000+ pdbs I need a way to
 define them individually. I've tried variations on %s' % (resi) and
 bymolec but I can't seem to figure out how to get them parsed separately
 without specifying a number. I've also tried using index to create a tuples
 list and iterating from that but I keep hitting the same issue. I've
 attached a couple of the attempted scripts so you can laugh at my google
 derived python skills.

 I've been trying to figure this out for a week now and I'm completely
 stumped. If anyone could nudge me in the right direction, even if it's some
 Pymolwiki article I missed, I would appreciate it immensely.

 Thanks for your time,
 Katherine


 --

 Nil illegitimo carborundum - Didactylos




 --
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Re: [PyMOL] what is an object colored ?

2013-11-25 Thread Jason Vertrees
Jon,

You can also iterate over a selection and show the color index for each
color

iterate *, color

You can then color by those indices, eg:

color 26

Cheers,

-- Jason


On Mon, Nov 25, 2013 at 5:42 AM, Jonathan Grimes
jonat...@strubi.ox.ac.ukwrote:


  dear all,

   i am having implementing these instructions.

   i would like to work out what color an object is……

   how is this defined …..

  s[names][1][5][0][1]
 
  equals your object name.

   if I have an object called A1…i am unsure how to
make A1 equal to s[names][1][5][0][1]


   many thanks

   jon


 Dr. Jonathan M. Grimes,
 NDM Senior Reseach Fellow
 University Research Lecturer
 DIAMOND Research Fellow

 Division of Structural Biology
 Wellcome Trust Centre for Human Genetics
 University of Oxford
 Roosevelt Drive,
 Oxford OX3 7BN, UK

 Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
 Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547

 On 12 Dec 2012, at 17:24, Jason Vertrees jason.vertr...@schrodinger.com
 wrote:

  Hi Jon,
 
  ive been given a pse file.and i am trying to work out what color
an object is..
 
i used the command
 
  get cartoon_color, pT_A
 
   and got back
 
  get: cartoon_color = default in object pT_A
 
  You're right, that's not very helpful. This will get you the answer,
  but it's not very straightforward:
 
  s = cmd.get_session()
 
  print cmd.get_color_tuple(s[names][1][5][0][2])
 
  To make sure you have right object ensure that,
 
  s[names][1][5][0][1]
 
  equals your object name.
 
  Cheers,
 
  -- Jason
 
  --
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  Director of Core Modeling Product Management
  Schrödinger, Inc.
 
  (e) jason.vertr...@schrodinger.com
  (o) +1 (603) 374-7120




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Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282

2013-11-24 Thread Jason Vertrees
Hi,

Is there any chance you can send me your input file(s)? Also, please let me
know what computer, video card, and architecture (32-bit/64-bit) you're
running on.

Cheers,

-- Jason


On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский croov...@gmail.comwrote:

 Hello
 I run PyMol 1.6.0 on windows 7 and I get this error:
 ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282
 or
 ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282

 over and over again.
 Is there any way to get rid of that? That's really annoying.

 crooveck


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Re: [PyMOL] ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=1282

2013-11-24 Thread Jason Vertrees
Hi Pawel,

I suggest making sure that your video drivers are up to date at all times
when using software like PyMOL. Mobile video cards notoriously badly
implement the OpenGL spec.

If that's a bug in our part, we'll try to track it down.

Cheers,

-- Jason


On Sun, Nov 24, 2013 at 3:42 PM, Павел Томашевский croov...@gmail.comwrote:

 2013/11/24 Jason Vertrees jason.vertr...@schrodinger.com:
  Hi,
 Hi Jason

  Is there any chance you can send me your input file(s)? Also, please let
 me
  know what computer, video card, and architecture (32-bit/64-bit) you're
  running on.

 So basically this problem occurs every time I start pymol, even
 without loading any input files.
 My computer is Dell Latitude E6400, running Windows 7 64-bits, I have
 Nvidia Quadro NVS160M.
 I've installed newest drivers a few days ago, but the problem still exists.

 If it matters... I've obtained PyMol executables (already compiled)
 from
 http://www.lfd.uci.edu/~gohlke/pythonlibs/3msnvi49/pymol-1.6.0.0.win-amd64-py2.7.exe
 .
 Executable comes with integrated Python 2.7 distribution...


  Cheers,
 
  -- Jason

 Cheers
 Pawel


 
 
  On Sat, Nov 23, 2013 at 2:47 PM, Павел Томашевский croov...@gmail.com
  wrote:
 
  Hello
  I run PyMol 1.6.0 on windows 7 and I get this error:
  ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns
  err=1282
  or
  ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=1282
 
  over and over again.
  Is there any way to get rid of that? That's really annoying.
 
  crooveck
 
 
 
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Re: [PyMOL] Font problem

2013-11-22 Thread Jason Vertrees
Hi Justin,

We'll fix that, too.

Cheers,

-- Jason


On Fri, Nov 22, 2013 at 1:24 AM, Justin Lecher j.lec...@fz-juelich.dewrote:

 On 22/11/13 01:02, Thomas Holder wrote:
  Hi,
 
  this is fixed now in the sourceforge SVN repository.
 
  Cheers,
Thomas
 

 Thanks for working quickly on it, but it isn't fixed here.

 There some things I observe,

 The font geometry changes according to the window geometry. That means a
 tall  thin window creates tall, stretched fonts. I would say, that font
 geometry should be independent from the window size.

 Probably coming from the same source in the code, the fonts get ugly
 when maximizing a window on a 27'' screen.

 This scaling problem also depends on use_shaders.

 I am using rev. 4052


 Regards,
 Justin


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 phone: +49 2461 61 2117




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Re: [PyMOL] Pymol sas

2013-11-21 Thread Jason Vertrees
Neshat,

Warren wrote the surfacing algorithm years ago. A little more discussion on
the algorithm can be found here (
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07124.html)
and here (http://www.pymolwiki.org/index.php/Get_Area).

Cheers,

-- Jason


On Tue, Nov 12, 2013 at 2:17 AM, neshat haq neshat...@gmail.com wrote:

 Hi,
 I could not find the the algorithm by which pymol calculates the solvent
 ASA.
 What I understood is that pymol adds the vdw radii of atom and probe,
 makes the sphere around the center of selected atoms, puts some dots and
 according to the density of dots it calculates the SASA.
 or it simply uses the Richard  Lee algorithm of rolling water.
 Please clarify my doubts.
 --
 Best regards
 Neshatul Haque
 PhD, Dpt of Biotechnology
 university of hyderabad


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Re: [PyMOL] Font problem

2013-11-21 Thread Jason Vertrees
Justin,

You're right, they are ugly! We're fixing that ASAP.

Thanks for bringing this up.

Cheers,

-- Jason


On Thu, Nov 21, 2013 at 8:10 AM, Justin Lecher j.lec...@fz-juelich.dewrote:

 Hi,

 label fonts look ugly here with use_shaders=1. When switching on
 use_display_lists=1 it looks good again. But the two options are
 exclusive so I get a performance penalty for the gain of good looking
 fonts.
 After ray tracing the fonts look great in both cases.

 Is there a way to improve the font rendering during shader activated mode?

 thanks
 Justin

 --
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 Institute of Complex Systems
 ICS-6 Structural Biochemistry
 Research Centre Juelich
 52425 Juelich, Germany
 phone: +49 2461 61 2117




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Re: [PyMOL] UCSD pymol workshop

2013-11-21 Thread Jason Vertrees
Hi Spencer,

We're happy to help. Please email me offline and I'll see how we can assist.

Cheers,

-- Jason


On Wed, Nov 20, 2013 at 5:30 PM, Spencer Bliven sbli...@ucsd.edu wrote:

 We've been discussing putting together a PyMol workshop for the UCSD
 undergrad bioinformatics club (http://ubic.ucsd.edu/). I wanted to ping
 this list and see if anyone in the San Diego area would be interested,
 either as attendants or as an instructor or assistant.

 I would like hearing if anyone has resources they found particularly
 useful when learning to use pymol - tutorials, slides, etc.

 Thanks!

 Spencer




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Re: [PyMOL] How to make outlines to spheres drawn in PyMOL ?

2013-11-19 Thread Jason Vertrees
Anasuya,

set ray_trace_mode, 1

Cheers,

-- Jason

On Tue, Nov 19, 2013 at 12:24 AM, Anasuya Dighe
anas...@mbu.iisc.ernet.in wrote:

 Dear users,
  I was interested in knowing if there is an option or setting in PyMOL which 
 is
 able to make an outline to spheres.
  I am aware of the show spheres command and have used it extensively to show
 C-alpha atoms of amino acids as spheres.
  I am curious to know how I could make an outline to the C-alpha atoms in a
 particular selection. Also, once the outline is made, how might I be able to
 change the color of such an outline ?

 Please let me know.

 Thanks,

 Anasuya


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Re: [PyMOL] apply spectrum per MODEL in PyMOL script

2013-11-11 Thread Jason Vertrees
Hi Jerome,

fetch 1nmr, discrete=1, async=0
as ribbon
set all_states
for x in range(cmd.count_states()): cmd.color(str(x), state %s % x)

You can substitute the spectrum command for the color command.

Cheers,

--- Jason

On Sat, Nov 9, 2013 at 8:54 PM, Jerome BENOIT g62993...@rezozer.net wrote:
 Hello List,

 is there a way in PML script to apply a specific spectrum to each MODEL (as 
 define in PDB data file) ?

 Thanks in advance,
 Jerome

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Re: [PyMOL] default values in pymol?

2013-11-11 Thread Jason Vertrees
Hi Neshatul,

# print out the vdw values used for a given selection

iterate my_selection, vdw

Use alter to change the values:

alter my_selection, vdw=vdw+2.0

Cheers,

--Jason

On Sat, Nov 9, 2013 at 4:17 PM, neshat haq neshat...@gmail.com wrote:
 Can anyone tell where can I get the default values of van der wall radii (or
 other radii) used in pymol, for atoms and combinations of atoms, like
 C, N, O, C=O, CH3, ..etc

 --
 Best regards
 Neshatul Haque
 PhD, Dpt of Biotechnology
 university of hyderabad

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Re: [PyMOL] [WAS: polygonal ring] cyclic peptide

2013-11-05 Thread Jason Vertrees
Hi Jerome,

PyMOL doesn't yet handle cyclic peptides. It's an open case we hope to
resolve soon.

Cheers,

-- Jason

On Tue, Nov 5, 2013 at 1:47 AM, Jerome BENOIT g62993...@rezozer.net wrote:
 Hello Again,

 let rephrase my question:
 does PyMOL have support for cyclic peptide (ex. 2NS4) ?

 Thanks,
 Jerome

 On 29/10/13 17:37, Jerome BENOIT wrote:
 Hello List,

 So far I use PyMOL to visualize polygonal chain through an expurged PDB data 
 file when the chain is not ring.
 Now I would like to visualize chain rings: what is the best way to make 
 PyMOL understand that the two end points coincide ?

 Thanks in advance,
 Jerome

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Re: [PyMOL] [WAS: polygonal ring] cyclic peptide

2013-11-05 Thread Jason Vertrees
Jerome,

One has already been filed internally. If you'd like, feel free to
open on on the open-source tracker
(https://sourceforge.net/p/pymol/feature-requests/).

Cheers,

-- Jason

On Tue, Nov 5, 2013 at 9:54 AM, Jerome BENOIT g62993...@rezozer.net wrote:
 Hello,

 thanks for the reply.

 May a ticket be filled ?

 Jerome

 On 05/11/13 15:34, Jason Vertrees wrote:
 Hi Jerome,

 PyMOL doesn't yet handle cyclic peptides. It's an open case we hope to
 resolve soon.

 Cheers,

 -- Jason

 On Tue, Nov 5, 2013 at 1:47 AM, Jerome BENOIT g62993...@rezozer.net wrote:
 Hello Again,

 let rephrase my question:
 does PyMOL have support for cyclic peptide (ex. 2NS4) ?

 Thanks,
 Jerome

 On 29/10/13 17:37, Jerome BENOIT wrote:
 Hello List,

 So far I use PyMOL to visualize polygonal chain through an expurged PDB 
 data file when the chain is not ring.
 Now I would like to visualize chain rings: what is the best way to make 
 PyMOL understand that the two end points coincide ?

 Thanks in advance,
 Jerome

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Re: [PyMOL] cylindrical helices

2013-11-01 Thread Jason Vertrees
Andreas,

That's an interesting find. PyMOL is clearly being fooled by the secondary
structure assignment. I don't think it's PyMOL's responsibility to address
egregious cases like this—rare and non-standard.

You can run 'dss' to update the secondary structure to something more
reasonable or you can use the 'alter' command to update the secondary
structure assignments. That should improve the result.

Cheers,

-- Jason


On Fri, Nov 1, 2013 at 7:33 AM, Andreas Förster docandr...@gmail.comwrote:

 Dear all,

 I've just been baffled for a while with a pdb that showed a strange
 behavior upon changing the representation from cylindrical cartoon
 helices to normal cartoon helices.  It seemed to me that helices were
 disappearing.

 A picture of the effect is here:
 http://www.msf.bio.ic.ac.uk/images/helices.png

 The arrows show pairs of normal helices merged into single short
 cylindrical helices.

 At some point, I realized the problem was the definition of pairs of
 helices as one continuous secondary-structure element (encircled).
 Running dss on the file fixed everything.

 I'm left wondering whether PyMOL should realize it's being fooled by the
 secondary structure predictions in egregious cases like this.  I looked
 hard at the structure with cylindrical helices and started to interpret
 differences to a homologous structure, which seemed to have additional
 helices, and in perpendicular orientations.

 Best regards.


 Andreas




 --
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Re: [PyMOL] Is object enabled or disabled?

2013-10-29 Thread Jason Vertrees
Hi Chris,

if objName in cmd.get_names(enabled_only=1):
  print objName is enabled

Cheers,

-- Jason

On Tue, Oct 29, 2013 at 5:50 AM, Christoffer Norn ch.n...@gmail.com wrote:
 Hi All,
 How can I, from the command line, get information on whether a object is 
 enabled or disabled? I need this to flip through thousands of designed 
 proteins — and with this many proteins, mouse-clicking to enable/disable them 
 becomes a bit cumbersome.
 Thanks,
 Chris
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Re: [PyMOL] neutral aminoacids

2013-10-11 Thread Jason Vertrees
Osvaldo,

To make PyMOL pick fragments from another location just edit the path
at the top of pymol/modules/chempy/fragments/__init__.py.

The fab command is in pymol/modules/pymol/editor.py.

Cheers,

-- Jason



On Thu, Oct 10, 2013 at 11:38 PM, Osvaldo Martin aloctavo...@gmail.com wrote:
 BTW, there is an easy option to make cmd.fab() to pick the fragments from an
 alternative location? (just to avoid modifying the original fragments files)

 thanks,

 Osvaldo.

 On Fri, Oct 11, 2013 at 12:32 AM, Osvaldo Martin aloctavo...@gmail.com
 wrote:

 Ok, I will try editing those files.

 Cheers,

 Osvaldo.



 On Fri, Oct 11, 2013 at 12:12 AM, Jason Vertrees
 jason.vertr...@schrodinger.com wrote:

 Hi Osvaldo,

 This isn't built in yet. But, if you need to do that, you can edit the
 Python picked files found here:

 pymol/data/chempy/fragments

 Cheers

 -- Jason

 On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin aloctavo...@gmail.com
 wrote:
 
  I am using the comand cmd.fab() to create small peptides. There is an
  easy
  option to add neutral aminoacids? The default behaviour is to add
  charged
  amino acids with the charge of the free amino acid in solution at pH =
  7
  i.e. Lys and Arg protonated and Glu, Asp and His unprotonated.
 
  Thanks in advance.
 
 
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Re: [PyMOL] selection residues with an exact b-factor value

2013-10-10 Thread Jason Vertrees
Hi Mike,

We didn't implement the equals operator, but the less than and greater than
operators are strict comparisons so you can do the following:

select my_exact_b, not (b0.5 or b0.5)

Cheers,

-- Jason


On Thu, Oct 10, 2013 at 9:34 PM, Osborne Michael 
michael.osbo...@umontreal.ca wrote:

 Hello Pymolers
 I think this is an easy one, but I can't seem to get this to work.
 I'd like to select residues with a bfactor equal to a certain value, say
 0. However something like:
 select aa, b = 0
 does not work
 although
 select aa, b  0.5
 does work.
 Cam someone show me how to do this?
 Cheers

 Mike



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Re: [PyMOL] neutral aminoacids

2013-10-10 Thread Jason Vertrees
Hi Osvaldo,

This isn't built in yet. But, if you need to do that, you can edit the
Python picked files found here:

pymol/data/chempy/fragments

Cheers

-- Jason

On Thu, Oct 10, 2013 at 2:41 PM, Osvaldo Martin aloctavo...@gmail.com wrote:

 I am using the comand cmd.fab() to create small peptides. There is an easy
 option to add neutral aminoacids? The default behaviour is to add charged
 amino acids with the charge of the free amino acid in solution at pH = 7
 i.e. Lys and Arg protonated and Glu, Asp and His unprotonated.

 Thanks in advance.

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Re: [PyMOL] load surface

2013-09-27 Thread Jason Vertrees
Hi Alexander,

See http://www.pymolwiki.org/index.php/Wfmesh.

Cheers,

-- Jason


On Fri, Sep 27, 2013 at 3:05 PM, Alexander Rose alexander.r...@weirdbyte.de
 wrote:

 Hi,

 I have create a surface (vertices and faces) in some external program and
 am now looking for a format to convert it to so that PyMOL can natively
 load it. Any suggestion is much appreciated.


 Best
 Alexander


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Re: [PyMOL] Background colors in PyMOL 1.6

2013-09-20 Thread Jason Vertrees
Hi Nils,

Thomas will soon fix the return values of the get command for color to
properly contain the 0x prefixes. In the meantime, please add them
yourself if this is causing lots of problems:

# prepend the result with 0x

x = 0x%s % (cmd.get(bg_rgb_top))

# set the color

cmd.set(bg_rgb_bottom, x)

Cheers,

-- Jason



On Fri, Sep 20, 2013 at 11:36 AM, Nils NN n...@gmx.ch wrote:



 Hi Jason,
 thanks for the reply.
 Your method works well for the single color background.
 For the gradient BG however the problem still remains:
 PyMOLset bg_gradient, 1
 PyMOLget bg_rgb_top
 - this returns '4d', which seems to be the hex-value.

 However when I try to set the bg_rgb_top/bottom value (regardless if I use
 hex or rgb-list) I still get an endless output of:
 Setting-Error: type read mismatch (color) 663
 Setting-Error: type read mismatch (color) 663
 Setting-Error: type read mismatch (color) 663
 Setting-Error: type read mismatch (color) 663
 Setting-Error: type read mismatch (color) 663
 ...

 This message keeps flooding the output shell until I close the program. I
 guess this is rather a bug than intended?

 Best,
 Nils



 Gesendet: Donnerstag, 19. September 2013 um 17:39 Uhr
 Von: Jason Vertrees jason.vertr...@schrodinger.com
 An: Nils NN n...@gmx.ch
 Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
 
 Betreff: Re: [PyMOL] Background colors in PyMOL 1.6

 Hi Nils,

 We've updated how PyMOL stores colors in sessions. You can try,

 cmd.get_color_tuple(cmd.get(bg_rgb))

 or if you need it as a list:

 list(cmd.get_color_tuple(cmd.get(bg_rgb)))

 Cheers,

 -- Jason

 On Thu, Sep 19, 2013 at 5:17 PM, Nils NN n...@gmx.ch wrote:

 Hello,

 I recently installed PyMOL 1.6 on my Debian machine. I have noticed that
 the description of the background colors has somehow changed. The command
 get bg_color returns [R,G,B] values in all previous versions, while since
 1.6 it only returns values  like black (which messes up some of my
 plugins and scripts). I'm not sure if this some kind of bug or a new way of
 handling colors...
 When I try to set the background gradient colors (set bg_rgb_top/bottom) I
 get an endless output of Setting-Error: type read mismatch (color) 664 -
 I have to kill and restart the program to get rid of the message. Same
 happens with my scripts using cmd...
 Can someone confirm these problems? Perhaps I'm doing something wrong here.

 Thanks in advance,
 Nils





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Re: [PyMOL] Background colors in PyMOL 1.6

2013-09-19 Thread Jason Vertrees
Hi Nils,

We've updated how PyMOL stores colors in sessions. You can try,

cmd.get_color_tuple(cmd.get(bg_rgb))

or if you need it as a list:

list(cmd.get_color_tuple(cmd.get(bg_rgb)))

Cheers,

-- Jason


On Thu, Sep 19, 2013 at 5:17 PM, Nils NN n...@gmx.ch wrote:

 Hello,

 I recently installed PyMOL 1.6 on my Debian machine. I have noticed that
 the description of the background colors has somehow changed. The command
 get bg_color returns [R,G,B] values in all previous versions, while since
 1.6 it only returns values  like black (which messes up some of my
 plugins and scripts). I'm not sure if this some kind of bug or a new way of
 handling colors...
 When I try to set the background gradient colors (set bg_rgb_top/bottom) I
 get an endless output of Setting-Error: type read mismatch (color) 664 -
 I have to kill and restart the program to get rid of the message. Same
 happens with my scripts using cmd...
 Can someone confirm these problems? Perhaps I'm doing something wrong here.

 Thanks in advance,
 Nils






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Re: [PyMOL] C-aplha c-alpha distances

2013-09-10 Thread Jason Vertrees
Hi Ananya,

This is easily doable in PyMOL.

If you've already aligned the two structures and, let's stay they're
called protein1 and protein2, then use rms_cur:

rms_cur protein1 and guide, protein2 and guide


If the initial and final structures are in the same object loaded from
disk then you can easily copy the last state to a new object using
create then use rms_cur:

# extract state 20 from my_trajectory and make it state 1
# in final_copy. Here I use 20, but you use whichever
# state is your final state.

create final_copy, my_trajectory, 20, 1

# do the RMS calculation

rms_cur initial, final_copy


Cheers,

-- Jason




On Tue, Sep 10, 2013 at 10:21 AM, Ananya Chatterjee ananya...@yahoo.in wrote:
 Dear all,

 I have aligned two structures (one the initial structure and another one is
 the final structure after MD simulation) in pymol, now I want to measure the
 C-alpha- C-alpha distances of each residue between the initial and the final
 structure of the MD simulation. Is it possible to do it by pymol, if yes
 then how to do it. Please help me in this regard I am very new to this
 field.

 Thank u in advance,

 Ananya

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Re: [PyMOL] Alpha Channels in Pymol Movies

2013-07-25 Thread Jason Vertrees
Hi Jordan,

If ray_trace_frames is on, and ray_opaque_background is off then
during the moviemaking process PyMOL uses the background color in the
movie.

At present, I think your only workaround is to export the PNGs with
transparencies and use a professional-quality movie exporter, like
Adobe Premier Pro (or similar).

Cheers,

-- Jason



On Tue, Jul 23, 2013 at 7:23 PM, Jordan Willis jwillis0...@gmail.com wrote:
 Hello,

 I'm using MacPymol 1.5.0.4

 When I save a ray traced .PNG file with set ray_opaque_background, 0 It does 
 gives me a transparent background when I put the picture into other apps, 
 e.g. Powerpoint. However, when I save it as a .mov file, I can see that pymol 
 is trying for a transparent background (I can see each frame as a 
 checkerboard), but the finished product is a solid black background that 
 looks terrible. Has anyone encountered this problem and have a possible 
 solution or workaround?

 Jordan



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Re: [PyMOL] Pymol OpenGL ES?

2013-07-17 Thread Jason Vertrees
Hi Paul,

We have plans to create the Android port, too (and have already have
the core cross compiled). But, we chose not to commit to it at that
time because the Android tablet space wasn't mature enough. We hope to
revisit that decision soon.

Cheers,

-- Jason

On Wed, Jul 17, 2013 at 11:13 AM, Paul Paukstelis pauks...@umd.edu wrote:
 Hi Jason,

 I did realize there was an iPad version, but I guess I was wondering if
 there was perhaps something more general. For example, I'm natively
 running linux on a Galaxy Note 10.1, and there will likely be more linux
 tablets popping up. For me (and likely others now or in the future),
 pymol would really make it a complete mobile device.

 --p

 On 07/17/2013 12:02 PM, Jason Vertrees wrote:
 Hi Paul,

 It's been done already. See, PyMOL on the iPad (http://pymol.org/mobile).

 Cheers,

 -- Jason

 On Wed, Jul 17, 2013 at 10:55 AM, Paul Paukstelis pauks...@umd.edu wrote:
 Just out of curiosity, are there any plans to port pymol over to use
 OpenGL ES to bring it to more mobile devices?

 --
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 Assistant Professor
 University of Maryland
 Chemistry  Biochemistry Dept.
 Center for Biomolecular Structure  Organization
 pauks...@umd.edu
 301-405-9933


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Re: [PyMOL] python module in pymol

2013-07-09 Thread Jason Vertrees
Hi Pascal,

PyMOL treats .pml and .py files differently. The cluster_count
script was written as a .py file as needs to be used as such.

run cluster_count.py

cluster_count PO4

worked just fine when run as a Python file.

Cheers,

-- Jason

On Tue, Jul 9, 2013 at 6:06 AM, Pascal Auffinger
p.auffin...@ibmc-cnrs.unistra.fr wrote:
 Hi,

 I tried to use the cluster_count script
 (http://www.pymolwiki.org/index.php/Cluster_Count)
 in a pymol.pml file. Unfortunately I get the following message:
 ---
 PyMOLcluster_count PO4
 Traceback (most recent call last):
   File /home/sws2/Desktop/pymol/modules/pymol/parser.py, line 464, in
 parse
 exec(layer.com2+\n,self.pymol_names,self.pymol_names)
   File string, line 1
 cluster_count PO4
^
 SyntaxError: invalid syntax
 ---
 (PO4) is a selection of five atoms

 When I use the same script as a pymol plugin, it works fine
 when I type in the command cluster_count PO4

 Any idea ???

 Thanks for helping,

 Pascal



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 IBMC/CNRS
 15 rue René Descartes
 67084 Strasbourg Cedex

 p.auffin...@ibmc-cnrs.unistra.fr
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Re: [PyMOL] Trouble with mutagenesis script

2013-07-02 Thread Jason Vertrees
Hi Dan,

You're missing a slash. You have:

PyMOL.exe -qc mutate.py -- digly.pdb digly A/2 ASN


where you should have

PyMOL.exe -qc mutate.py -- digly.pdb digly A/2/ ASN

When the residue is properly selected you'll see this:

Selected!
 Mutagenesis: 4 rotamers loaded.
 ExecutiveRMS: RMS =0.083 (4 to 4 atoms)
 Mutagenesis: 12 rotamers loaded.

where the RMS will change based on your residues.

Cheers,

-- Jason

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Re: [PyMOL] Pymol DLP 3D

2013-06-28 Thread Jason Vertrees
Hi Colin,


  Does anyone have any experience in running pymol in 3D using a DLP
 projector? I have an Optoma EW610ST, running from a windows seven machine
 using a Geforce GT620 GPU. The computer and projector are connected via
 HDMI but at present I am not able to configure any 3D output.


GeForce cards are incapable of presenting windowed OpenGL 3D at 120 Hz. You
need a Quadro card. The NVidia 3D Vision (
http://www.nvidia.com/object/3d-vision-main.html) page should have all the
info you need.

Cheers,

-- Jason

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Re: [PyMOL] Anaglyph colours sorted (kind of)

2013-06-27 Thread Jason Vertrees
Hi Gary,

I think you misunderstood.

First, with a good video card, use Setting  Rendering  Modernize for
the fastest and highest quality on screen rendering. In fact, it's
essentially as good as ray tracing but without shadows. If your
machine cannot handle this, the fallback is immediate mode rendering,
which PyMOL has been using for years. Machines with older and lower
quality video cards sometimes cannot handle this rendering technique:
they're simply incapable of using such drawing techniques.

 Point 4 should now be:
 4) do not use 'ray' when trying to use anaglyph stereo. This is a shame 
 because an anaglyph image for a slide or printout might be useful.

You have this backwards. The 'ray' command works just fine in anaglyph
mode. I've made countless 3D images using 'ray' and anaglyph mode.


 Some irreversible colour changes are frustrating after working for hours on 
 molecular structures, and then finding anaglyph does not work. That’s why I'd 
 like to find a 'reset' command for the settings – edit all settings. 
 Initialise wipes out all my hard work (molecules, objects, selections, maps, 
 etc etc). Currently I just have to revert to the last saved pse file.

Since we do not have 'undo' for things like colors you have to save
keep saving your session files so you don't lose any color changes.


 Any idea why using modern shaders does not work with anaglyph and might this 
 be improved later?

Again, modern shaders do indeed work with PyMOL–I use them all the
time–your video card just has to be good enough and you need to be
using PyMOL v1.5 or later.

Cheers,

-- Jason



 From: Jason Vertrees jason.vertr...@schrodinger.com
 Date: Wednesday, 26 June 2013 21:53
 To: Gary Hunter gary.hun...@um.edu.mt
 Cc: Thomas Holder thomas.hol...@schrodinger.com, 
 pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
 Subject: Re: [PyMOL] Anaglyph colours sorted (kind of)

 Hi Gary,


 1) do not use a black background


 Agreed. Something like gray works well in my experience. Don't forget in 
 techniques like anaglyph and chromadepth color takes on another meaning–it 
 encodes depth or separation. It's useful to keep this in mind.



 2) do not use setting  rendering  modernize


 If you have a modern video card that supports shaders well, Setting  
 Rendering  Modernize will give you better performance and much prettier 
 graphics. If, however, you're on a laptop with an old Intel graphics card, 
 stick to immediate mode rendering ('set use_shaders, 0').



 3) be careful with setting quality too high (especially on spheres)


 Again, using Setting  Rendering  Modernize will actually give you pixel 
 perfect spheres drawn quickly. But, in immediate mode, you are correct.


 To create the highest-quality movies or images, make sure you ray trace your 
 images. This can be done with the 'ray', and 'png' commands or as movie 
 creation time if 'ray_trace_frames' is set.


 To reinitialize PyMOL just run the reinitialize command.

 Cheers,

 -- Jason




 On 18/06/2013 09:59, Thomas Holder thomas.hol...@schrodinger.com wrote:

 Hi Gary,
 
 actually PyMOL should be optimized for red/cyan and not green/magenta.
 There is no option to change the colors, sorry.
 
 In PyMOL 1.5 anaglyph has been improved and there are is an
 anaglyph_mode settings which defaults to 4 (optimized anaglyph).
 Other reasonable values are 3 (half-color) and 1 (gray).
 
 http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
 
 If you really need to change the colors, you could take the open-source
 code and tweak the anaglyph_mode matrix in layer1/Scene.c
 
 Hope that helps.
 
 Cheers,
   Thomas
 
 Gary Hunter wrote, On 06/17/13 09:53:
  Is there a way to customise the colours used in anaglyph stereo mode?
  Anaglyph mode has been optimised for green/magenta glasses but I have
  lots of red/cyan ones so I'd like to change the colours used if I can.
  Gary
 
  Prof. Gary J. Hunter,
  Department of Physiology and Biochemistry
  University of Malta, Msida, MSD 2080, Malta.
  phone: +356 2340 2917
  phone: +356 21316655 (secretary),  Fax: +356 21310577
  http://www.um.edu.mt/ms/physbiochem
 
 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor
 
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Re: [PyMOL] Anaglyph colours sorted (kind of)

2013-06-26 Thread Jason Vertrees
Hi Gary,


1) do not use a black background


Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning–it
encodes depth or separation. It's useful to keep this in mind.



 2) do not use setting  rendering  modernize


If you have a modern video card that supports shaders well, Setting 
Rendering  Modernize will give you better performance and much prettier
graphics. If, however, you're on a laptop with an old Intel graphics card,
stick to immediate mode rendering ('set use_shaders, 0').



 3) be careful with setting quality too high (especially on spheres)


Again, using Setting  Rendering  Modernize will actually give you pixel
perfect spheres drawn quickly. But, in immediate mode, you are correct.


To create the highest-quality movies or images, make sure you ray trace
your images. This can be done with the 'ray', and 'png' commands or as
movie creation time if 'ray_trace_frames' is set.


To reinitialize PyMOL just run the reinitialize command.

Cheers,

-- Jason




 On 18/06/2013 09:59, Thomas Holder thomas.hol...@schrodinger.com
 wrote:

 Hi Gary,
 
 actually PyMOL should be optimized for red/cyan and not green/magenta.
 There is no option to change the colors, sorry.
 
 In PyMOL 1.5 anaglyph has been improved and there are is an
 anaglyph_mode settings which defaults to 4 (optimized anaglyph).
 Other reasonable values are 3 (half-color) and 1 (gray).
 
 http://pymol.org/dsc/dokuwiki/doku.php?id=setting:anaglyph_mode
 
 If you really need to change the colors, you could take the open-source
 code and tweak the anaglyph_mode matrix in layer1/Scene.c
 
 Hope that helps.
 
 Cheers,
   Thomas
 
 Gary Hunter wrote, On 06/17/13 09:53:
  Is there a way to customise the colours used in anaglyph stereo mode?
  Anaglyph mode has been optimised for green/magenta glasses but I have
  lots of red/cyan ones so I'd like to change the colours used if I can.
  Gary
 
  Prof. Gary J. Hunter,
  Department of Physiology and Biochemistry
  University of Malta, Msida, MSD 2080, Malta.
  phone: +356 2340 2917
  phone: +356 21316655 (secretary),  Fax: +356 21310577
  http://www.um.edu.mt/ms/physbiochem
 
 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor
 
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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-20 Thread Jason Vertrees
Hi David,

If you save a session file in the latest version of PyMOL there is never
the expectation that prior versions can read that file. Such forward
compatibility (of the older versions) is not supported. We do support,
however, backward compatibility which is when newer versions of PyMOL
read older session files.

Cheers,

-- Jason


On Wed, Jun 19, 2013 at 4:18 PM, David Hall li...@cowsandmilk.net wrote:

 I still have this problem:
 session saved in 1.6 with a black background; opens in 1.5 (and earlier)
 with a red background

 Many of my collaborators use old versions of pymol, frequently installed
 onto their machines when they were bought X years ago, and this essentially
 makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
 least not without getting weird e-mails asking why I have a sudden affinity
 for the color red).

 -David




 On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder 
 thomas.hol...@schrodinger.com wrote:

 This is fixed in SVN rev 4032.

 Cheers,
   Thomas

 Thomas Holder wrote, On 06/15/13 10:45:
  Hi Rob,
 
  this has not been fixed yet, I'm really sorry. We'll look into this
  ASAP. It only affects the open-source code, apparently we missed
  something when syncing with the incentive codebase.
 
  Cheers,
Thomas
 
  On Jun 14, 2013, at 9:23 PM, Robert Campbell 
 robert.campb...@queensu.ca wrote:
  Hello Thomas and David,
 
  Was there any resolution of this?  I've just compiled the latest
 version
  from SVN and I have the same problem opening files created under
 version
  1.5.0.  This is on Debian testing (32-bit).
 
  Cheers,
  Rob
 
  On Fri, 2013-04-26 19:15  EDT,  David Hall li...@cowsandmilk.net
  wrote:
 
  Hi Thomas,
 
  I'm running into issues with color compatibility between 1.6 and
  earlier versions when opening pses
  (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
  Setting-Error: type read mismatch (color) 6
  Setting-Error: type read mismatch (color) 663
  Setting-Error: type read mismatch (color) 664
  (b) background color disparity:
  saved in 1.5 with black background; opens in 1.6 with a white
 background
  saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a red
  background
 
  These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
  others who would like to beta test can use devel:languages:python repo
  in openSUSE:
 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 
  -David

 --
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 PyMOL Developer
 Schrödinger Contractor


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Re: [PyMOL] PyMOL 1.6 pre-release announcement

2013-06-20 Thread Jason Vertrees
Bob,

Sure, feel free to send those to Thomas.

Cheers,

-- Jason


On Thu, Jun 20, 2013 at 9:06 AM, Robert Hanson hans...@stolaf.edu wrote:

 (yes, I meant forward compatibility there)

 Jason, in our 100+ PyMOL session files that we can now read into Jmol we
 have a few files that don't seem to have backward compatibility to PyMOL
 1.3 from the open source version 1.6.0.0. Mostly it has to do with CGOs and
 measurements. Should I just send them to you and/or Thomas?

 Bob



 On Thu, Jun 20, 2013 at 7:36 AM, Jason Vertrees 
 jason.vertr...@schrodinger.com wrote:

 Hi David,

 If you save a session file in the latest version of PyMOL there is never
 the expectation that prior versions can read that file. Such forward
 compatibility (of the older versions) is not supported. We do support,
 however, backward compatibility which is when newer versions of PyMOL
 read older session files.

 Cheers,

 -- Jason


 On Wed, Jun 19, 2013 at 4:18 PM, David Hall li...@cowsandmilk.netwrote:

 I still have this problem:
 session saved in 1.6 with a black background; opens in 1.5 (and earlier)
 with a red background

 Many of my collaborators use old versions of pymol, frequently installed
 onto their machines when they were bought X years ago, and this essentially
 makes it so I cannot use pymol 1.6 as I cannot share sessions with them (at
 least not without getting weird e-mails asking why I have a sudden affinity
 for the color red).

 -David




 On Tue, Jun 18, 2013 at 7:37 AM, Thomas Holder 
 thomas.hol...@schrodinger.com wrote:

 This is fixed in SVN rev 4032.

 Cheers,
   Thomas

 Thomas Holder wrote, On 06/15/13 10:45:
  Hi Rob,
 
  this has not been fixed yet, I'm really sorry. We'll look into this
  ASAP. It only affects the open-source code, apparently we missed
  something when syncing with the incentive codebase.
 
  Cheers,
Thomas
 
  On Jun 14, 2013, at 9:23 PM, Robert Campbell 
 robert.campb...@queensu.ca wrote:
  Hello Thomas and David,
 
  Was there any resolution of this?  I've just compiled the latest
 version
  from SVN and I have the same problem opening files created under
 version
  1.5.0.  This is on Debian testing (32-bit).
 
  Cheers,
  Rob
 
  On Fri, 2013-04-26 19:15  EDT,  David Hall li...@cowsandmilk.net
  wrote:
 
  Hi Thomas,
 
  I'm running into issues with color compatibility between 1.6 and
  earlier versions when opening pses
  (a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
  Setting-Error: type read mismatch (color) 6
  Setting-Error: type read mismatch (color) 663
  Setting-Error: type read mismatch (color) 664
  (b) background color disparity:
  saved in 1.5 with black background; opens in 1.6 with a white
 background
  saved in 1.6 with a blackground; opens in 1.5 (and earlier) with a
 red
  background
 
  These are run on openSUSE 12.3 with SVN rev 4028 . On a side note,
  others who would like to beta test can use devel:languages:python
 repo
  in openSUSE:
 
 https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
 
  -David

 --
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 PyMOL Developer
 Schrödinger Contractor


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Re: [PyMOL] Leapmotion ?

2013-06-18 Thread Jason Vertrees
Hi Aurélien,

We demoed the LeapMotion controller with PyMOL at the last ACS meeting.
Getting it hooked up to PyMOL  wasn't too hard, thanks to Thomas. In our
hands it wasn't ready for routine use: it was very erratic. The device
didn't do well in a real world setting as it would recognize all sorts of
things as Pointables--like my watch or reflections. We are waiting for the
platform to mature a bit more before diving back in.

Do let us know of your progress, as it's a really neat device with
interesting potential.

Cheers,

Jason

On Wednesday, June 19, 2013, Aurélien Grosdidier wrote:

 Hi all,

 We're planning to try PyMol with the leap motion device
 (https://www.leapmotion.com/). Has anyone already succeeded to do so ?

 Best,

 Aurélien.


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Re: [PyMOL] PyMOL measurements

2013-05-31 Thread Jason Vertrees
Hi Bob,

We added this a year or two ago:

set dynamic_measures, 1

In newer versions of PyMOL this is enabled by default.

Cheers,

-- Jason


On Fri, May 31, 2013 at 8:27 AM, Robert Hanson hans...@stolaf.edu wrote:

 Is there a way to tie measurement ends to specific atoms, so that when the
 structure is tweaked, those measurements update automatically?

 --
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 Chair, Chemistry Department
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Re: [PyMOL] how to get cealign outputs for mulitple structures

2013-05-30 Thread Jason Vertrees
Hi Jacob,

Use the result from cmd.cealign and an alignment object. Here's an
example:


# fetch two proteins

fetch 1cll 1ggz, async=0

# use a python block

python

# cealign the two structures and create a corresponding alignment object

result = cmd.cealign(1cll, 1ggz, object=aln)

# print out the values from the result

print result.keys()
for key in result:
  print %s: %s % (key, result[key])

# end the python block

python end

# now access those atoms in the alignment

select 1cll and aln

# or count the atoms in 1ggz and aln

print cmd.count_atoms(1ggz and aln)

Cheers,

-- Jason




On Thu, May 30, 2013 at 2:07 PM, Jacob Pessin
jacob.pes...@einstein.yu.eduwrote:

  Hi all,

 can anyone suggest a straightforward way of collecting the cealign output
 in bulk, (RMS, #atoms compared), using alignto doesn't even print this to
 screen (I tried adjusting quiet=, to no avail).


 thanks in advance

 jacob

 https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554#
 https://owa.einstein.yu.edu/owa/?ae=Itema=Opent=IPM.Noteid=RgDDT2ZJXulBTI8H5G%2fACk3UBwBPSkr8RdqeRa4tSfsjXcRlSCziAABPSkr8RdqeRa4tSfsjXcRlAAAPdWIns=Draftpspid=_1369930182703_402002554#


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Re: [PyMOL] how to face cartoon

2013-05-10 Thread Jason Vertrees
Hi DJ,

It sounds like you're using the transparency setting instead of
cartoon_transparency. For example instead of

movie_fade transparency,  1, 0., 40, 1.

you likely want

movie_fade cartoon_transparency,  1, 0., 40, 1.

Cheers,

-- Jason


On Fri, May 10, 2013 at 3:50 AM, Dhananjay dhananjay.c.jo...@gmail.com wrote:
 Dear all,

 I am trying to animate set of proteins.
 Each protein has two conformations.
 I wanted to show first confirmation as cartoon, followed by fade out it and
 fade in the second confirmation.

 I could use movie_fade.py script successfully, however, it fades the surface
 to cartoon.

 I just want to fade out first confirmation and fade in and display the
 second one.

 Any suggestion please.

 Thanking you in advance.

 -- DJ



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Re: [PyMOL] trouble with fading for sticks in a movie

2013-04-26 Thread Jason Vertrees
Hi Yarrow,

set_bond stick_transparency, 0.5, myObj

Cheers,

-- Jason

On Fri, Apr 26, 2013 at 11:03 AM, Yarrow Madrona amadr...@uci.edu wrote:

 Hi,

 I have previously been able to do a fake fade on surface transparency by
 doing the following:
 where testout is an object in pymol.

 mdo 449: set transparency, 1, testout
 mdo 550: show surface, testout
 mdo 551: set transparency, 0.7, testout
 mdo 552: set transparency, 0.6, testout
 mdo 553: set transparency, 0.5, testout
 mdo 554: set transparency, 0.4, testout
 mdo 555: set transparency, 0.3, testout
 mdo 556: set transparency, 0.3, testout
 mdo 557: set transparency, 0.1, testout
 mdo 558: set transparency, 0, testout


 The surface will slowly come to life between frames 449 and 558. However,
 if I try doing this with
 set stick_transparency, nothing happens. I have tried to do this using
 scenes, however the object simply disappears instead of fading. I would
 love some help on this. I am interested in python scripting as well as I
 know a little python but not sure how to implement it in pymol. Thanks!


 -
 Yarrow Madrona

 Graduate Student
 Molecular Biology and Biochemistry Dept.
 University of California, Irvine
 Natural Sciences I, Rm 2403
 Irvine, CA 92697



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Re: [PyMOL] Problems with H_add when theres alternate conformations present

2013-04-19 Thread Jason Vertrees
Hi Esben,

It's up to you to decide how you want to handle this. You have a few options.

You can remove unwanted alternate conformations, for example:

remove not alt ''+'A'

then run your script.


Or you can specify PyMOL only add hydrogens to a certain set of conformations:

# only h_add to alt conformations labeled 'C'

h_add 1zw9 and alt 'C'


To only add hydrogens to default or 'A' conformers do the following:

h_add 1zw9 and alt ''+'A'


Cheers,

-- Jason


On Thu, Apr 18, 2013 at 3:59 AM, Esben Jannik Bjerrum
esbenjan...@rocketmail.com wrote:
 Hi Pymol Users
 I have a problem with wrong atom assignment, and subsequently wrong
 addition of hydrogens, if theres alternate conformations present. I hope
 anyone else has experience with this or suggestions for troubleshooting.
 I have developed some scripts that downloads pdb-files from a list, add
 hydrogens to them, and otherwise prepares them for further usage. However,
 if theres alternate conformations present, the atoms on the backbone gets a
 wrong charge assignemt or something, breaking the subsequent addition of
 hydrogens. It seems to happen at PDB load time.

 Example steps to reproduce
 fetch 1zw9
 zoom resi 12
 h_add 1zw9

 the hydrogen on the nitrogen in the backbone peptide bond doesn't make a
 planer configuration, and if I save the object, the oxygen is assigned a -1
 charge. This makes troubles in my subsequent workflow.

 I've tried to delete the alternate conformations inside PyMOL before adding
 hydrogens, but that doesnt fix the problem. I can fix the problem by
 removing the alternate conformations from the PDB file before I load it into
 pymol, but I would rather fix it inside pymol in my scripts.

 Best Regards
 Esben Jannik Bjerrum

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Re: [PyMOL] CEalign parameter d0 and d1

2013-04-17 Thread Jason Vertrees
Hi Quyen,

It's been a few years since I wrote that but here is what I recall:

D0 is a constant cutoff that represents the upper bound of dissimilarity
for the difference of two distance matrices A_i and B_j, rooted at
subsequences i to i+8 and j to j+8, respectively. Raising this value allows
for sloppier fragments being considered.

D1 is a constant cutoff that represents the upper bound of dissimilarity
for the entire path being considered. In fact, it's equal to path_score /
(window_size * path_length).

 So, D0 ensure that incoming fragments are still good. D1 ensures that as
we extend the current alignment the total quality of the current alignment
remains good.

After this, all N top scoring paths are stored in the path cache and the
best path is returned.

Cheers,

-- Jason


On Wed, Apr 17, 2013 at 3:34 AM, QT rdirect...@gmail.com wrote:

 Dear all,

 I have a question regarding CEalign d0 and d1 parameter.  What exactly are
 their functions?

 I don't know enough C++ to decipher the algorithm but they are used
 findPath() in ccealignmodule.cpp.  It seems that that d0 controls a
 similarity matrix and d1 the path length.  A d1 below a certain number does
 indeed make cealign return RMSD over smaller set of residues and there is a
 lower bound for d1 where cealign will fail to align.  D0 behaves
 similarly.  The default is 2 and 3 for d0 and d1.  I'm going to guess that
 those numbers are also dimensionless.

 Will it be useful to tune the parameter d0 and d1?

 Best,
 Quyen


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Re: [PyMOL] CGO fixed in space

2013-04-15 Thread Jason Vertrees
Hi Tim,

We don't yet have advanced screen-stabilized objects. In the meantime consider,

wizard message, Your Message Here

Cheers,

-- Jason

On Mon, Apr 15, 2013 at 6:43 PM, Someone Else tno...@gmail.com wrote:
 Hi,

 is it possible to define a CGO object (e.g. a text) that wouldn't move when
 a user rotates the scene? For example, a graphics title in the top left
 corner

 Tim



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Re: [PyMOL] Howto fake mouse events in pymol

2013-04-01 Thread Jason Vertrees
Hi Camilo,

Currently we only offer this level of access via the C-library, so it's not
accessible to end-users.

The current workaround is to use the move and rotate commands.

Cheers,

-- Jason


On Sun, Mar 31, 2013 at 10:31 AM, Camilo Andrés Jimenez Cruz 
camilo.jimen...@gmail.com wrote:

 Hi all.

 I am wondering if it is possible to fake mouse events in pymol. I would
 like to be able to simulate a click/drag in a specific position of the
 viewport. Thanks!

 -- Camilo Jiménez


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[PyMOL] Invitation to visit at ACS New Orleans

2013-03-27 Thread Jason Vertrees
Greetings,

If you will be at the April ACS meeting in New Orleans, please feel free to
stop by the Schrödinger booth (#400). I will be there much of the time
answering questions, demoing new features, and generally discussing science
and visualization.

Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad,
and even a sneak peek of Leap Motion (https://www.leapmotion.com/)
controller integration with PyMOL.

Cheers,

-- Jason

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Re: [PyMOL] Invitation to visit at ACS New Orleans

2013-03-27 Thread Jason Vertrees
Hi Sabuj,

Do you have it working under linux?


Yes, I have demonstrated the same functionality on Ubuntu (12.10). Ubuntu
is the only Linux distro currently supported by Leap.

Cheers,

-- Jason

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Re: [PyMOL] How to hide the object control panel

2013-03-24 Thread Jason Vertrees
Matthias,

As David said, try setting internal_gui to 0.

Or, try saving your session as a .psw instead of .pse.

Cheers,

Jason

Sent from my Android. Please excuse the concision and any typos.
On Mar 24, 2013 6:55 PM, Matthias Haffke matze_haf...@hotmail.com wrote:

 Dear all,

 this might be a simple question, but I would like to know how to hide the
 object control panel on the right side in the PyMol window.
 I would like to give a full screen presentation using scenes and it would
 be nice to have more space and remove the object control panel. Switching
 full_screen on does not do the job unfortunately - the object control
 panel remains visible.

 Many thanks already if anyone knows the solution,

 Matthias


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Re: [PyMOL] How to ray trace clipped image without clipping spheres.

2013-03-11 Thread Jason Vertrees
Hi Yarrow,

This is a known problemhttp://sourceforge.net/p/pymol/feature-requests/53/.
We'll try to fix this soon.

Cheers,

-- Jason


On Mon, Mar 11, 2013 at 2:05 PM, Yarrow Madrona amadr...@uci.edu wrote:

 Hi,

 Does anyone know how to ray trace an image of an active site in sphere
 representation that is clipped, without getting a weird result that I
 assume comes from clipping the spheres? It looks like unfilled circles.

 Thank you

 -Yarrow


 --
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 University of California, Irvine
 Natural Sciences I, Rm 2403
 Irvine, CA 92697





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Re: [PyMOL] pymol install

2013-03-04 Thread Jason Vertrees
Hi Yeping,

Check out
http://www.pymolwiki.org/index.php/Linux_Install#Compile_and_install.

Cheers,

-- Jason


On Mon, Mar 4, 2013 at 8:17 PM, yp sun sunyep...@yahoo.com.cn wrote:

 Dear pymol users,

 I try to install pymol in Linux system as following

 (1) download pymol-v1.5.0.1.tar.bz2 and decompress it to /opt directory.
 (2) go into /opt/pymol/setup directiry and enter the command setup.sh

 Then I see the install success information:

 
 Creating ./pymol startup script with
 PYMOL_PATH=/opt/pymol/setup
 
 If you need to move PyMOL in the future,
 re-run ./setup.sh afterwards.
 
 You may now want to copy or link:
 /opt/pymol/setup/pymol
 to something like /usr/local/bin/pymol
 
 Enjoy!

 However, when I type pymol command, I get the error information:

 ./pymol: line 14: /opt/pymol/setup/ext/bin/python: No such file or
 directory
 ./pymol: line 14: exec: /opt/pymol/setup/ext/bin/python: cannot execute:
 No such file or directory

 Could you tell me why?

 Thanks!

 Yeping Sun
 CAS Key Laboratory of Pathogenic Microbiology  Immunology
 INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
 NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china


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Re: [PyMOL] [PyMol] How to visualize surface within a given radius

2013-03-04 Thread Jason Vertrees
Greetings,

Please also investigate the following settings:

# needs a real atom selection
surface_carve_selection

# distance from the above selection to cull surfaces
surface_carve_cutoff

I looked at your data and there is a small problem. You have a few points
where one atom is mapped to multiple surface points. Thus, when you show it
as surface two pocket fragments show up. When you hide it they both hide.

Also of interest is PyMOL's ability to render pockets and cavities on its
own (Settings  Surface  Cavities  Pockets).

Cheers,

-- Jason


On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared jared.samp...@nyumc.orgwrote:

  Hi Yarrow -

  If you add br.  to the show surface command, you will get more
 continuous surfaces, as the selection will be made by residue instead of by
 atom.

 show surface, br. protein within 0.5 of pocket_selection


  If you don't want to show the surface from a particular residue (e.g. if
 it's masking something else you want to show), you can hide surface for a
 selection.

  hide surface, resi 225+347


  Cheers,
 Jared

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 212-263-7898
 http://kong.med.nyu.edu/




  On Mar 4, 2013, at 2:37 PM, Yarrow Madrona amadr...@uci.edu wrote:

 Thank you for your help Thomas,

 Using your settings I get a lot of partial surfaces

 Showing the surface around the Pocket selection like this:

 show surface, protein within 0.5 of pocket_selection

 worked well but I still see a piece of surface that I really don't want to
 show up. I guess I can take it out in photoshop but that just seems wrong.
 I have attached it.

 -Yarrow



 Hi Yarrow,
 should be as simple as:
 PyMOL hide surface
 PyMOL show surface, (organic around 8.0)
 PyMOL set transparency, 0.3
 PyMOL set two_sided_lighting
 See also:
 http://pymolwiki.org/index.php/Selection_Algebra
 Hope that helps.
 Cheers,
  Thomas
 Yarrow Madrona wrote, On 03/03/13 18:34:

 Hello,
 Does anyone know how to visualize a surface within a given radius from

  a

 ligand binding site? In chimera you can limit the display surface

  within

 0-X angstrom of a ligand. This allows you to see the surface

  surrounding

 the ligand without the rest of the protein.
 I guess you could create a new selection of residues around a ligand

  and

 show this surface but I wondered if there are any other ways of doing

  this.

 --
 Thomas Holder
 PyMOL Developer
 Schrödinger Contractor

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Re: [PyMOL] Lighting script request

2013-02-18 Thread Jason Vertrees
Hi Vitaly,

In our later versions of PyMOL there's a setting called edit_light that
controls which light may be moved by the mouse in 3-button Lights Mode. To
enable 3-button Lights Mode, just click Mouse  3-Button Lights. Use
shift+mouse to move the light around.

To control which lights are being manipulated:

# let there be 3 lights

set light_count, 3

# move the second specular light

set edit_light, 2

Now, in 3-button Lights mode, the mouse will move light 2.

The default light is ambient which cannot be moved. If you have 3 lights on
(ambient and two specular), then you can move the two specular two lights
by setting edit_light to 1 or 2.

Cheers,

-- Jason


On Sun, Feb 17, 2013 at 12:22 AM, V.V. vvos...@gmail.com wrote:

 Occasionally I need to play around with the number of lights and their
 vectors to get nice rendering. It's not something I do often, so every
 time I need to scour through the mailing list to recall Pymol
 definitions of light sources (the page on light badly needs
 updating). So... Can someone write a script that would grab the light
 data from the settings and present it as a separate object? A reverse
 action, where dragging the points of the light vector would update the
 lightX values would also be nice.

 Thank you,
 Vitaly


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Re: [PyMOL] Zoom + Fading simultaneously in movie

2013-02-11 Thread Jason Vertrees
Hi João,

You'll need to use the mdo command to fade while zooming. The easiest way
is to use the movie_fades script (
http://www.pymolwiki.org/index.php/Movie_fade) from the PyMOLWiki.

Cheers,

-- Jason


On Sat, Feb 9, 2013 at 4:48 AM, João Rodrigues anar...@gmail.com wrote:

 Hi all,

 I'm trying to make a short movie here and I came across something I can't
 find on the internet how to do it.. I want to zoom in a region of the
 protein (done easily) and at the same time fade its surface (also easily
 done on its own, thanks Tsjerk).

 Is this possible or we cannot have two actions in the same frame?

 Sorry for the limited jargon for movie making!

 Best,

 João


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Re: [PyMOL] Managing Viewport Location

2013-02-08 Thread Jason Vertrees
Hi Wilson,

The following works for me:

# put the PyMOL window at 100,100 on startup

./pymol -X 100 -Y 100

I don't think we can programmatically move the OpenGL window once it's
started up, however.

On MacOS X 10.8 and the windowing system overrides these values; Linux and
Windows should operate correctly.

Cheers,

-- Jason


On Fri, Feb 8, 2013 at 4:04 PM, Wilson Omesiete womesi...@gmail.com wrote:

 Is it possible to control the screen location of the viewport during run
 time through the API? Currently I am using...

 import os, wx, __main__

 app = wx.App()
 os.environ['PYMOL_PATH'] = C:\Python27\PyMOL

 __main__.pymol_argv = [ 'pymol', -qx] # Quiet and no GUI
 import pymol
 pymol.finish_launching()

 app.MainLoop()

 ...to load PyMol without the external GUI in quiet mode. I tried passing
 -qxX 30Y 50 in argv, but that change causes PyMol to load forever, also
 that would only give control over the initial position if it worked.

 --
 Wilson Omesiete
 School of Biochemistry
 Georgia Institute of Technology


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Re: [PyMOL] cross hair for non-bonded atoms

2013-01-30 Thread Jason Vertrees
Hi Pascal,

hide nonbonded

Cheers,

Jason

Sent from my Android. Please excuse the concision and any typos.
On Jan 30, 2013 1:10 PM, Pascal Auffinger 
p.auffin...@ibmc-cnrs.unistra.fr wrote:

 Hi,

 Just wondering how to remove the cross hair that is shown for each
 non-bonded atom
 (for example water molecules).

 Thanks,

 Pascal


 -
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 IBMC/CNRS
 15 rue René Descartes
 67084 Strasbourg Cedex

 p.auffin...@ibmc-cnrs.unistra.fr
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Re: [PyMOL] Hight-quality visualisation

2013-01-27 Thread Jason Vertrees
Hi James,

In particular I wounder to know how I could decrease width of contour

 black line (appeared in set ray_trace_mode) ?


Please modulate the ray_trace_gain setting to adjust the thickness of the
outline. Please do not rely upon 3rd party software until you've tried this
easier solution.

For other neat rendering tricks, please see the PyMOLWiki's Gallery (
http://www.pymolwiki.org/index.php/Gallery).

Cheers,

-- Jason

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Re: [PyMOL] Active stereo on an iMac?

2013-01-25 Thread Jason Vertrees
Hi Joachim,

To my knowledge Apple does not support stereoscopic 3D. This has been a
longstanding issue they still refuse to address.

Cheers,

-- Jason


On Fri, Jan 25, 2013 at 11:34 AM, Joachim Reichelt 
joachim.reich...@helmholtz-hzi.de wrote:

 Dear Mac-User

 is it possible to use active stereo, e.g. NVIDIA shutter glasses + ASUS
 3D Monitor on the latest iMac?
 The GT 640M/650M are on the list under
 http://www.nvidia.de/object/3d-vision-requirements-de.html

 --
 Joachim Reichelt


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Re: [PyMOL] Piecewise rotations while viewing in surface

2013-01-25 Thread Jason Vertrees
Hi Alex,

We'll look into making this faster/smarter. To let you know, whenever you
move an atom, it deforms the surface and causes a recalculation. The bigger
your structure and higher quality the surface the longer this takes.

Cheers,

-- Jason


On Tue, Jan 22, 2013 at 10:34 AM, Alex Truong atru...@bu.edu wrote:

 Hi All,

 This isn't really a problem per se, I'm just wondering. Is there any way
 to more efficiently code the rotation protocol when the items being viewed
 are in surface view? Maybe my computer isn't fast/strong enough or
 something, but it seems whenever I try tweaking the position of one
 subunits in relation to other subunits while everything is in surface view,
 two redraws occur, and it's difficult for me to adjust with precision
 because there's so much latency between positionings. Just a thought.
 again, it's not really much of an issue, because I can just retoggle a new
 view or something as a workaround, but it seems like manipulations while in
 surface view can get a little GPU/CPU intensive. Are the redraws necessary?

 Alex


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Re: [PyMOL] names of the residues

2013-01-25 Thread Jason Vertrees
Hi Ahmet,

If your PDB is named 1foo and has one chain this should work:

iterate first 1foo and poly, resn

iterate last 1foo and poly, resn

Otherwise you'll need to specify the selection more carefully, but first
and last should still be appropriate.

Cheers,

-- Jason



On Fri, Jan 25, 2013 at 4:16 PM, Ahmet yıldırım ahmedo...@gmail.com wrote:

 Dear users,

 How can I learn the names of the residues that make up the N- and C-
 terminals of a structure using Pymol?

 Thanks in advance
 --
 Ahmet Yıldırım


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Re: [PyMOL] new line in label

2013-01-24 Thread Jason Vertrees
Hi Abhinav,

It's currently not feasible. Please see the previous discussion on this:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08942.html.

Cheers,

-- Jason


On Thu, Jan 24, 2013 at 11:04 AM, Abhinav Kumar
abhin...@slac.stanford.eduwrote:

  Hi,
 I want to create a label that has a line break inside it. For example
 Asn\n102.
 Is there a way to do it?
 The command 'label selection Asn\n102' does not work.
 --
  Thanks,
 Abhinav

  JCSG@SSRL, SLAC
 (650) 926-2992


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Re: [PyMOL] Write vector graphics of session

2013-01-15 Thread Jason Vertrees
Greetings,

There seems to be some significant interest in vector graphics output.
To track this, I created a poll on the PyMOL website
(http://pymol.org/vector_poll) where you can cast your vote on which
format you prefer. Poll results will help advise development efforts.

Cheers,

-- Jason

On Tue, Jan 15, 2013 at 6:32 AM, Martin Hediger ma@bluewin.ch wrote:
 I'm no expert but I guess my favorite would be EPS. Converting to PDF, if
 required, is easy on the Mac.

 Best regards
 Martin




 On 14.01.13 23:53, Jason Vertrees wrote:

 Martin,

 That would be a nice feature. Which format would you and the others
 prefer: SVG, PDF, or EPS?

 Cheers,

 -- Jason

 On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch wrote:

 Hi PyMOL users
 Can PyMOL write a vector based picture of a session? Does not require to
 be very fancy, but vector based would be cool. Something like in the
 old days with molscript.

 Best regards
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Re: [PyMOL] Write vector graphics of session

2013-01-14 Thread Jason Vertrees
Martin,

That would be a nice feature. Which format would you and the others
prefer: SVG, PDF, or EPS?

Cheers,

-- Jason

On Sat, Jan 12, 2013 at 6:31 AM, Martin Hediger ma@bluewin.ch wrote:
 Hi PyMOL users
 Can PyMOL write a vector based picture of a session? Does not require to
 be very fancy, but vector based would be cool. Something like in the
 old days with molscript.

 Best regards
 Martin

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Re: [PyMOL] stick/ribbon rendering not working

2013-01-10 Thread Jason Vertrees
Hi Abhinav,

Does this setting help:

set cylinder_shader_ff_workaround, 1

If not, can you please send me a screenshot showing the problem?

Cheers,

-- Jason


On Wed, Jan 9, 2013 at 5:40 PM, Abhinav Kumar
abhin...@slac.stanford.edu wrote:
 Hi,
 I recently upgraded my desktop to Ubuntu 12.10.

 When I load a pdb in pymol, it comes up with line rendering as usual, but if
 I try to do a stick or ribbon rendering, it does not do it. In fact the
 stick operation hides the residue.

 These are the graphics specifics written by pymol.
 OpenGL graphics engine:
   GL_VENDOR: nouveau
   GL_RENDERER: Gallium 0.4 on NV84
   GL_VERSION: 3.0 Mesa 9.0
  Detected 4 CPU cores.  Enabled multithreaded rendering.

 Any help please.

 --
 Thanks,
 Abhinav

 JCSG@SSRL, SLAC
 (650) 926-2992


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Re: [PyMOL] unittest for get_coordinate function

2013-01-10 Thread Jason Vertrees
Hi Martin,

 I wonder, what is a most meaningful way of programmatically determining
 that a line of text in an arbitrary file contains atomic coordinates?
 The context of this question is that I plan to write a program that
 reads two files containing coordinates and has to perform operations on
 pairs of coordinates r1 and r2, where ri is the coordinate value from
 file i.

 [snip]

You ask about reading and testing coordinate data from files in
various formats. There are two things I can think of to consider.
First, each file format will have a different definition and therefore
properties for extracting data. Some, like the PDB will be
column-based, so you'll need to focus on getting your columns exactly
right. Others might be binary (MTZ) or dictionaries (CIF) in which
higher-order parsing might be necessary. Thus, for each format, you'd
need a specific test which will be defined by that format. Second, and
this happens all the time, many application writers will produce files
that are nearly properly formatted--read incorrectly formatted--and
will break a strict parser. If you're working on a large set of files,
I suggest you write a scrubber that you can apply across your files
to ensure they're properly formatted before use.

If you're lucky, your format will come with a nicely defined BNF grammar.

Good luck.

Cheers,

-- Jason

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Re: [PyMOL] Atom renaming within selection

2013-01-03 Thread Jason Vertrees
James,

alter my_sele, name=CA

PyMOL might act quirky after doing that, though.

Cheers,

-- Jason

On Thu, Jan 3, 2013 at 8:37 AM, James Starlight jmsstarli...@gmail.com wrote:
 Dear Pymol users!


 I want to rename all atoms within selection to the selected name. I've
 found that the renamecommand can do it but the syntax of that comand
 is not quite understood for me :( Could you provide me with some
 example ? e.g my mollecule consist of 120 carbon atoms named as the
 C1, C2... C120.  I want to rename all atoms to CA ( the same index for
 all atoms).


 Thanks for help


 James

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Re: [PyMOL] Memory not released after load and delete of structure

2012-12-20 Thread Jason Vertrees
Hi Martin,

Which version of PyMOL are you using?

Cheers,

-- Jason

On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote:
 Dear PyMOL users
 In a directory are PDB files of combined size equal to around 3MB. When
 I load all files into PyMOL, I observe that the required RAM of PyMOL
 (MacOS X 10.6) increases by roughly this amount.
 When I delete all objects, the RAM requirement remains the same and when
 I then reload all structures, the RAM requirement increases even further.
 I'm currently using PyMOL to batch process a number of files where a
 structure is loaded, modified and then deleted again from the objects
 list. This then results in RAM requirements of over 1GB and together
 with other applications, I run out of memory.
 Is there a way I can prevent PyMOL from behaving this way?

 Best regards and thanks for any help
 Martin

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Re: [PyMOL] Memory not released after load and delete of structure

2012-12-20 Thread Jason Vertrees
Martin,

That sounds like a memory leak in v1.3. Can you try a newer version of
PyMOL and let us know if it still happens? We've fixed lots of bugs
since v1.3.

Also, is your script simply iterating over structures and deleting
them when done? You sure you're not missing a cleanup step somewhere?
(Any chance we can see the script or a stub of it?)

Cheers,

-- Jason

On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote:
 Hi Jason,
 I'm using PyMOL 1.3.

 Best regards
 Martin





 On 20.12.12 15:53, Jason Vertrees wrote:

 Hi Martin,

 Which version of PyMOL are you using?

 Cheers,

 -- Jason

 On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote:

 Dear PyMOL users
 In a directory are PDB files of combined size equal to around 3MB. When
 I load all files into PyMOL, I observe that the required RAM of PyMOL
 (MacOS X 10.6) increases by roughly this amount.
 When I delete all objects, the RAM requirement remains the same and when
 I then reload all structures, the RAM requirement increases even further.
 I'm currently using PyMOL to batch process a number of files where a
 structure is loaded, modified and then deleted again from the objects
 list. This then results in RAM requirements of over 1GB and together
 with other applications, I run out of memory.
 Is there a way I can prevent PyMOL from behaving this way?

 Best regards and thanks for any help
 Martin


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Re: [PyMOL] wierd bug in Ubuntu 12.10

2012-12-17 Thread Jason Vertrees
Hi Stephan,

I use Ubuntu 12 and haven't had any problems with PyMOL. I do have
problems with my mouse in all apps, but that's not PyMOL's fault.

Do you know anyone else with these problems? Have you asked around the
Ubuntu community?

Cheers,

-- Jason

On Sun, Dec 16, 2012 at 10:37 AM, lloyd riggs lloyd.ri...@gmx.ch wrote:

 Dear All,

 I have a wierd bug with pymol after a recent update to Ubuntu 12.10.  If I 
 use any auxiliary (not in pymol) software such as notepads, gedit, etc..Pymol 
 then does some sort of switch if it is open at the same time for selections.  
 It changes from residue, to atom, to whole molecule in the selection, 
 depending on how much or how many times you go and type something in gedit.  
 It then does not allow you to rotate the molecule, or change the menu 
 selections anymore.  I then have to re-start the computer, or re-install 
 pymol to re-set the normal operations.  This is extremely problematic, as 
 pymol is a good program to quickly look at specific residues, etc...when 
 doing massive text based tabulations of specific residues, and a necessary 
 orientation and check visually is needed on the side to keep track of things. 
  Needless to say the uses for anything else, such as making images, etc..

 Has anyone experienced this, or more importantly, does anyone have a patch or 
 bug fix.

 Sincerely,

 Stephan Watkins

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Re: [PyMOL] what is an object colored ?

2012-12-12 Thread Jason Vertrees
Hi Jon,

  ive been given a pse file.and i am trying to work out what color
an object is..

i used the command

  get cartoon_color, pT_A

   and got back

  get: cartoon_color = default in object pT_A

You're right, that's not very helpful. This will get you the answer,
but it's not very straightforward:

s = cmd.get_session()

print cmd.get_color_tuple(s[names][1][5][0][2])

To make sure you have right object ensure that,

s[names][1][5][0][1]

equals your object name.

Cheers,

-- Jason

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Re: [PyMOL] make bond between two atoms

2012-12-11 Thread Jason Vertrees
Hena,

 I created two objects as follows:

 pseudoatom A1, pos=[10.0, 10.0, 100.0]
 pseudoatom A2, pos=[10.0, 10.0, -200.0]

 I want to create a bond between these two atoms. Could you please help me? I
 need to display a 2 fold axis passing through these points.

You can create a distance measure between them as shown here,
http://www.pymolwiki.org/index.php/Pseudoatom. Or you can do this:

pseudoatom foo1, pos=[0,0,0], name=CA
pseudoatom foo2, pos=[1,1,1], name=CB

create foo, foo1 or foo2

bond fooCA, fooCB

which creates a single object from the two pseudoatoms and bonds the
two pseudoatoms.

Cheers,

-- Jason

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Re: [PyMOL] Help with alignments

2012-12-11 Thread Jason Vertrees
Hi Jon,

align prot1 and chain A, prot2 and chain X

'super' and 'cealign' should work similarly.

Cheers,

-- Jason

On Tue, Dec 11, 2012 at 7:35 AM, Jonathan Grimes
jonat...@strubi.ox.ac.uk wrote:

  I am wanting to align proteins based on superposition of
  particular chains.  Is it possible to do the superposition based
  on the chains, but to move, in this case the entire complex ???

  Thanks
   Jon

 Sent from my iPad

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Re: [PyMOL] Rendering memory errors

2012-12-10 Thread Jason Vertrees
Hi Stephan Lloyd Watkins,

 I am no longer able to use the rendering plugin , which is a vlauble asset as 
 I am at this moment in the midst of making some publication quality figures.

Which rendering plugin are you referring to? What type of computer are
you using?


 Additional, the standard ray trace option will only work if I use a white 
 background, and zoom out further than would make a good image, ie a 300 amino 
 protein about 1 inch square on an 8x8 inch window (visual field).

How are you ray tracing? Using the 'ray' command? Clicking the 'ray'
button? What happens if you do not use a white background? These bugs
sound like they're related to the plugin, not PyMOL itself. Can you
share your PyMOL session file with me?


 As it is both the rendering types, I assume it is some change to memory 
 utilized by the shaders, as it crashes everytime.  I have a similar problem 
 now with gimp as well, however the memory cap is easy to see and maxes out 
 around 3-4 G before crashing, however there is a 16 G memory, along with 4G 
 on the GPU so I do not know where the errors come from.  I do not get the 
 errors on VMD, however prefer Pymol for the ease of use and also the images 
 are nice.

If you have Intel-based hardware you might try the following settings
upon startup:

set use_shaders, 0
set sphere_mode, 0

and then try your rendering plugin.

Cheers,

-- Jason

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[PyMOL] Project Upgrades

2012-12-06 Thread Jason Vertrees
Greetings,

This is just a quick note to let you know that the server hosting the
PyMOLWiki has recently been upgraded. In general the site should be
faster. If you see any problems, please let me know.

If anyone is curious, the PyMOLWiki is still highly utilized. It's
been viewed over 9.6 million times and often gets more than 2,000
unique visitors each day.

Next, we've upgraded the open-source project page on SourceForge.
Please be aware that some links will have moved. Likewise, if you see
any problems, please let us know. The conversion will probably take a
little time, so please be patient.

Cheers,

-- Jason

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Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

2012-12-04 Thread Jason Vertrees
Hi Rye,

set connect_cutoff, 0.5

load 1.xyz

produces different bonding than if you left the connect_cutoff value
to its default, 0.35. Set it to 0.85 and then load the file and you'll
see the Unknown atoms in the middle bonded as well.

Cheers,

-- Jason

On Tue, Dec 4, 2012 at 11:33 AM, Rye Terrell ryeterr...@ryeterrell.net wrote:

 Hi Jason,

 Thanks for the tip. I still couldn't get it to work. I'll google around some
 more, but here's the file. Thanks for any help.

 Cheers,
 Rye


 On Mon, Dec 3, 2012 at 4:34 PM, Jason Vertrees
 jason.vertr...@schrodinger.com wrote:

 Hi Rye,

 How about connect_cutoff in Å? There's also connect_mode
 (http://www.pymolwiki.org/index.php/Connect_mode).

 If you send me a copy of your file I can look at it.

 Cheers,

 -- Jason

 On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell ryeterr...@ryeterrell.net
 wrote:
  I have a silicon bulk system. Pymol indicates that a handful of the
  atoms
  are bonded to each other. Many bonds are not indicated. Is there some
  value
  I can adjust that will make pymol indicate that more atoms are bonded? I
  usually do this by setting some cutoff radius, but googling around has
  yielded no results. I see that there is a way to bond atom pairs
  manually,
  but that would be incredibly tedious given the number of bonds there
  should
  be.
 
  Thanks for any help!
  Rye
 
 
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Re: [PyMOL] setting the cutoff radius that determines when atoms are bonded

2012-12-03 Thread Jason Vertrees
Hi Rye,

How about connect_cutoff in Å? There's also connect_mode
(http://www.pymolwiki.org/index.php/Connect_mode).

If you send me a copy of your file I can look at it.

Cheers,

-- Jason

On Mon, Dec 3, 2012 at 4:03 PM, Rye Terrell ryeterr...@ryeterrell.net wrote:
 I have a silicon bulk system. Pymol indicates that a handful of the atoms
 are bonded to each other. Many bonds are not indicated. Is there some value
 I can adjust that will make pymol indicate that more atoms are bonded? I
 usually do this by setting some cutoff radius, but googling around has
 yielded no results. I see that there is a way to bond atom pairs manually,
 but that would be incredibly tedious given the number of bonds there should
 be.

 Thanks for any help!
 Rye

 --
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Re: [PyMOL] iPad pymol questions

2012-11-28 Thread Jason Vertrees
Hi Steve.

 I am a new subscriber to the pymol listserv.  I did look around a bit on the 
 listserv site, but did not find a way to search previous postings and 
 responses, so did not find if there is a known answer to my question.

Welcome to the PyMOL community.


 Minor question: is there a way to search the pymol message archive, and if 
 so, how to do it?

Yes, try here 
http://sourceforge.net/search/?group_id=4546type_of_search=mlists.
You get there by mousing over Mailing Lists on the pymol-users
archive page 
(http://sourceforge.net/mailarchive/forum.php?forum_name=pymol-users).


 Major question: I have been playing with the iPad version of pymol from 
 Schrodinger.  I know how to search pbd for structures,and how to view 
 structures I have already found and saved to my pymol app folder on Dropbox.  
 But I need to show some structures to an audience where I may not have wifi 
 access for my iPad, and I would like to have the pymol iPad app locally save 
 structure files so I can use them when I am off line.  Is there a way to do 
 this with the iPad?

Currently you need to be online to access your data. We'll fix this
for the next release.


Cheers,

-- Jason

--
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Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

2012-11-27 Thread Jason Vertrees
Mike,

 Although I am curious now if I had a pdb that lacks hydrogens, like I did in 
 this case,
 what pymol facilities are there for adding them? Apparently you have some 
 editing

h_add object_name

Type, help h_add or check out h_add on the PyMOLWiki
(http://www.pymolwiki.org/index.php/H_Add).

Cheers,

-- Jason

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Re: [PyMOL] ribbon trace, visualizing polymers (resent)

2012-11-27 Thread Jason Vertrees
Hi Erik,

Can you please send me a copy of one of the problematic sessions?

Cheers,

-- Jason

On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson nelsoner...@gmail.com wrote:

 I use pymol to generate images of simple polymers by loading their
 coordinates as
 .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates.
 I connect
 them using the ribbon_trace option, and color them by varying b-factors in
 the .pdb
 file.

 I had created many different movies and figures this way, and I saved the
 sessions
 as .pse files. Just recently, I went back to view some of these sessions and
 they just
 loaded as blank screens.

 I tried creating more images as before - using the ribbon_trace option to
 connect the
 atoms - but it no longer works.

 I'm pretty sure I didn't change any options in pymol, so I'm wondering if
 pymol
 somehow updated itself, or some update of my mac airbook affected the pymol
 program. Neither of these seems very likely.

 What went wrong? Is there a way I can fix this?

 A more general question. It seems like there must be a better way to
 visualise a
 polymer, say as a ball an stick image. Is there a more straight forward way
 of doing
 this in pymol?

 Thanks, Erik

 --
 Erik Nelson

 Howard Hughes Medical Institute
 6001 Forest Park Blvd., Room ND10.124
 Dallas, Texas 75235-9050

 p : 214 645 5981
 f : 214 645 5948

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Re: [PyMOL] ribbon trace, visualizing polymers (resent)

2012-11-27 Thread Jason Vertrees
Hi Erik,

This is a known bug introduced in OS X 10.8 and some video cards. To
fix this just type,

  set cylinder_shader_ff_workaround, 1

and all should be well. PyMOL uses an official rendering optimization
but some systems have difficulty with it, hence our workaround.

This is automatically fixed in PyMOL v1.5.0.5 and later (and in the
recent open-source code).

Cheers,

-- Jason



On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson nelsoner...@gmail.com wrote:

 I use pymol to generate images of simple polymers by loading their
 coordinates as
 .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates.
 I connect
 them using the ribbon_trace option, and color them by varying b-factors in
 the .pdb
 file.

 I had created many different movies and figures this way, and I saved the
 sessions
 as .pse files. Just recently, I went back to view some of these sessions and
 they just
 loaded as blank screens.

 I tried creating more images as before - using the ribbon_trace option to
 connect the
 atoms - but it no longer works.

 I'm pretty sure I didn't change any options in pymol, so I'm wondering if
 pymol
 somehow updated itself, or some update of my mac airbook affected the pymol
 program. Neither of these seems very likely.

 What went wrong? Is there a way I can fix this?

 A more general question. It seems like there must be a better way to
 visualise a
 polymer, say as a ball an stick image. Is there a more straight forward way
 of doing
 this in pymol?

 Thanks, Erik

 --
 Erik Nelson

 Howard Hughes Medical Institute
 6001 Forest Park Blvd., Room ND10.124
 Dallas, Texas 75235-9050

 p : 214 645 5981
 f : 214 645 5948

 --
 Monitor your physical, virtual and cloud infrastructure from a single
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(e) jason.vertr...@schrodinger.com
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Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

2012-11-26 Thread Jason Vertrees
Hi Mike,

 I was trying to figure out what to eat today so naturally I started looking 
 for PDB libraries
 with food components.  I was looking for garlic related chemicals when I came 
 across this,

 http://molecules.gnu-darwin.org/

 which seems to have many pdb files. My question I guess is, what does pymol 
 have
 for an API to get molecule structures from various locations or do you just 
 have an
 interface for pdb.org? Besides deciding on what to eat today, I was curious if
 pymol has more generalized means of finding structure files.

We have an API for accessing structures remotely. For example,

   load 
http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
myMolecule

You could easily create a PyMOL plugin
(http://www.pymolwiki.org/index.php/Plugins_Tutorial) that takes
advantage of this site very simply using the load command and
formatted URLs.

I hope your meal was tasty.

Cheers,

-- Jason


 
  From: jason.vertr...@schrodinger.com
  Date: Fri, 2 Nov 2012 18:57:38 -0500
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] Mobile PyMOL Problem and Solution
 
  Greetings,
 
  On Oct 28th, the folks at the PDB made some changes to their PDB Web
  Services interface. This change broke Mobile PyMOL's ability to search
  for and download PDBs.

 I haven't bothered to look at this specific situation but this a problem 
 with many sites
 and automated interaction. NCBI has a nice eutils interface that has 
 remained stable
 for a while, I'd been trying to get more groups to offer a web interface 
 designed for
 automated interactions. FWIW,

 http://www.ncbi.nlm.nih.gov/books/NBK25500/


 Do you have automated access to this library for example,

 http://www.ncbi.nlm.nih.gov/Structure/index.shtml

 they also have their own viwer, for example,

 http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

 but pymol seems a bit more extensive.

 
  I have updated Mobile PyMOL and will soon resubmit it to the AppStore
  for verification and release. This process takes typically takes no
  less than 8 days. So, in the meantime for the 7,000 Mobile PyMOL users
  please use the following technique to acquire structures:
  (1) Using Safari on the iPad browse to the www.pdb.org and find the
  structure you want.
  (2) Click Download Files from the upper right hand side of the
  structure's page and then select PDB File (Text).
  (3) Click Open in PyMOL.
 
  Happily, as a long-term solution, I've established contact with the
  PDB Web Services Group and we'll now be made aware of future changes.
  The PDB is an extremely valuable resource in the community and I'm
  glad we could work this out.
 
  Cheers,
 
  -- Jason
 
  --
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Re: [PyMOL] Pymol in command mode - no output

2012-11-26 Thread Jason Vertrees
Hi Per,

You'll probably want to use something like this:

# load the file

load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb,
myMolecule

# ray trace and save the image; you need to do this since you're running
# PyMOL headlessly

png ~/foo.png, height=768, width=1024, ray=1


As far as missing output that's most likely because you're running
remotely and the stdout/stderr are being piped elsewhere. This is
common on clusters.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 10:28 AM, Per Larsson per.lars...@sbc.su.se wrote:
 Hi Pymol-users,

 I'm running a pml-script file to render some images on a remote server, using 
 pymol 1.4, but I do not get any output at all. And no error message, so it is 
 hard to troubleshoot, unfortunately.

 To reduce the complexity of my script, I have reduced it to basically just 
 loading a pdb-file and saving as a png-image (two lines in the pml-script), 
 but even that does not work. Any suggestions?

 I envoke the whole thing using
 $pymol -c script.pml


 Thanks
 /Per




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Re: [PyMOL] cgo object tutorials

2012-11-26 Thread Jason Vertrees
Hi Heng,

 Hi, I am just wondering if there are some useful pymol cgo tutorials
 available ? such as how to visualize a  3D triangle object(vertex and
 triangle files are known ) in Pymol?

See https://www.google.com/?q=pymol%20cgo. There is a chapter
subsection on CGOs and also a few scripts the demonstrate their usage.


 In addition, is the pymol volume visualize (http://pymol.org/volume)
 available for educational use ?

Volume visualization is available in the Incentive version and
open-source builds, but not the free Educational version.

Cheers,

-- Jason

--
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Re: [PyMOL] (no subject)

2012-11-26 Thread Jason Vertrees
Hi Mary,

Just a hint for any future lists you might be on: most modern email
lists, including pymol-users, have footers with links to subscription
options. You simply click that to get to a subscription page where you
can unsubscribe.

In this case, I removed you from the list to save you the hassle.

Cheers,

-- Jason

On Mon, Nov 26, 2012 at 5:30 PM, Mary Hall mh...@potomacschool.org wrote:
 How do I remove myself from the PyMOL users list? I'd like to stop receiving
 emails.

 Thank you.

 M. Hall

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