Re: [PyMOL] PyMOL with Python 3

[Justin Lecher]

On 07/12/15 10:42, Justin Lecher wrote:
> On 07/12/15 10:23, Spencer Bliven wrote:
>> Nice work! It will be very nice to have python3 compatibility in the future.
>>
>> It would be nice to organize a section of the pymol-script-repo for
>> python3-compatible scripts once this gets merged to SVN.
>>
> 
> I think, we can make most of the scripts work on py2 and 3
> simultaneously. I will create a new branch in the repo. I someone likes
> to help, you are very welcome to send PRs. Please send one PR per script
> for the ease of reviews.
> 
> Justin
> 
> 

Hi,

I updated all scripts except of two for python2 and 3 compatibility.

isoslider.py and frame_slider.py are using tk. Although 2to3 is able to
convert the code I am not familiar with implementing it in a cross ABI
compatible way. So contributions are welcome here.

Justin



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Re: [PyMOL] PyMOL with Python 3

[Justin Lecher]

On 07/12/15 10:23, Spencer Bliven wrote:
> Nice work! It will be very nice to have python3 compatibility in the future.
> 
> It would be nice to organize a section of the pymol-script-repo for
> python3-compatible scripts once this gets merged to SVN.
> 

I think, we can make most of the scripts work on py2 and 3
simultaneously. I will create a new branch in the repo. I someone likes
to help, you are very welcome to send PRs. Please send one PR per script
for the ease of reviews.

Justin




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Re: [PyMOL] Using Python 3.4.3 Shell

[Justin Lecher]

On 09/11/15 09:05, Tom Aharoni wrote:
> Hey :)
> 
> I would like to work with pymol commands such as 
> cmd.distance() etc using Python 3.4.3 Shell. 
> 
> However when I try "import pymol" i get this message:
> 
> Traceback (most recent call last):
>   File "", line 1, in 
> import pymol
> ImportError: No module named 'pymol'
> 
> I would very appreciate your help.
> 

Hi,

simply you can't right now as pymol is not python3 ready yet.

Justin


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Re: [PyMOL] What legal license does PyMOL's logo available under?

[Justin Lecher]

On 28/05/15 19:26, Thomas Holder wrote:
> Hi Brenton,
> 
> the logo is currently not available under any license, it's a trademark of 
> Schrödinger. This means you can't upload it on Wikimedia Commons.
> 
> Cheers,
>   Thomas
> 

Hi Thomas,

That brings up an interesting question about the usage in distro
packages. At least Fedora and Gentoo are using it separately from the
svn repo.

Cheers,
Justin



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Re: [PyMOL] Compile Errors on SVN 4111

[Justin Lecher]

On 19/03/15 20:45, Thomas Holder wrote:
> Hi Justin,
> 
> unfortunately, not everyone is on Gentoo... see comment about distutils and 
> CXXFLAGS here:
> https://sourceforge.net/p/pymol/bugs/159/#58a5

Hi Thomas,

absolutely right, scipy is also suffering from this. There is an open
bug at distutils upstream [1]. Interestingly, setting CXXFLAGS for pymol
works. Don't know why though.

Justin



1)
http://bugs.python.org/issue1222585



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Re: [PyMOL] Compile Errors on SVN 4111

[Justin Lecher]

On 19/03/15 16:52, Tim Travers wrote:
> 
> Hi,
> 
> I also had problems compiling this last night. According to the
> following (see "Compile and install" towards the bottom),
> you have to callfirst:
> export CPPFLAGS="-std=c++0x"
> before doing the build call.
> 
> I used:
> export CPPFLAGS="-std=c++11x"
> so depends on your compiler.
> 
> HTH,
> Tim
> 

Hi,

Actually CPPFLAGS work but are the wrong ones. CPPFLAGS are the
C-PreProcessor flags which apply to C and CXX code. Things like -I... or
-D... should go there. The --std=c++11x flag as the name suggests is
only for CXX code. So adding --std=c++11x to CXXFLAGS would be more
appropriate. Works here on Gentoo systems flawlessly.

Justin




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[PyMOL] Pymol wiki search is not working

[Justin Lecher]

Hi everyone,

is it just me or is the pymol wiki search broken?

Simple search for e.g. "color" doesn't yield anything. Only if there is a page
with exactly the search term as name, you will get a hit.

In other wikis you will get also hit for search term inside the article as it
was before also in the Pymol wiki.

Could this be fixed?

thanks,

Justin

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Re: [PyMOL] PyMOLWiki Update

[Justin Lecher]

On 20/06/14 17:45, Jason Vertrees wrote:
> Hi Suzanne,
> 
> Everything should look and act exactly like it has in the past, including the
> address.
> 
> Cheers,
> 
> -- Jason
> 

Hi,

I just saw some weirdness when I try to access

https://www.pymolwiki.org/

That doesn't look like pymol stuff.

Cheers,
Justin

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Re: [PyMOL] Making nmr-like ensemble from several pdbs

[Justin Lecher]

On 27/08/14 07:56, James Starlight wrote:
> Hi
> 
> both of them are present in my ensemble. the problem is not here- if it
> possible i could upload the ensemble.pdb to some server if someone could
> check it.
> 
> James
> 

Hi,

Go for some paste bins or do a gist on github.

Justin


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Re: [PyMOL] Making nmr-like ensemble from several pdbs

[Justin Lecher]

On 27/08/14 07:43, James Starlight wrote:
> and than how to quick merged aligned conformers back to the NMR ensemble
> including TER record between each model in it?
> 
>

Hi James,

in addition you need the "MODEL #" [1] - "ENDMDL" [2] entry.

Justin

1)
http://wwpdb.org/documentation/format33/sect9.html#MODEL

2)
http://wwpdb.org/documentation/format33/sect9.html#ENDMDL



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Re: [PyMOL] cartoon_transparency issue

[Justin Lecher]

On 25/08/14 18:42, Markus Heller wrote:
> Hello,
> 
> Attached is a crop of a figure create with the latest PyMOL under Windoze 7 
> 64 bit.  When setting cartoon_transparency, I get a gray band on the 
> cartoons.  Where does this come from, and how do I get rid of it?
> 
> Thanks and Cheers
> Markus
> 
> Here's my code:
> 
> # reset everything
> delete all
> 
> # white background
> bg_color white
> 
> # show valences
> set valence, 1
> 
> # show valences inside rings, 0 = centered, 1 = inside set valence_mode, 1
> 
> # antialias
> set antialias = 1
> 
> # load the PDB files
> 
> load ... example PDB
> 
> # turn on grid mode and set it up
> set grid_mode, 1
> 
> # hide everything
> hide everything
> 
> # select protein
> select prot, polymer
> 
> # color everything
> color white
> 
> # show cartoon ribbon for protein
> show cartoon
> 
> # don't show backbone for cartoons
> set cartoon_side_chain_helper, on
> 
> # keep standard helix, strand, loop representations # other options: cartoon 
> loop, cartoon rect, # cartoon oval , cartoon tube cartoon automatic
> 
> # color cartoon white and set transparency set cartoon_color, white set 
> cartoon_transparency, 0.7
> 
> # select residue of interest
> select roi, resi 27+31+34+37+41
> 
> # show sticks for ROIs
> show sticks, roi
> 
> # hide non-polar H
> hide (h. and (e. c extend 1))
> 
> # color ROIs
> color atomic
> color yellow, (name C* and roi)
> 
> # show H-bonds between sidechains and assign to slots dist Hbo-sc, resi 37, 
> resi 41, mode = 2
> 
> # hide alls labels
> hide labels
> 
> # color all dashes green
> set dash_color, green
> 
> # deselect all to avoid little pink squares deselect
> 
> 
> 
> 
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Hi markus,

just raytrace you figure using the "ray" command.

Justin

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Re: [PyMOL] Font problem

[Justin Lecher]

On 11/03/14 07:52, Justin Lecher wrote:
> On 10/03/14 21:52, Thomas Holder wrote:
>> Hi Justin,
>>
>> this is fixed in SVN rev 4070, sorry that it took so long.
>>
>> Cheers,
>>   Thomas
>>
> 
> Hi Thomas,
> 
> Thanks a bunch. I will try it out tomorrow on my 3D machine.
> 
> Cheers,
> Justin
> 


Looks beautiful now. Thanks a lot Thomas,
Justin

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Re: [PyMOL] Font problem

[Justin Lecher]

On 10/03/14 21:52, Thomas Holder wrote:
> Hi Justin,
> 
> this is fixed in SVN rev 4070, sorry that it took so long.
> 
> Cheers,
>   Thomas
> 

Hi Thomas,

Thanks a bunch. I will try it out tomorrow on my 3D machine.

Cheers,
Justin

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Re: [PyMOL] Font problem

[Justin Lecher]

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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Re: [PyMOL] Font problem

[Justin Lecher]

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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[PyMOL] Font problem

[Justin Lecher]

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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Re: [PyMOL] commands history

[Justin Lecher]

On 11/11/13 08:43, Folmer Fredslund wrote:
> Dear Chandan,
> 
> The command "log_open" will start writing a log file of events happening.
> 
> If you want a specific name for the logfile you write "log_open myfile.pml"
> 
> In that file the commands you type will be saved, as well as actions
> from menus (not sure how many, but I think most of them).
> 

Hi,

I have this as the first lines in my ~/.pymolrc

import datetime
_logdate = datetime.datetime.strftime(datetime.datetime.now(),
"%y%m%d%H%M%S")
cmd.log_open(filename="pymol-%s.pml"%_logdate)


Justin

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Re: [PyMOL] Stereo (quad-buffered) and fixed object (Sequence, Sidebar) are suboptimal

[Justin Lecher]

On 15/07/13 18:56, Thomas Holder wrote:
> Hi Justin,
> 
> we fixed this in sourceforge SVN today. Please recompile and check if it
> works for you. Thanks.
> 
> Cheers,
>   Thomas

Thanks Thomas,

works perfectly now!

Cheers,
Justin

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[PyMOL] Stereo (quad-buffered) and fixed object (Sequence, Sidebar) are suboptimal

[Justin Lecher]

Hi,

Static objects like the sidebar and the sequence are only rendered for
one eye. This results in some unpleasant optical effects due to one eye
seeing different things as the other when having stereo switched on.

Is it possible to render those objects for both eyes?

Thanks
Justin


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ICS-6 Structural Biochemistry
Research Centre Juelich
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Re: [PyMOL] Help to compile u3d converter - IDTF to U3D on linux 64

[Justin Lecher]

On 04/03/13 12:21, Troels Emtekær Linnet wrote:
> Dear Pymolers.
> 
> I am playing around with creating a pdf file with 3 D graphics.
> I am saving in *idtf* format, which I convert to *u3d, *and then include
> in pdf through latex.
> 
> I can do this on windows, but I can't compile IDTFConverter *on linux 64.*
> 
> I have made this progress
> 
> http://pymolwiki.org/index.php/3d_pdf#Linux_install
> 
> But when I compile, I get.

Hi,

try this one

http://www2.iaas.msu.ru/tmp/u3d/u3d-1.4.3.tar.gz

it only has problems with gcc-4.7 but I can provide a patch if needed.

Justin

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[PyMOL] cartoo_transparency per selection

[Justin Lecher]

Hi,

Can I set the transparency level on residue basis? I should, shouldn't I?

If I do

>set cartoon_transparency, 0, chain a
 Setting: cartoon_transparency set for 1100 atoms in object "3sw1".

it seems that pymol sets something(at least this is what the prompt
says) but nothing changes visually. Bug of feature?

Thanks for help,

Justin


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phone: +49 2461 61 2117




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Re: [PyMOL] Open Source PyMOL v1.5.0.1

[Justin Lecher]

On 14/02/12 10:44, fukami...@chugai-pharm.co.jp wrote:
> set cylinder_shader_ff_workaround

thanks for that trick. It solved the problem.

justin

-- 
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52425 Juelich, Germany
phone: +49 2461 61 2117




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Re: [PyMOL] Open Source PyMOL v1.5.0.1

[Justin Lecher]

On 14/02/12 09:29, Lecher, Justin wrote:
> Hi Jason,
> 
> I found a bug. If you set Display -> Quality -> Maximum Quality turns
> the display around. That means the back is in the front and small, and
> the front, larger parts are in the back.
> 
> 
> justin

To be more precise, it seems that this only occurs with sticks
representation. All others are nice and super fast.

justin

-- 
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Research Centre Juelich
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Re: [PyMOL] Open Source PyMOL v1.5.0.1

[Justin Lecher]

Hi Jason,

I found a bug. If you set Display -> Quality -> Maximum Quality turns
the display around. That means the back is in the front and small, and
the front, larger parts are in the back.


justin
-- 
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Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117




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Re: [PyMOL] Open Source PyMOL v1.5.0.1

[Justin Lecher]

On 13.02.2012 20:27, Jason Vertrees wrote:
> Greetings,
> 
> It is my pleasure to announce the release of open source PyMOL
> v1.5.0.1. The source code has been committed to the open-source
> repository. It is revision 3976. An svn tag and downloadable bz2
> source file were also created. All of this is accessible form the
> PyMOL project page on SourceForge
> (http://sourceforge.net/projects/pymol/).
> 
> Before upgrading PyMOL -- please -- upgrade your video drivers! NVidia
> and AMD/ATI cards are known to work well. But, Intel Mobile and other
> low-end cards might have issues with the new rendering. The majority
> of rendering anomalies are fixed by simply upgrading your video
> drivers.
> 
> You should be able to pull and build just like normal. You will need Python 
> 2.7.
> 
> Some simple testing on my Linux machine shows the following
> improvements in real-time rendering performance for a large protein
> (58,000 atom Gro-EL, PDB 1AON) with the new open-source PyMOL code:
> 
> Lines:
>240% increase (81 FPS to 270 FPS)
> Spheres:
>864% increase (28 FPS to 270 FPS)
> Sticks:
>2100% increase (8 FPS to 180 FPS)
> Cartoon:
>3757% increase (27 to 270 FPS)
> Surface:
>2600% increase (10 to 270 FPS)
> Mesh:
>33% (180 FPS to 270 FPS)
> 
> Your numbers will be different. This Linux machine has a powerful card
> used for development
> (http://www.amd.com/us/products/workstation/graphics/ati-firepro-3d/v8800/Pages/v8800.aspx).
> It was generously donated by AMD. If you use an AMD/ATI card and PyMOL
> works for you it's because AMD/ATI helped out. You may want to thank
> them. What I've seen is that the more powerful your card the greater
> the _difference_ in speed. That is, low-end cards should see
> improvements in the range of tens to hundreds of percent while more
> powerful cards should register improvements like mine, in the
> thousands of percent for some representations.
> 
> To quickly test performance of the new code on your machine just load
> a large structure (eg. 1AON; 3R8O and 3R8T) and quickly
> rotate/translate it. To see the refresh rate, type "set
> show_frame_rate". The refresh rate shows up in the lower right hand
> corner. Compare the frame rate, smoothness, and rendering quality when
> the setting "use_shaders" is turned off and when it's turned on.
> Compare different representations, each time turning on and off the
> "use_shaders" setting.
> 
> You can quickly update old PyMOL session files to the new rendering by
> clicking, Settings > Rendering > Modernize after loading the old
> session file. PyMOL will flip all the right settings to update
> rendering. If the new code doesn't render properly, you can revert to
> the old style rendering by typing:
> 
>  set use_shaders, 0
> 
>  set sphere_mode, 0
> 
> 
> Please let us know how it goes.
> 
> Cheers,
> 
> -- Jason, Blaine & the PyMOL Team
> 


Hi Jason,

thanks for the work.

I cannot compile the molfile support:

x86_64-pc-linux-gnu-gcc -pthread -Ofast -pipe -ftracer -march=corei7-avx
-mtune=corei7-avx -mcx16 -msahf -mno-movbe -maes -mpclmul -mpopcnt
-mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mavx
-msse4.2 -msse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64
--param l2-cache-size=8192 -frecord-gcc-switches -g -funroll-loops
-Wimplicit-function-declaration -fPIC -D_PYMOL_MODULE -D_PYMOL_INLINE
-D_PYMOL_FREETYPE -D_PYMOL_LIBPNG -D_PYMOL_OPENGL_SHADERS
-D_PYMOL_VMD_PLUGINS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS
-D_CGO_DRAWARRAYS -D_PYMOL_GL_CALLLISTS -DOPENGL_ES_2 -Iov/src -Ilayer0
-Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -I/usr/include/freetype2
-Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src
-Imodules/cealign/src -Imodules/cealign/src/tnt -Igenerated/include
-Igenerated/src -I/usr/include/python2.7 -c
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o
build-2.7/temp.linux-x86_64-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In function
‘read_basis_metadata’:
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:208:11: error:
‘molfile_qm_metadata_t’ has no member named ‘have_esp’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:209:11: error:
‘molfile_qm_metadata_t’ has no member named ‘have_npa’
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:211:11: error:
‘molfile_qm_metadata_t’ has no member named ‘have_internals’
error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1


Thanks,

justin



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Re: [PyMOL] cartoon_sidechain_helper

[Justin Lecher]

Strange, yesterday I did a quick test and it didn't work. But here on my
main machine everything is fine.
Sorry for the noice.

jsutin


On 13/11/11 17:48, Jason Vertrees wrote:
> Hi Justin,
> 
> It works; see 
> http://www.pymolwiki.org/index.php/File:Cartoon_side_chain_helper_on.png.
> You just have to color by atom type after coloring by secondary
> structure:
> 
> set cartoon_sidechain_helper, on
> 
> C > Color > by ss > Helix (red) Sheet (yellow) Loop (green)
> 
> C > Color > by element > ...
> 
> Cheers,
> 
> -- Jason
> 
> On Sun, Nov 13, 2011 at 7:11 AM, Justin Lecher  wrote:
>> Hi,
>>
>> while trying this
>>
>> http://kpwu.wordpress.com/2011/11/12/pymol-sidechain-helper-in-the-cartoon-view/
>>
>> I recognised that the "color by atom type" function doesn't work anymore
>> if the sidechain helper is on. Bug or feature? Could we enable it?
>>
>> Thanks justin
>>
>> --
>> Justin Lecher
>> Institute of Complex Systems
>> ICS-6 Structural Biochemistry
>> Research Centre Juelich
>> 52425 Juelich, Germany
>> phone: +49 2461 61 2117
>>
>>
>>
>> --
>> RSA(R) Conference 2012
>> Save $700 by Nov 18
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>>
> 
> 
> 




-- 
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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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[PyMOL] cartoon_sidechain_helper

[Justin Lecher]

Hi,

while trying this

http://kpwu.wordpress.com/2011/11/12/pymol-sidechain-helper-in-the-cartoon-view/

I recognised that the "color by atom type" function doesn't work anymore
if the sidechain helper is on. Bug or feature? Could we enable it?

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] Antw.: Put scripts in a svn folder

[Justin Lecher]

Hi,

That days I simply copied the scripts from the wiki into the repo. After
that many scripts got updated in the wiki, so we need to synchronize it
again. I am sorry but I lost the interest because I wanted it to be
community based not as my own project.

Currently the repo is set to be open for any commit. Of course this has
know security implications but doesn't need selected commiters.
If we would select one or some trusted commiter we could do it on github
in a nice way. The main repo could be closed to commit access for the
trusted ones. If someone wants to add/modify something the main repo can
be forked, modified and request pull (http://help.github.com/fork-a-repo/).

justin



On 11/10/11 5:45 PM, Troels Emtekær Linnet wrote:
> I personally think git hub is a good suggestion.
> 
> And we need you wikiguys (Jason etc. ) to catch the idea and implement
> it. :-)
> 
> Security is an issue, and I also believe that you need to control this.
> I don't know if github is able to make securities in groups of a owner
> of a script and some "super users". 
> So only a few users can change the script.
> Would it possible to have the same user credentials to the github as the
> wiki?
> 
> Host / mirror.
> As far as I know, one can find each file at a github webpage.
> So, maybe the pymolwiki could show that file in a window at the wiki?
> 
> People with github experience should throw in some experience. :-)
> 
> Best
> Troels
> 
> 
> 
> 
> Troels Emtekær Linnet
> Slotsvej 2
> 4300 Holbæk
> Mobil: +45 60210234
> 
> 
> 
> 2011/11/10 Jason Vertrees  <mailto:jason.vertr...@schrodinger.com>>
> 
> Hi Justin,
> 
> > I started this some time ago and also announced it on the mailing
> list. But
> > it didn't caught much interest.
> 
> The idea didn't get much traction because it was ahead of its time. I
> think now is its time.
> 
> The plugin manager that Thomas is creating will be able to aggregate
> scripts from various locations and install them on the fly without one
> needing to restart PyMOL. Do you mind working with Thomas to help
> integrate with the git-hub repo?
> 
> Downloading scripts and running them creates a security hazard. So, we
> need to be careful about that.
> 
> Some points to consider for the repository:
>  * it should mirror or host the code from the PyMOLWiki, not fork it
>  * be secure from misuse (can anyone commit or just you?)
> 
> What do you think?
> 
> Cheers,
> 
> -- Jason
> 
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) jason.vertr...@schrodinger.com
> <mailto:jason.vertr...@schrodinger.com>
> (o) +1 (603) 374-7120 
> 
> 
> --
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
> ___
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> <mailto:PyMOL-users@lists.sourceforge.net>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> 
> 




-- 
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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] Volumes video

[Justin Lecher]

On 13/04/11 21:24, Jason Vertrees wrote:
> Hi all,
> 
> Just a quick note to let you know that I posted a small 5 minute
> (silent) basic volumes usage video.  The video is on YouTube
> (http://www.youtube.com/watch?v=tuAo_8-_HIc) and linked to from the
> PyMOLWiki (http://www.pymolwiki.org/index.php/Volume) for discussion.
> 
> Also, the new volumes can be used to make movies (see the MPEGs at the
> bottom of http://pymol.org/volume_gallery).  Volumes don't yet ray
> trace.  We've got a preliminary version of raytracing in, but it's not
> yet ready for release (ie, it's not yet good enough).
> 
> Anyone using volumes, feel free to update the PyMOLWiki pages with
> anything you've learned.  I'll try to keep facilitating as time
> permits.
> 
> Cheers,
> 
> -- Jason
> 

Thanks Jason,

the volume rendering rocks!

I tried it with APBS electrostatic maps. This gives a quite intersting
representation mode.

Thanks justin


-- 
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Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
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Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

[Justin Lecher]

Hi Jason,

could you please use PYMOL_DATA to determine the location of the shaders
dir? it is actually stored in PYMOL_DATA/shaders and with PYMOL_DATA !=
PYMOL_PATH/data it fails.

Thanks justin
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ICS-6 Structural Biochemistry
Research Centre Juelich
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phone: +49 2461 61 2117




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Re: [PyMOL] New plugin: MSMS plugin for PyMOL

[Justin Lecher]

On 21/03/11 22:57, Hongbo Zhu wrote:
> Dear PyMOLers,
> 
> As many of you might be aware of, MSMS is an excellent program developed 
> by Michel Sanner for computing protein surface, especially solvent 
> excluded surface (SES). (see http://mgltools.scripps.edu/packages/MSMS/ 
> ). Due to its outstanding usability, Robert Campbell had already 
> provided several very helpful PyMOL scripts about MSMS (see 
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ ).
> 
> I have also been using the MSMS program heavily in my work and developed 
> a MSMS plugin for PyMOL with a graphical user interface (GUI). If you 
> have interest, please take a look at the plugin at:
> ---
> http://www.pymolwiki.org/index.php/MSMS
> ---
> Features:
> MSMS can be configured and invoked in the GUI.
> The triangulated protein SES can be rendered as mesh or/and vertices 
> plus normal vectors.
> The color of surface mesh or vertices can also be configured.
> 
> Your feedback and suggestions are particularly welcome!
> 
> Best regards,
> Hongbo
> 
> --
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Hi Hongbo,

it is officially included in Gentoo Linux now [1]. It would be nice, if
you could drop me a mail, in case you changed something, so that I can
create a bumped version.

thanks justin

[1] http://packages.gentoo.org/package/sci-chemistry/pymol-plugins-msms
Might take some hours to appear there

-- 
Justin Lecher
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 fetch

[Justin Lecher]

On 12/07/10 20:24, Vivek Ranjan wrote:
> Hello,
> 
> There is a script supercell at
> "http://pymolwiki.org/index.php/Supercell";. It uses the following
> example:
> 
> run supercell.py
> fetch 2x19, async=0
> 
> Where is "2x19"... I mean the pdb file for this example is in which
> directory under pymol ?
> 
> 

The fetch command directly fetches the pdb file from the online database.

-- 
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Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385




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Re: [PyMOL] Please remove my emal address from your bulletin board

[Justin Lecher]

On 23/04/10 10:04, Greg Landrum wrote:
> The best part is that you sent this message, where you tell Dave that
> he shouldn't post unsubscribe requests to the list, to the list.
> 
> 

I recognised that it is a common problem with unsubscriptions from
mailing lists, so a public reminder how to unsubscribe can't be bad.

justin




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Re: [PyMOL] Please remove my emal address from your bulletin board

[Justin Lecher]

On 23/04/10 06:00, Charles David Stout wrote:
> Dear PyMol developers,
> 
> PyMol is an awesome program, but I'm a casual user.  Please remove my 
> email address from your bulletin board.
> Thanks
> Dave Stout
> 4-22-10
> 
> d...@scripps.edu
> 
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justin





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[PyMOL] PYNMR or NMR support in Pymol

[Justin Lecher]

Hello Jayson,

as I saw you are starting to implement crystallographic specific
elements like fetching maps from the EDS, what about putting some NMR
related features on top. The most important would be to get something
like the old pyNMR plugin to show NOE restrains. What do you think about
this idea?
Perhaps it is a small fix to get the pyNMR code working with the newer
versions of pymol.

Thanks justin




-- 
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ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385




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Re: [PyMOL] subversion 3897 compile error in Cmd.c

[Justin Lecher]

Hi Hari,

the distutils based build is fine.

justin



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Re: [PyMOL] CEalign - PyMOL Build

[Justin Lecher]

+1 from me



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Re: [PyMOL] Pre-release version of the PyMOL-APBS plugin

[Justin Lecher]

On 28/01/10 21:31, Michael Lerner wrote:
> Hi all,
> 
> I've been working with Jason Vertrees on a new version of the PyMOL-APBS
> plugin and it's now ready for pre-release.

Hi,

that's really good news, that you are going to develop the plugin in a
more public accessible manner!

For all gentoo user, you can find the plugin in the sci overlay as

sci-chemistry/pymol-apbs-plugin.

There is a version for revision 11 as well as a live ebuild available.

Thanks justin

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Research Centre Juelich GmbH,
52425 Juelich,Germany
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Re: [PyMOL] Problem Compiling Pymol 1.2.x

[Justin Lecher]

Stephen P. Molnar wrote:
> Here's teh end of the log file that I recorded.  I really don't have
> anyplace to which to upload the entire 125 kb log file.

Hi Stephen,

as Donnie already mentioned, we cannot help if we could not see the
_complete_ build.log. From the part you past, it looks succesfull. So
please try to provide us the log, in worst case compress it and attach
it to your mail.
What exactly is the output if you start it in a shell?

Justin



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[PyMOL] graphic bug?

[Justin Lecher]

Hi all, Warren,

I have this graphic problem with pymol

http://dev.gentooexperimental.org/~jlec/paste/pymol.png

I don't know since when it appears, but it is quite nasty. When I rotate
the molecule it is fine but after a second it became like this. Is this
a problem of pymol or of my setup?


pymol HEAD of svn
linux-2.6.30
xorg-server-1.6.3
intel-driver-2.8.0


Thanks justin


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Research Centre Juelich GmbH,
52425 Juelich,Germany
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Re: [PyMOL] Error: unknown type

[Justin Lecher]

> I've updated it on the Wiki.
> 

So anyone likes to try git and update the repo?




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Research centre Juelich GmbH,
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Re: [PyMOL] GIT'r Done

[Justin Lecher]

Waren points me to the fact, that it might be good to explain how to work with 
the github. I wrote a little
howto, but there are alot more in the web, which can be easily be found via 
google. I think nonetheless it
is a good starting point to contribute to our script repo.

http://tinyurl.com/cy7wj8

If anyone has suggestions feel free to edit the howto. Questions about 
unresolved things are also welcome.

Thanks justin


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Research centre Juelich GmbH,
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Re: [PyMOL] GIT'r Done

[Justin Lecher]

Jason Vertrees schrieb:
> Justin,
> 
> Thanks for taking the initiative to import the Script Library into git. 
>   It's great to see more and more of the PyMOL community giving back.
> 
> Now users can simply get a copy of all the scripts with one easy git 
> command.  I posted some details below the main menu of the Script 
> Library (http://pymolwiki.org/index.php/Category:Script_Library) on git.
> 
> I expect that if the community adopts the idea then the PyMOLWiki will 
> be used for documentation, photos and information related to the 
> scripts, while git will hold the actual code.
> 
> Cheers,
> 
> -- Jason
> 
> 
> 

Hi all,

just to clarify. Everyone can push back things into the Github. You just have 
to create an account at
GitHub, deposit a public ssh key and use this clone command:

git clone g...@github.com:jlec/Pymol-script-repo.git


If have already checked out the repo using the public access, open 
REPO_ROOT/.git/config in your
favorite editor and change

[remote "origin"]
   url = git://github.com/jlec/Pymol-script-repo.git
   fetch = +refs/heads/*:refs/remotes/origin/*

to

[remote "origin"]
   url = g...@github.com:jlec/Pymol-script-repo.git
   fetch = +refs/heads/*:refs/remotes/origin/*


and everything is fine.



Thanks,

justin
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Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385




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[PyMOL] GitHub for pymol-scripts

[Justin Lecher]

Dear all,

yesterday I created a GitHub to collect and enlarge the scripts collection for 
pymol. I started to 
import the already posted ones from the pymolwiki.org.
In my opinion this is a smooth way to maintain the code of the scripts and it 
is a good addition to the 
wiki pages. I'd like everyone to check out the repo and contribute.

http://github.com/jlec/Pymol-script-repo/tree/master

If you have problem with git, just mail me.

Thanks justin


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Research Centre Juelich GmbH,
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phone: +49 2461 61 5385



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[PyMOL] image on pymol.org

[Justin Lecher]

Hi Warren,

some time ago I asked for the script you used for the image on pymol.org and I 
lost it somewhere. Could
you post it again, please?

Thanks, justin

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[PyMOL] (no subject)

[Justin Lecher]

Hello all especially Warren,

What does

"Sorry, time-sequential stereo 3D not available"

mean. It is printed out when I start pymol. I am using current HEAD.

Thanks justin


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Re: [PyMOL] writing selection to a external file

[Justin Lecher]

Tsjerk Wassenaar schrieb:

Hi,

This should've gone to the list... (isn't there an option "send
replies to list rather than to poster" to the mailing list?)

Tsjerk

  

Depends on the list, but there is a nifty addon for thunderbird

http://alumnit.ca/wiki/index.php?page=ReplyToListThunderbirdExtension

Justin



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[PyMOL] [SOLVED] python traceback from apbs plugin and one more question

[Justin Lecher]

Justin Lecher schrieb:

Hi all,
I am using the latest svn version of Pymol with python 2.5.2. Now I get
following traceback when clicking the set grid button of the apbs plugin:

Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/pmg_tk/__init__.py", line 35,
in run
PMGApp(pymol_instance,skin).run(poll)
  File "/usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py", line 170, 
in run

self.root.mainloop()
  File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1023, in mainloop
self.tk.mainloop(n)
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1751, in __call__
_reporterror(self.func, args)
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1777, in _reporterror
msg = exc_type + ' Exception in Tk callback\n'
TypeError: unsupported operand type(s) for +: 'type' and 'str'


I am not that familiar with python, so that I couldn't figure out where
it comes from.

Thanks for help,
jusitn


My fault, once again a mis formated pdb output from modeller!


But one more question, how is the new picture on the pymol homepage
made? The one in the middle? I love the light settings!

Thanks justin



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[PyMOL] python traceback from apbs plugin

[Justin Lecher]

Hi all,
I am using the latest svn version of Pymol with python 2.5.2. Now I get
following traceback when clicking the set grid button of the apbs plugin:

Traceback (most recent call last):
  File "/usr/lib/python2.5/site-packages/pmg_tk/__init__.py", line 35,
in run
PMGApp(pymol_instance,skin).run(poll)
  File "/usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py", line 170, 
in run

self.root.mainloop()
  File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1023, in mainloop
self.tk.mainloop(n)
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1751, in __call__
_reporterror(self.func, args)
  File "/usr/lib/python2.5/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1777, in _reporterror
msg = exc_type + ' Exception in Tk callback\n'
TypeError: unsupported operand type(s) for +: 'type' and 'str'


I am not that familiar with python, so that I couldn't figure out where
it comes from.

Thanks for help,
jusitn



--
Justin Lecher
Institute for  Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385




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[PyMOL] pymolrc

[Justin Lecher]

Hi all,

Just want to know if there are only per user pymolrc files at ~/.pymolrc 
or could there be a system wide configuration e.g. /etc/pymolrc. or 
somewhere else?


Thanks,
justin





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Re: [PyMOL] How to use PyMOL without GUI ?

[Justin Lecher]

Yang, Zheng schrieb:


Dear All,

 

Would you please remind me how to start PyMOL in Linux, without the 
GUI, only command lines?  Just like Matlab, we using ‘matlab -nojvm’ 
to disable the graphic interface.


 

I am running PyMOL to ray-trace a figure. But the protein is too big. 
It always run out of memory. So I am thinking to send the job to a 
linux server which has larger RAM.


 


Thank you so much for your help!

 


Best,

Zheng



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just type:

pymol -c SKRIPT

or

pymol -q -c SKRIPT  if you want no output.


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Re: [PyMOL] problem with .pml file

[Justin Lecher]

type
@yourpmlfile.pml

Hally Shaffer schrieb:
> I installed pymol onto a linux system.  I can open the program, open the pdb
> file, and open a .pse file, but I cannot open the .pml file which contains the
> manipulations that I've already made. Any suggestions?
>
> --
> Hally Shaffer
> <>< Graduate Student
> Georgia Institute of Technology
> School of Chemistry and Biochemistry
> gth8...@mail.gatech.edu
>
>
>
>
>
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Re: [PyMOL] Calculation of Domain Volume in Pymol

[Justin Lecher]

For all the gentoo guys out there:
I wrote an ebuild for msms. Any Bugs and suggestions should be reported
to me for further improvement.


Robert Campbell schrieb:
> Dear Buz,
>
> On Fri, 04 Jan 2008 15:43:41 -0500, Buz Barstow 
> wrote:
>
>   
>> Dear all,
>>
>> I'd like to very accurately calculate the volume of a selection in  
>> pymol, or with tools that are callable by pymol? Could anyone suggest  
>> a program or algorithm?
>> 
>
> MSMS will calculate areas and volumes.  I have written a python script that
> you can run from within PyMOL to call msms.  You can find it
> (msms_pymol.py) at my scripts web page:
>
>   http://pldserver1.biochem.queensu.ca/~rlc/work/pymol
>  
> It does not use the pdb_to_xyzrn script supplied with msms -- that
> conversion is now built in to the python script.
>
> After "running" the script to load it, then you can do:
>
>   calc_msms_area object_name
>
> with options for changing the selection for calculating the area, the probe
> radius and density.  
>
> Because I was most interested in the calculation of surface areas,
> including buried surface areas, the initial MSMS calculation is only run on
> the complete object.  That is what volume will be reported.  
>
> For example, to calculate the surface area of chain A of a protein that is
> buried by chain B, first create two objects:
>
>   create protein_A, protein & chain A
>   create protein_B, protein & chain B
>
> Then run:
>
>   calc_msms_area protein_A,protein_A within 4. of protein_B,probe=1.4
>
> This will therefore report the volume of all of protein_A, but for the
> surface areas, only the part of A that is buried by B.
>
> Cheers,
> Rob
>   



---
---
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Sitz der Gesellschaft: Jülich
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Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Dr. Sebastian M. Schmidt
---
---
inherit eutils

DESCRIPTION="This allows you to run msms as a standalone application. A wrapped 
version of the library comes with MGLTools"
SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86Linux2_2.6.1.tar.gz";
HOMEPAGE="http://mgltools.scripps.edu";
RESTRICT="primaryuri"
LICENSE="academical free"
SLOT="0"
KEYWORDS="~x86"
IUSE=""

RDEPEND=""
DEPEND="${RDEPEND}"

src_install() {
insinto /usr/lib/msms/
doins atmtypenumbers
exeinto /usr/lib/msms/
doexe pdb_to_xyzr pdb_to_yzrn msms.i86Linux2.2.6.1
dosym /usr/lib/msms/pdb_to_xyzr /bin/pdb_to_xyzr
dosym /usr/lib/msms/pdb_to_xyzrn /bin/pdb_to_xyzrn
dosym /usr/lib/msms/msms.i86Linux2.2.6.1 /usr/bin/msms
dodoc README ReleaseNotes
doman msms.1
}