pymol-users Mailing List for PyMOL Molecular Graphics System (Page 2)

Hi PyMOLers,
I am trying to use the built-in functionality to draw a user-defined ellipsoid and I am doing this by adding an extra ANISOU line in my PDB. Here is a test case:
ATOM 2 CA ALA D 500 -1.217 1.844 -2.065 1.00 1.00 CAANISOU 2 CA ALA D 500 26170 51470 166480 20820 -91370 -57530 CATEREND
The upper triangle of my un-diagonalized, symmetric matrix looks like this:
26.167 2.082 -9.137 5.147 -5.753 16.648
I had read in the PDB format documentation that: 1) The values are given as U[1,1], U[2,2], U[3,3], U[1,2], U[1,3], U[2,3] 2) And that the values are scaled by a factor of 10**4
I've tried the "show ellipsoid" example on the PyMOL-Wiki which worked fine. I just can't seem to get this to work. As well, I've tried the Ellipsoid python script but the resulting CGO that it draws doesn't seem to be correct.
Any help would be greatly appreciated.
Sean 		 	 		 

Hi,
I'm trying to install PyMOL-v1.5.0.4-Linux-x86_64 on Linux Mint 13.
After successful unpacking, "sh"-ing and copying into /usr/local/bin/pymol
I tried to execute Pymol from the terminal, but error came out:
vitali@vs-Think ~/install/pymol $ pymol
/home/vitali/install/pymol/pymol.exe: 1:
/home/vitali/install/pymol/pymol.exe: Syntax error: ")" unexpected
What am I doing wrong? I tried to google, but nothing similar came up.
Thanks,
Vitali

Hi Ananya,
if you really want CA-CA distances of *each residue*, it will be a few
lines of scripting:
xyz_initial = cmd.get_model('initial & guide').get_coord_list()
xyz_final = cmd.get_model('final_copy & guide').get_coord_list()
from chempy import cpv
for xyz_pair in zip(xyz_initial, xyz_final):\
 print cpv.distance(*xyz_pair)
Hope that helps.
Cheers,
 Thomas
Jason Vertrees wrote, On 09/10/13 20:21:
> 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 <ana...@ya...> 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
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Jordan,
if the movie has not been interpolated yet, they are interchangeable.
But if you change camera positions in an already interpolated movie,
"interpolate" will do nothing, but "reinterpolate" will.
Example:
unset movie_auto_interpolate
unset movie_auto_store
fragment ala
set_view ( 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0,\
 0.000000227, -0.000000007, -50.0, 6.538792133, \
 0.220408708, 0.0, 40.0, 100.0, -20.0 )
view 0, store
set_view ( 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0,\
 0.000000194, -0.000000011, -50.0, -6.024504662, \
 0.514286995, 0.0, 40.0, 100.0, -20.0 )
view 1, store
mset 1x100
view 0, recall, 0
mview store, 1
view 1, recall, 0
mview store, 100
# now interpolate 1 -> 100
mview interpolate
# change camera in frames 30 and 60
view 1, recall, 0
mview store, 30
view 0, recall, 0
mview store, 60
# does nothing, frame 30 and 60 will jump
mview interpolate
# will interpolate 1 -> 30 -> 60 -> 100
mview reinterpolate
Hope that helps.
Cheers,
 Thomas
Jordan Willis wrote, On 09/09/13 08:00:
> Hello,
> 
> I'm all over the place with storing scenes, views, states etc.
> 
> One thing I can't get to the bottom of, especially going through the
> documentation, is when one should use interpolate vs. reinterpolate.
> In Movie School 5, they seem to be used interchangeably. It seems to
> me that it should be if I'm storing a view on an object for the first
> time it should be interpolate, and everything else should be
> reinterpolate.
> 
> I have a feeling this is what's causing some issues with my complex
> movie.
> 
> Does anyone have a simple explanation of when to use one or the
> other?
> 
> J
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Jordan,
impressive Movie :) I don't exactly know what the problem is, it's a lot
of code. But a few thoughts:
"rotate" and "translate" have a "camera" argument and can either work in
model space, or in camera space. Default is camera=1. So if you want
those to operate independant of camera view, you should work in model
space (camera=0).
The "broken line" is before you jump to frame 430. This means, you
already have an interpolated camera position at frame 430 which
influences all (camera space) object rotations after this point. I
suggest to interpolate only in the very end of the movie.
set movie_loop, 0
mview reinterpolate
mview reinterpolate, object=*
I guess you know about the settings "movie_auto_interpolate", and
"movie_auto_store".
Cheers,
 Thomas
Jordan Willis wrote, On 09/10/13 01:38:
> Hello,
> 
> I'm trying to incorporate a camera zoom together with some other object
> motions. The object motions work fine, but when I incorporate a zoom and
> interpolate the camera views, the scenes seem to jump ahead of the
> object motions.
> 
> For instance, say at frame 50 is when I change colors and text and the
> object has completed spinning. However, when I incorporate a camera
> motion several frames down the pipeline, the color change will happen at
> around frame 30 before it should.
> 
> Here is the line of the code that gives me trouble (real names of
> objects rewritten in pseudocode)
> 
> frame 400
> super sele1, sele2
> super sele3, sele2
> pseudoatom title_5, object1
> hide nonbonded, title_5
> translate [0,40,0], object=title_5
> label title_5, "With unique somatic mutations that altered framework and
> CDR3 structure"
> show labels, title_5
> set_view (\
> -0.992779553, -0.119716585, 0.004772634,\
> -0.055808492, 0.426833898, -0.902588844,\
> 0.106016770, -0.896369994, -0.430436313,\
> 0.000191912, 0.000052718, -182.240753174,\
> 7.153404236, -15.651230812, 4.890758514,\
> 133.269271851, 231.092132568, -20.000000000 )
> mview store, object=object1
> mview store, object=object2
> mview store, object=object3
> mview reinterpolate, object=object1
> mview reinterpolate, object=object2
> mview reinterpolate, object=object3
> scene 012, store
> mview store, 400, scene=012
> #broken line
> mview reinterpolate, scene=012
> 
> The last line where I interpolate the camera motion along with the
> object motions throws everything off for the entire movie. Even if I
> don't do these two motions together and divide them up into separate
> scenes. This sort of problem is mentioned on the
> wiki http://pymolwiki.org/index.php/MovieSchool_5 at the very bottom:
> 
> " the PyMOL GUI may not have caught up to the correct place before
> saving the scene information."
> 
> 
> and recommends you store frame and scene numbers together...which I
> thought I did. I've also tried reordering when to store the camera
> motion etc. Does anyone have a solution to this problem?
> 
> For the complete movie script:
> 
> https://github.com/jwillis0720/msd_move/blob/master/makemovie.pml
> 
> 
> 
> If you want to actually run the movie all the files are there and you
> could check out the repo:
> 
> gi...@gi...:jwillis0720/msd_move.git
> 
> 
> and running makemovie.pml replacing path = "path/to/the/git/repo"
> 
> I would really appreciate the help,
> J
> ------------------------------------
> Jordan Willis
> Vanderbilt Medical Center
> jwi...@gm... <mailto:jwi...@gm...>
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear Bernhard,
I'm certainly not one of the Pymol 3D experts, but I've done a a few 3D 
movies in Pymol for presentations with a 3D projector. It's not much 
different from creating non-3D videos, only difference is the movies 
contains the two images side-by-side. Youtube assumes 'Cross-Eye Stereo' 
by default. After uploading the video to YouTube you have to set a 
special 3D-tag to be recognized as a 3D movie (see below). This is the 
workflow how I would do it:
1) create scenes & movie in PyMOL and write out consecutive frames 
(PNGs) with 'Cross-Eye Stereo' activated
2) Merge the PNG-frames to a (video-compressed) movie using a suitable 
program of your choice (e.g. VirtualDub) employing a compression codec 
(e.g. MJPEG)
(for help on video formats supported by YouTube see: 
https://support.google.com/youtube/troubleshooter/2888402?hl=en&ref_topic=2888648)
3) Upload the Video to Youtube, add the following tag: yt3d:enable=true.
(for help on YouTube formatting tags see: 
https://support.google.com/youtube/answer/146402?hl=en&ref_topic=2888648)
I also found a tutorial which describes the process coming from a 
slightly different background than structural biology ;-) but the 
procedure is similar. Maybe this is helpful...
http://www.3dsview.com/2011/12/12/3ds-view-tutorial-how-to-convert-3ds-videos-to-youtube-3d/
Good luck!
Christoph
Bernhard Rupp schrieb:
> Dear Pymol Experts,
>
> As an activity for the International Year of Crystallography 2014 , a
> colleague of mine
> would like to produce a 3D movie that can be uploaded to the YouTube 3D
> channel from pymol
> and/or povray. We would like to know if this is (a routine action / possible
> / or a development task). If the former, where to go for instructions?
>
> Best regards, BR
>
> ----------------------------------------------------------------------------
> ------------
> Bernhard Rupp
> Marie Curie Incoming International Fellow
> Innsbruck Medical University
> Schöpfstrasse 41
> A 6020 Innsbruck – Austria
> +43 (676) 571-0536
> ber...@i-...
> ----------------------------------------------------------------------------
> ------------
> Dept. of Forensic Crystallography
> k.-k. Hofkristallamt
> Vista, CA 92084
> 001 (925) 209-7429
> br...@ru...
> br...@ho...
> http://www.ruppweb.org/
> -----------------------------------------------------------------------
>
>
>
>
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
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> 

Hi Spencer,
thanks for the feedback.
Do you know the "organic" keyword? This should usually match what you
consider the ligand. It will not distinguish between covalently bound
and not covalently bound, though.
select ligand, organic & !(bymol polymer)
select ptm, organic & (bymol polymer)
Cheers,
 Thomas
Spencer Bliven wrote, On 09/11/13 01:14:
> Excellent! I had previously been using things like 'not elem c+n+o+h+s'
> in my scripts. Using 'metal' will match my intent much better.
> 'Sidechain' will be appreciated as well.
> 
> I would suggest 'ligand' and 'ptm' selectors to distinguish nonbonded
> and covalently bonded hetatms. Although I'm not sure how non-standard
> amino acids would fit in to those terms.
> 
> -Spencer
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Dear Pymol Experts,
As an activity for the International Year of Crystallography 2014 , a
colleague of mine 
would like to produce a 3D movie that can be uploaded to the YouTube 3D
channel from pymol 
and/or povray. We would like to know if this is (a routine action / possible
/ or a development task). If the former, where to go for instructions?
Best regards, BR
----------------------------------------------------------------------------
------------
Bernhard Rupp 
Marie Curie Incoming International Fellow
Innsbruck Medical University 
Schöpfstrasse 41
A 6020 Innsbruck – Austria
+43 (676) 571-0536
ber...@i-...
----------------------------------------------------------------------------
------------
Dept. of Forensic Crystallography
k.-k. Hofkristallamt
Vista, CA 92084
001 (925) 209-7429
br...@ru...
br...@ho...
http://www.ruppweb.org/
-----------------------------------------------------------------------

Excellent! I had previously been using things like 'not elem c+n+o+h+s' in
my scripts. Using 'metal' will match my intent much better. 'Sidechain'
will be appreciated as well.
I would suggest 'ligand' and 'ptm' selectors to distinguish nonbonded and
covalently bonded hetatms. Although I'm not sure how non-standard amino
acids would fit in to those terms.
-Spencer
On Sun, Sep 8, 2013 at 4:54 AM, Thomas Holder <tho...@sc...
> wrote:
> Greetings,
>
> we added "backbone", "bb." and "sidechain", "sc." keywords (SVN rev
> 4041). They select polymer (protein and nucleic acid) backbone and
> sidechain atoms, based on PDB atom names. The internal GUI menu items
> with "main chain" and "side chain" use the new keyword, which adds
> nucleic acid support for those since they previously only considered
> protein atom names.
>
> Cheers,
> Thomas
>
> Thomas Holder wrote, On 08/13/13 17:56:
> > Greetings,
> >
> > this is a quick announcement that we added the "metals" keyword to the
> > selection language (SVN code revision 4039).
> >
> > Since PyMOL's selection language is one of the powerful core features
> > that make so many complex tasks so easy, we plan to add more useful
> > keywords and operators. For example selecting by x,y,z coordinates, or
> > selecting by secondary structure element. If you have a good idea for a
> > new keyword or operator, please file a feature request on sourceforge.
> >
> > Cheers,
> > Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger Contractor
>
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
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> Archives: http://www.mail-archive.com/pym...@li...
>

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 <ana...@ya...> 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
>
> ------------------------------------------------------------------------------
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e) Jas...@sc...
(o) +1 (603) 374-7120

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

Hello,
I'm trying to incorporate a camera zoom together with some other object motions. The object motions work fine, but when I incorporate a zoom and interpolate the camera views, the scenes seem to jump ahead of the object motions.
For instance, say at frame 50 is when I change colors and text and the object has completed spinning. However, when I incorporate a camera motion several frames down the pipeline, the color change will happen at around frame 30 before it should.
Here is the line of the code that gives me trouble (real names of objects rewritten in pseudocode)
frame 400
super sele1, sele2 
super sele3, sele2
pseudoatom title_5, object1
hide nonbonded, title_5
translate [0,40,0], object=title_5
label title_5, "With unique somatic mutations that altered framework and CDR3 structure"
show labels, title_5
set_view (\
 -0.992779553, -0.119716585, 0.004772634,\
 -0.055808492, 0.426833898, -0.902588844,\
 0.106016770, -0.896369994, -0.430436313,\
 0.000191912, 0.000052718, -182.240753174,\
 7.153404236, -15.651230812, 4.890758514,\
 133.269271851, 231.092132568, -20.000000000 )
mview store, object=object1
mview store, object=object2
mview store, object=object3
mview reinterpolate, object=object1
mview reinterpolate, object=object2
mview reinterpolate, object=object3
scene 012, store 
mview store, 400, scene=012
#broken line
mview reinterpolate, scene=012
The last line where I interpolate the camera motion along with the object motions throws everything off for the entire movie. Even if I don't do these two motions together and divide them up into separate scenes. This sort of problem is mentioned on the wiki http://pymolwiki.org/index.php/MovieSchool_5 at the very bottom:
" the PyMOL GUI may not have caught up to the correct place before saving the scene information."
and recommends you store frame and scene numbers together...which I thought I did. I've also tried reordering when to store the camera motion etc. Does anyone have a solution to this problem?
For the complete movie script:
https://github.com/jwillis0720/msd_move/blob/master/makemovie.pml
If you want to actually run the movie all the files are there and you could check out the repo:
gi...@gi...:jwillis0720/msd_move.git
and running makemovie.pml replacing path = "path/to/the/git/repo"
I would really appreciate the help,
J
------------------------------------
Jordan Willis
Vanderbilt Medical Center
jwi...@gm...

Hi Christoph,
as I wrote yesterday (reply to Engin's first message), the sequence
viewer background issue is fixed in the latest open-source code. The
problem appeared in version 1.6.0.0, no earlier version should be affected.
Cheers,
 Thomas
Christoph Parthier wrote, On 09/09/13 11:19:
> Hi again,
> 
> A short "revision" on the 'background color' problem (when setting 
> background color to 'white' the background of the alternative command 
> text window (ESC key) remains black and text is not visible).
> 
> Anyone else experiencing this problem?
> 
> I (now) think it is unrelated to the sequence number color issue. And it 
> seems unrelated to the operating system used. It rather seems to be 
> related to the graphics card/driver used and the PyMOL version used (see 
> below).
> 
> I checked two computers with different NVIDIA graphics cards, several 
> NVIDIA drivers and Linux and Windows, respectively.
> 
> Results:
> 
> Linux 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 304.88) / PyMOL 1.6.0.0 
> Incentive Build: problem occurs
> Linux 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 304.88) / PyMOL 1.5.0.5 
> Incentive Build: OK - no problem!
> 
> Windows 7 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 307.45) / PyMOL 
> 1.6.0.0 Incentive Build: problem occurs
> Windows 7 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 311.66) / PyMOL 
> 1.6.0.0 Incentive Build: problem occurs
> 
> Linux 32-bit / NVIDIA Quadro FX 1000 (NVIDIA driver 173.14.30) / PyMOL 
> 1.6.0.0 Incentive Build: OK - no problem!
> 
> Hope this helps to narrow-down the issue.
> 
> Thanks,
> Christoph
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi again,
A short "revision" on the 'background color' problem (when setting 
background color to 'white' the background of the alternative command 
text window (ESC key) remains black and text is not visible).
Anyone else experiencing this problem?
I (now) think it is unrelated to the sequence number color issue. And it 
seems unrelated to the operating system used. It rather seems to be 
related to the graphics card/driver used and the PyMOL version used (see 
below).
I checked two computers with different NVIDIA graphics cards, several 
NVIDIA drivers and Linux and Windows, respectively.
Results:
Linux 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 304.88) / PyMOL 1.6.0.0 
Incentive Build: problem occurs
Linux 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 304.88) / PyMOL 1.5.0.5 
Incentive Build: OK - no problem!
Windows 7 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 307.45) / PyMOL 
1.6.0.0 Incentive Build: problem occurs
Windows 7 64-bit / NVIDIA Quadro 4000 (NVIDIA driver 311.66) / PyMOL 
1.6.0.0 Incentive Build: problem occurs
Linux 32-bit / NVIDIA Quadro FX 1000 (NVIDIA driver 173.14.30) / PyMOL 
1.6.0.0 Incentive Build: OK - no problem!
Hope this helps to narrow-down the issue.
Thanks,
Christoph
I wrote:
> Hi,
>
> I experience the same with WinPyMOL 1.6.0.0 Incentive Build (running 
> under Windows 7, NVidia Quadro 4000) - but not under Linux PyMOL 1.6.0.0.
>
> In addition I have the following related problem in WinPyMOL 1.6.0.0: 
> when setting the background color (of the graphics window) to white, 
> the background of the text console (switching with ESC key) remains 
> black. In this case the text in this window is not visible at all 
> (because it assumes it has white background and thus text color is 
> inverted). When the background color is set to 'light grey' the text 
> color becomes 'dark grey' (still on black background...).
>
> I have not experienced this problem in previous WinPyMOL Incentive 
> Builds.
>
> Christoph
>
>
>> Hi everybody,
>>
>> Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue
>> numbers in the sequence if the background is set to white. I have been
>> playing with all the seq_view_* settings (thanks for documenting them
>> clearly within the Edit All Settings window!), especially
>> seq_view_label_color, and this setting works if the background is not
>> set to white. If the background is white (regardless of opaque
>> background or not), many colors I tried display no font (or likely black
>> font), *but* some colors do, and some colors display incorrect colors.
>>
>> RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and
>> white for sequence numbers do not show. Grey, purple and brown look
>> fine, but pink is a dimmed light blue, orange is green, and aquamarine
>> is brown. After having too much fun with these colors, I thought I
>> report this.
>>
>> Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version
>> catches an error as it is starting, which may be related:
>> libpng warning: iCCP: known incorrect sRGB profile
>>
>> Working on a Mac 10.6.8.
>>
>> Best,
>> Engin
>>
>> ------------------------------------------------------------------------------ 
>>
>> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
>> Discover the easy way to master current and previous Microsoft 
>> technologies
>> and advance your career. Get an incredible 1,500+ hours of step-by-step
>> tutorial videos with LearnDevNow. Subscribe today and save!
>> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk 
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>

Hello,
I'm all over the place with storing scenes, views, states etc. 
One thing I can't get to the bottom of, especially going through the documentation, is when one should use interpolate vs. reinterpolate. In Movie School 5, they seem to be used interchangeably. It seems to me that it should be if I'm storing a view on an object for the first time it should be interpolate, and everything else should be reinterpolate. 
I have a feeling this is what's causing some issues with my complex movie. 
Does anyone have a simple explanation of when to use one or the other?
J

Greetings,
we added "backbone", "bb." and "sidechain", "sc." keywords (SVN rev
4041). They select polymer (protein and nucleic acid) backbone and
sidechain atoms, based on PDB atom names. The internal GUI menu items
with "main chain" and "side chain" use the new keyword, which adds
nucleic acid support for those since they previously only considered
protein atom names.
Cheers,
 Thomas
Thomas Holder wrote, On 08/13/13 17:56:
> Greetings,
> 
> this is a quick announcement that we added the "metals" keyword to the
> selection language (SVN code revision 4039).
> 
> Since PyMOL's selection language is one of the powerful core features
> that make so many complex tasks so easy, we plan to add more useful
> keywords and operators. For example selecting by x,y,z coordinates, or
> selecting by secondary structure element. If you have a good idea for a
> new keyword or operator, please file a feature request on sourceforge.
> 
> Cheers,
> Thomas
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Hi Engin,
the sequence viewer background and font colors are fixed in the latest
open-source code (SVN rev 4041) and will be fixed in the next PyMOL release.
Cheers,
 Thomas
Engin Özkan wrote, On 09/04/13 19:59:
> Hi everybody,
> 
> Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue 
> numbers in the sequence if the background is set to white. I have been 
> playing with all the seq_view_* settings (thanks for documenting them 
> clearly within the Edit All Settings window!), especially 
> seq_view_label_color, and this setting works if the background is not 
> set to white. If the background is white (regardless of opaque 
> background or not), many colors I tried display no font (or likely black 
> font), *but* some colors do, and some colors display incorrect colors.
> 
> RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and 
> white for sequence numbers do not show. Grey, purple and brown look 
> fine, but pink is a dimmed light blue, orange is green, and aquamarine 
> is brown. After having too much fun with these colors, I thought I 
> report this.
> 
> Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version 
> catches an error as it is starting, which may be related:
> libpng warning: iCCP: known incorrect sRGB profile
> 
> Working on a Mac 10.6.8.
> 
> Best,
> Engin
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

What about the following commands:
select mystuff, resi 1-3 and m1
select otherstuff, resi 7-9 and m2
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rro...@co...
On 9/5/2013 3:40 PM, Alessia Visconti wrote:
> Dear pyMOL users,
> I'm puzzled about how to solve an apparently simple task.
>
> I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to 
> select two different sets of atoms from each of them.
> Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] 
> from m2.
>
> I tried several combinations of "load" and "select", but no option worked.
> The last selection is always applied to both molecules. I also Googled 
> it, without any success.
>
> Does anyone know if its possible to make a selection in isolation over 
> a given molecule?
> Any suggestion will be highly appreciated!
>
> Thanks in advance,
> Alessia
>
>
> ------------------------------------------------------------------------------
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> Discover the easy way to master current and previous Microsoft technologies
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Hi Allesia,
I am not quite sure how to want to select the atoms, but if you want to have the selected atoms of both m1 and m2 in the same selection (here s1), then try this:
select s1, (m1 and id 1-3) or (m2 and id 7-9)
if you want two different selections, just do
select s1, m1 and id 1-3
select s2, m2 and id 7-9
Hope that helps,
Bernhard
On Sep 5, 2013, at 12:40 PM, Alessia Visconti <ale...@gm...> wrote:
> Dear pyMOL users,
> I'm puzzled about how to solve an apparently simple task. 
> 
> I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select two different sets of atoms from each of them.
> Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from m2.
> 
> I tried several combinations of "load" and "select", but no option worked.
> The last selection is always applied to both molecules. I also Googled it, without any success.
> 
> Does anyone know if its possible to make a selection in isolation over a given molecule?
> Any suggestion will be highly appreciated!
> 
> Thanks in advance,
> Alessia
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
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It helped a lot, thank you very much.
Alessia
On 5 September 2013 22:20, Bernhard Lechtenberg <
ble...@sa...> wrote:
> Hi Allesia,
>
> I am not quite sure how to want to select the atoms, but if you want to
> have the selected atoms of both m1 and m2 in the same selection (here s1),
> then try this:
> select s1, (m1 and id 1-3) or (m2 and id 7-9)
>
> if you want two different selections, just do
> select s1, m1 and id 1-3
> select s2, m2 and id 7-9
>
> Hope that helps,
> Bernhard
>
> On Sep 5, 2013, at 12:40 PM, Alessia Visconti <ale...@gm...>
> wrote:
>
> > Dear pyMOL users,
> > I'm puzzled about how to solve an apparently simple task.
> >
> > I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select
> two different sets of atoms from each of them.
> > Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9]
> from m2.
> >
> > I tried several combinations of "load" and "select", but no option
> worked.
> > The last selection is always applied to both molecules. I also Googled
> it, without any success.
> >
> > Does anyone know if its possible to make a selection in isolation over a
> given molecule?
> > Any suggestion will be highly appreciated!
> >
> > Thanks in advance,
> > Alessia
> >
> ------------------------------------------------------------------------------
> > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> > Discover the easy way to master current and previous Microsoft
> technologies
> > and advance your career. Get an incredible 1,500+ hours of step-by-step
> > tutorial videos with LearnDevNow. Subscribe today and save!
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk_______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
>
>

Dear pyMOL users,
I'm puzzled about how to solve an apparently simple task.
I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select
two different sets of atoms from each of them.
Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from
m2.
I tried several combinations of "load" and "select", but no option worked.
The last selection is always applied to both molecules. I also Googled it,
without any success.
Does anyone know if its possible to make a selection in isolation over a
given molecule?
Any suggestion will be highly appreciated!
Thanks in advance,
Alessia

Hi,
I experience the same with WinPyMOL 1.6.0.0 Incentive Build (running 
under Windows 7, NVidia Quadro 4000) - but not under Linux PyMOL 1.6.0.0.
In addition I have the following related problem in WinPyMOL 1.6.0.0: 
when setting the background color (of the graphics window) to white, the 
background of the text console (switching with ESC key) remains black. 
In this case the text in this window is not visible at all (because it 
assumes it has white background and thus text color is inverted). When 
the background color is set to 'light grey' the text color becomes 'dark 
grey' (still on black background...).
I have not experienced this problem in previous WinPyMOL Incentive Builds.
Christoph
> Hi everybody,
>
> Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue
> numbers in the sequence if the background is set to white. I have been
> playing with all the seq_view_* settings (thanks for documenting them
> clearly within the Edit All Settings window!), especially
> seq_view_label_color, and this setting works if the background is not
> set to white. If the background is white (regardless of opaque
> background or not), many colors I tried display no font (or likely black
> font), *but* some colors do, and some colors display incorrect colors.
>
> RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and
> white for sequence numbers do not show. Grey, purple and brown look
> fine, but pink is a dimmed light blue, orange is green, and aquamarine
> is brown. After having too much fun with these colors, I thought I
> report this.
>
> Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version
> catches an error as it is starting, which may be related:
> libpng warning: iCCP: known incorrect sRGB profile
>
> Working on a Mac 10.6.8.
>
> Best,
> Engin
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies
> and advance your career. Get an incredible 1,500+ hours of step-by-step
> tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> 

Hi Yeping,
I confirm that this is broken is 1.5, but works fine in 1.6. It seems
that this was a bug in the early version of the lines shader. So until
you have the change to upgrade, I suggest to disable the line shader:
PyMOL> unset line_use_shader
Cheers,
 Thomas
sunyeping wrote, On 09/04/13 17:21:
> Dear all
> 
> I want to make line presentation in pymol looks more thicker so I enter
> "set line_width, 3", but the lines in the viewer window don't show any
> change. Have you meet such circumstance? The pymol (version 1.5.0.1) is
> installed in centos5.9 system and other functions seem well. Thanks.
> 
> Yeping Sun
> 
> Institute of Microbiology, Chinese Academy of Sciences
-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

Thanks, Vaheh. As I did say that in my first post, actually purple, 
brown, forest etc. work too. But none of the primary colors (RGB or 
CMYK) does. And a number of them (like pink) give wrong colors.
And thanks for confirming the issue.
Engin
On 9/4/13 4:03 PM, Oganesyan, Vaheh wrote:
> Engin,
>
> If you go to Edit_all and change the seq_view_label_color to grey the numbers will become visible with white bkgr.
>
> Vaheh
>
>
>
>
> -----Original Message-----
> From: Engin Özkan [mailto:eo...@st...]
> Sent: Wednesday, September 04, 2013 4:40 PM
> To: pym...@li...
> Subject: Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
>
> I forgot to explicitly say, this is only for the Sequence View panel, which has a black background regardless of the background parameter. And it applies to both sequence numbers and chain labels. Sequences themselves are displayed correctly.
>
> Engin
>
> On 9/4/13 12:59 PM, Engin Özkan wrote:
>> Hi everybody,
>>
>> Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue
>> numbers in the sequence if the background is set to white. I have been
>> playing with all the seq_view_* settings (thanks for documenting them
>> clearly within the Edit All Settings window!), especially
>> seq_view_label_color, and this setting works if the background is not
>> set to white. If the background is white (regardless of opaque
>> background or not), many colors I tried display no font (or likely
>> black font), *but* some colors do, and some colors display incorrect colors.
>>
>> RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and
>> white for sequence numbers do not show. Grey, purple and brown look
>> fine, but pink is a dimmed light blue, orange is green, and aquamarine
>> is brown. After having too much fun with these colors, I thought I
>> report this.
>>
>> Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version
>> catches an error as it is starting, which may be related:
>> libpng warning: iCCP: known incorrect sRGB profile
>>
>> Working on a Mac 10.6.8.
>>
>> Best,
>> Engin
>>
>> ----------------------------------------------------------------------
>> -------- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL
>> 2012, more!
>> Discover the easy way to master current and previous Microsoft
>> technologies and advance your career. Get an incredible 1,500+ hours
>> of step-by-step tutorial videos with LearnDevNow. Subscribe today and save!
>> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.c
>> lktrk _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
>> http://www.mail-archive.com/pym...@li...
>
> ------------------------------------------------------------------------------
> Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more!
> Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
> To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Engin,
If you go to Edit_all and change the seq_view_label_color to grey the numbers will become visible with white bkgr.
 Vaheh
-----Original Message-----
From: Engin Özkan [mailto:eo...@st...]
Sent: Wednesday, September 04, 2013 4:40 PM
To: pym...@li...
Subject: Re: [PyMOL] Sequence numbers in MacPyMOL 1.6.0.0 with background set to white
I forgot to explicitly say, this is only for the Sequence View panel, which has a black background regardless of the background parameter. And it applies to both sequence numbers and chain labels. Sequences themselves are displayed correctly.
Engin
On 9/4/13 12:59 PM, Engin Özkan wrote:
> Hi everybody,
>
> Using MacPyMOL 1.6.0.0 Incentive Build, I no longer can see residue
> numbers in the sequence if the background is set to white. I have been
> playing with all the seq_view_* settings (thanks for documenting them
> clearly within the Edit All Settings window!), especially
> seq_view_label_color, and this setting works if the background is not
> set to white. If the background is white (regardless of opaque
> background or not), many colors I tried display no font (or likely
> black font), *but* some colors do, and some colors display incorrect colors.
>
> RGB/CMYK colors (black, red, green, blue, yellow, cyan, magenta) and
> white for sequence numbers do not show. Grey, purple and brown look
> fine, but pink is a dimmed light blue, orange is green, and aquamarine
> is brown. After having too much fun with these colors, I thought I
> report this.
>
> Same on PyMOLX11Hybrid, and fink-built 1.6.0.0, but fink-built version
> catches an error as it is starting, which may be related:
> libpng warning: iCCP: known incorrect sRGB profile
>
> Working on a Mac 10.6.8.
>
> Best,
> Engin
>
> ----------------------------------------------------------------------
> -------- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL
> 2012, more!
> Discover the easy way to master current and previous Microsoft
> technologies and advance your career. Get an incredible 1,500+ hours
> of step-by-step tutorial videos with LearnDevNow. Subscribe today and save!
> http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.c
> lktrk _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
> http://www.mail-archive.com/pym...@li...
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