pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] [pymol] Wrong Visualization of set Spheres

[Thomas H. <tho...@sc...>]

Hi Julian,

I think the problem is that you format the radius as an integer:

# wrong (%d)
cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
# correct (%f)
cmd.alter("helix%d" % i, expression="vdw=%f" % vdw_a)
# also correct:
cmd.alter("helix%d" % i, "vdw=vdw_a", space={'vdw_a': vdw_a})

Hope that helps.

You didn't break any support-requesting rules, your problem was well described, just a bit tricky to understand. The only thing you should add next time is PyMOL version and operating system (wasn't relevant for this problem, but you never know).

Cheers,
  Thomas

On Tue, May 7, 2019 at 3:40 PM Julian Krumm <s2j...@un...> wrote:
> 
> Dear Pymol-Team,
> 
> very new in this forum i come along with a specific problem.
> I wrote a little pymol-script:
> 
> 
> load /work/jkrumm/edgelook/0.00M/cter/40-helix-edge/helix-40.pqr
> 
> hide lines
> show cartoon
> 
> radius = 2.7
> vdw_a = 2.7
> 
> for i in range(401,413,1):\
> print(i)\
> vdw_a = vdw_a + 2.7\
> print(vdw_a)\
> cmd.create("helix%d" % i, "/helix-40///PRT`%d/PRT" % i)\
> cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
> rebuild
> 
> disable all
> 
> 
> for i in range(401,413,1):\
> cmd.set(name="sphere_transparency", value=0.0, selection="helix%d" % i)\
> cmd.show(representation="sphere", selection="helix%d" % i)\
> cmd.enable(name="helix%d" % i)
> 
> enable helix-40
> 
> set_view (\
>     0.246392056,   -0.601405144,    0.760001123,\
>    -0.951444209,   -0.299392790,    0.071540825,\
>     0.184513614,   -0.740724683,   -0.645971537,\
>     0.000000000,    0.000000000, -270.700958252,\
>     0.528925896,    8.660091400,   -2.648437977,\
>   100.995597839,  440.406250000,  -20.000000000 )
> 
> bg_color white
> set reflect, 0
> png ./test.png, width=2400, height=1200, dpi=300, ray=0
> 
> 
> It is reading the PRT-entrys out of the input file to new objects and then
> adjusts the proper radius.
> The radius of the protein spheres is incremented by 2.7 Å. Moreover the
> sphere center is shifted away from the C-terminus towards the N-terminus
> by a distance equal to its radius (not done by pymol).
> This should lead to the situation, that the surfaces of all
> protein-spheres cut succinctly in one point at the C-Terminus, which they
> do not.
> It comes to slightly deviations when the spheres are getting visualized.
> 
> I already checked the sphere-centers. They are placed right. Also the
> radii are set right. After i showed this to my advisor he is the same
> opinion that the problem has to be pymol-based. I can't explain and i hope
> You are able to help me with this problem.
> 
> Attached to this mail You will find the pymol-session and the input PQR.
> 
> Sincerely,
> JuK
> 
> 
> P.S. If i broke any rule of support-requesting or if any information is
> missing please let me know._______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe


--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] [pymol] Wrong Visualization of set Spheres

[Julian K. <s2j...@un...>]

Dear Pymol-Team,

very new in this forum i come along with a specific problem.
I wrote a little pymol-script:


load /work/jkrumm/edgelook/0.00M/cter/40-helix-edge/helix-40.pqr

hide lines
show cartoon

radius = 2.7
vdw_a = 2.7

for i in range(401,413,1):\
 print(i)\
 vdw_a = vdw_a + 2.7\
 print(vdw_a)\
 cmd.create("helix%d" % i, "/helix-40///PRT`%d/PRT" % i)\
 cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
rebuild

disable all


for i in range(401,413,1):\
 cmd.set(name="sphere_transparency", value=0.0, selection="helix%d" % i)\
 cmd.show(representation="sphere", selection="helix%d" % i)\
 cmd.enable(name="helix%d" % i)

enable helix-40

set_view (\
     0.246392056,   -0.601405144,    0.760001123,\
    -0.951444209,   -0.299392790,    0.071540825,\
     0.184513614,   -0.740724683,   -0.645971537,\
     0.000000000,    0.000000000, -270.700958252,\
     0.528925896,    8.660091400,   -2.648437977,\
   100.995597839,  440.406250000,  -20.000000000 )

bg_color white
set reflect, 0
png ./test.png, width=2400, height=1200, dpi=300, ray=0


It is reading the PRT-entrys out of the input file to new objects and then
adjusts the proper radius.
The radius of the protein spheres is incremented by 2.7 Å. Moreover the
sphere center is shifted away from the C-terminus towards the N-terminus
by a distance equal to its radius (not done by pymol).
This should lead to the situation, that the surfaces of all
protein-spheres cut succinctly in one point at the C-Terminus, which they
do not.
It comes to slightly deviations when the spheres are getting visualized.

I already checked the sphere-centers. They are placed right. Also the
radii are set right. After i showed this to my advisor he is the same
opinion that the problem has to be pymol-based. I can't explain and i hope
You are able to help me with this problem.

Attached to this mail You will find the pymol-session and the input PQR.

Sincerely,
JuK


P.S. If i broke any rule of support-requesting or if any information is
missing please let me know.

Re: [PyMOL] Minimum mesh spacing

[Thomas H. <tho...@sc...>]

Hi Vatsal,

The "min_mesh_spacing" setting only affects the "mesh" representation of molecules (molecular surface). To increase the mesh density of an isomesh, you need to upsample the map with the "map_double" command.

https://pymolwiki.org/index.php/Map_Double

Hope that helps.

Cheers,
  Thomas

> On Apr 26, 2019, at 12:42 AM, Vatsal Purohit <vat...@gm...> wrote:
> 
> Hello,
> 
> I've been trying to use the minimum mesh spacing feature on pymol to make my meshes more defined and it doesn't seem to do anything. 
> 
> I use .map.ccp4 files that I generated on ccp4 using .mtz files I generated on phenix. Any suggestions on what I might be doing wrong and what I could do to fix this would be really appreciated!
> 
> Regards,
> Vatsal 
> 
> -- 
> Vatsal Purohit
> 
> PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University
> PULSe-Biophysics and Structural Biology training group
> vp...@pu... | 346-719-9409
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Electron density map color

[Thomas H. <tho...@sc...>]

Hi Vatsal,

This is how you show positive and negative contour:

fetch 1ubq, diffmap, type=fofc, async=0
isomesh diffmesh, diffmap, 3.0
color green, diffmesh
set mesh_negative_color, red
set mesh_negative_visible

Example copied from:
https://pymolwiki.org/index.php/mesh_negative_visible

Cheers,
  Thomas


> On Apr 26, 2019, at 12:37 AM, Vatsal Purohit <vat...@gm...> wrote:
> 
> Hello,
> 
> I've been trying to color my Fo-Fc electron density maps in pymol with the positive Fo-Fc maps showing as green and negative Fo-Fc maps showing as red and having no luck with it. They either show up as red or green.
> 
> I generate my maps by converting .mtz from phenix to .ccp4 files on ccp4. Any suggestions about how I can try to color them individually this would be greatly appreciated!
> 
> Regards,
> Vatsal
> 
> -- 
> Vatsal Purohit
> 
> PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University
> PULSe-Biophysics and Structural Biology training group
> vp...@pu... | 346-719-9409
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] monitor same protein conformational change with multiple trajectory files

[Thomas H. <tho...@sc...>]

Hi Yu and David,

I like to throw in one of the many ways to do this inside PyMOL :-)

from pymol import cmd
# load 3000 files into the "multi" object
for i in range(3000): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
# if you want, fit to the first state
cmd.intra_fit('multi')

Morphing between each state is possible, but will take some time, and with the defaults you'll end up with 90000 states, which might be more than PyMOL can handle (also you'll have a 50 minute movie).

As a proof of concept, here is how you make a linear (faster than rigimol) morph with 3 interpolated states between each consecutive input state, for the first 100 of your files (yields 495 states):

from pymol import cmd
for i in range(100): cmd.load('file_{}.pdb'.format(i + 1), 'multi')
cmd.intra_fit('multi')
cmd.morph('morph', 'multi', state1=0, state2=0, refinement=0, steps=5, method='linear')

Hope that helps.

Cheers,
  Thomas


> On May 1, 2019, at 3:36 PM, David Gae <dd...@uc...> wrote:
> 
> Dear  Yu,
> 
> Try this  bash script and then run "pymol all.pdb” in your PDB directory. this might help you view your files as a trajectory. 
> 
> --------------------
> for i in {1..3000}
> do
> # change frame_$i.pdb to your file name. for example mine is frame_1.pdb
> [ -f "frame_$i.pdb" ] 
> z=frame_$i.pdb	
> sed  's/END/ENDMDL/g' $z > $z.r 
> { echo 'MODEL'; cat $z.r; } >$z.new
> 
> rm $z.r 
> done
> 
> cat *.new > all.pdb
> rm *.new
> ---------------------
> 
> I am sure there are many ways to do this inside pymol as well. you might want to look up https://pymolwiki.org/index.php/Main_Page
> 
> hope this helps,
> David
> 
>> On Apr 30, 2019, at 5:57 PM, Yu Qi <Yu...@du...> wrote:
>> 
>> Some background: I'm an undergraduate student and am doing research with my professor about modeling protein conformational changes. I am new to this field and and am actively learning how to use command lines, python and other relative tools. I have simulated how the protein will walk with CAMPARI and have gotten back 3000 trajectory (pdb) files, my question is: how do I use PyMOL to make a movie by using those trajectory files? Basically, I want to know how to visualize how the protein moved from the first pdb file to the second, then to the third, etc.
>> 
>> I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb, I aligned them first, then morphed them. I'm not sure how to go from there because I had a result file with 2 states and 2 frames, then when I tried to morph the result file with file_3.pdb, it did not work as I expected.
>> 
>> please let me know if you have questions, and I really appreciate the help.
>> 
>> Thank you for the help,
>> Yu
>> 
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Performing backend calculations within PyMOL

[Thomas H. <tho...@sc...>]

Hi Ali,

I would typically use a temporary object for that, which is loaded into the work space but never rendered:

def intra_rms_tempobj(filename):
    from pymol import cmd
    tmpname = cmd.get_unused_name('_tmpobj')
    cmd.load(filename, tmpname, zoom=0)
    try:
        return cmd.intra_rms(tmpname)
    finally:
        cmd.delete(tmpname)

It's also possible to create a new instance of the PyMOL backend, this is probably closer to what you were looking for:

def intra_rms_tempinstance(filename):
    import pymol2
    with pymol2.PyMOL() as p:
        p.cmd.load(filename)
        return p.cmd.intra_rms('*')

See also:
https://pymolwiki.org/index.php/Launching_From_a_Script#Independent_PyMOL_Instances_.28Context_Manager.29

Cheers,
  Thomas


> On May 3, 2019, at 2:24 AM, Ali Kusay <aku...@un...> wrote:
> 
> I have noticed that PyMOL can be used to perform fast calculations by using it in command line or through something like Jupyter notebook since it doesn’t have to worry about the graphical geometries. I am curious if this can be performed within the PyMOL program itself. For example, loading the python interpreter in PyMOL and using it load a multistate object and calculate RMSD through intra_fit without actually loading the object in the work space. I would appreciate your help, this would be immensely time saving for larger proteins while providing the convince of not having to leave the program.
>  
> Kin regards,
>  
> Ali Kusay
> PhD student 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] Performing backend calculations within PyMOL

[Ali K. <aku...@un...>]

I have noticed that PyMOL can be used to perform fast calculations by using it in command line or through something like Jupyter notebook since it doesn’t have to worry about the graphical geometries. I am curious if this can be performed within the PyMOL program itself. For example, loading the python interpreter in PyMOL and using it load a multistate object and calculate RMSD through intra_fit without actually loading the object in the work space. I would appreciate your help, this would be immensely time saving for larger proteins while providing the convince of not having to leave the program.

Kin regards,

Ali Kusay
PhD student

Re: [PyMOL] Space group Symmetry operators

[Jarrett J. <jar...@sc...>]

Hi Mark,

The first two digits of the code correspond to the zero-based index of the
symmetry operators list found here:
https://github.com/schrodinger/pymol-open-source/blob/master/modules/pymol/xray.py#L95
The following three digit pairs correspond to the X, Y, Z unit cell offsets
along that axis.

Jarrett J.

On Wed, May 1, 2019 at 1:07 PM Mark Saper <sa...@um...> wrote:

> PyMOL uses some preprogrammed space group operators to generate
> symmetry-related molecules.  These molecules are numbered
> _0100000, _0200000, _0300000.  I need to know which operators these
> correspond to for space group 18, P21212.
>
> Does anyone know where this can be found?  There are different orders of
> the operators depending on what book one consults.
>
> Thanks,
> Mark
> _______________________________________________
> Mark A. Saper, Ph.D.
> Associate Professor of Biological Chemistry, U-M Medical School
> Room 3220B, MSRB III   sa...@um...   +1 (734) 764-3353 mobile: (734)
> 276-6505
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Jarrett Johnson
PyMOL Developer
Schrödinger, Inc.

[PyMOL] Space group Symmetry operators

[Mark S. <sa...@um...>]

PyMOL uses some preprogrammed space group operators to generate symmetry-related molecules.  These molecules are numbered _0100000, _0200000, _0300000.  I need to know which operators these correspond to for space group 18, P21212.

Does anyone know where this can be found?  There are different orders of the operators depending on what book one consults.

Thanks,
Mark
_______________________________________________
Mark A. Saper, Ph.D.
Associate Professor of Biological Chemistry, U-M Medical School
Room 3220B, MSRB III   sa...@um...   +1 (734) 764-3353 mobile: (734) 276-6505

Re: [PyMOL] monitor same protein conformational change with multiple trajectory files

[David G. <dd...@uc...>]

Dear  Yu,

Try this  bash script and then run "pymol all.pdb” in your PDB directory. this might help you view your files as a trajectory. 

--------------------
for i in {1..3000}
do
# change frame_$i.pdb to your file name. for example mine is frame_1.pdb
[ -f "frame_$i.pdb" ] 
z=frame_$i.pdb	
sed  's/END/ENDMDL/g' $z > $z.r 
{ echo 'MODEL'; cat $z.r; } >$z.new

rm $z.r 
done

cat *.new > all.pdb
rm *.new
---------------------

I am sure there are many ways to do this inside pymol as well. you might want to look up https://pymolwiki.org/index.php/Main_Page

hope this helps,
David

> On Apr 30, 2019, at 5:57 PM, Yu Qi <Yu...@du...> wrote:
> 
> Some background: I'm an undergraduate student and am doing research with my professor about modeling protein conformational changes. I am new to this field and and am actively learning how to use command lines, python and other relative tools. I have simulated how the protein will walk with CAMPARI and have gotten back 3000 trajectory (pdb) files, my question is: how do I use PyMOL to make a movie by using those trajectory files? Basically, I want to know how to visualize how the protein moved from the first pdb file to the second, then to the third, etc.
> 
> I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb, I aligned them first, then morphed them. I'm not sure how to go from there because I had a result file with 2 states and 2 frames, then when I tried to morph the result file with file_3.pdb, it did not work as I expected.
> 
> please let me know if you have questions, and I really appreciate the help.
> 
> Thank you for the help,
> Yu
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>

[PyMOL] monitor same protein conformational change with multiple trajectory files

[Yu Qi <Yu...@du...>]

Some background: I'm an undergraduate student and am doing research with my professor about modeling protein conformational changes. I am new to this field and and am actively learning how to use command lines, python and other relative tools. I have simulated how the protein will walk with CAMPARI and have gotten back 3000 trajectory (pdb) files, my question is: how do I use PyMOL to make a movie by using those trajectory files? Basically, I want to know how to visualize how the protein moved from the first pdb file to the second, then to the third, etc.


I tried morphing two pdb files with one step from file_1.pdb to file_2.pdb, I aligned them first, then morphed them. I'm not sure how to go from there because I had a result file with 2 states and 2 frames, then when I tried to morph the result file with file_3.pdb, it did not work as I expected.


please let me know if you have questions, and I really appreciate the help.


Thank you for the help,

Yu

[PyMOL] Minimum mesh spacing

[Vatsal P. <vat...@gm...>]

Hello,

I've been trying to use the minimum mesh spacing feature on pymol to make
my meshes more defined and it doesn't seem to do anything.

I use .map.ccp4 files that I generated on ccp4 using .mtz files I generated
on phenix. Any suggestions on what I might be doing wrong and what I could
do to fix this would be really appreciated!

Regards,
Vatsal

-- 

Vatsal Purohit

PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University

PULSe-Biophysics and Structural Biology training group

vp...@pu... <pra...@pu...> | 346-719-9409

[PyMOL] Electron density map color

[Vatsal P. <vat...@gm...>]

Hello,

I've been trying to color my Fo-Fc electron density maps in pymol with the
positive Fo-Fc maps showing as green and negative Fo-Fc maps showing as red
and having no luck with it. They either show up as red or green.

I generate my maps by converting .mtz from phenix to .ccp4 files on ccp4.
Any suggestions about how I can try to color them individually this would
be greatly appreciated!

Regards,
Vatsal

-- 

Vatsal Purohit

PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University

PULSe-Biophysics and Structural Biology training group

vp...@pu... <pra...@pu...> | 346-719-9409

Re: [PyMOL] selecting a plane (perpendicular to zaxis)

[ahoneg <hon...@bi...>]

You can select by cordinates, e.g.

select my_selection, z>12.5 (see https://pymolwiki.org/index.php/Selection_Algebra)

So you can select for a range of z-coordinates:

select my_selection, z >12.5 and z< 15

best regards
Annemarie
____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



> On 24 Apr 2019, at 03:27, pym...@li... wrote:
> I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated
> Best Regards,
> Divya?
> 

Re: [PyMOL] selection of residues in protein using plane perpendicular to Z-axis

[Divya K. M. <dm...@gr...>]

Thanks Jared for your reply. I apologize for not clear. I want to use the plane to select the residues of interest in protein.


Best Regards,

Divya

________________________________
From: Jared Sampson <jar...@co...>
Sent: Tuesday, April 23, 2019 9:27 PM
To: Divya Kaur Matta
Cc: pymol-users
Subject: Re: [PyMOL] selection of residues in protein using plane perpendicular to Z-axis

Hi Divya -

It's not entirely clear what you're trying to do from your description.  Are you looking to select residues near the plane, or perhaps use the plane to divide residues into "of interest" and "not of interest"?  I think PyMOL can be useful here, but the approach will likely be different depending on your end goal.

Relatedly, if you want to visualize your plane, you can try the Plane Wizard<https://pymolwiki.org/index.php/Plane_Wizard> script, although that won't help with selecting atoms.

Cheers,
Jared


On April 23, 2019 at 7:46:49 PM, Divya Kaur Matta (dm...@gr...<mailto:dm...@gr...>) wrote:

Hi all,

I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated.


Best Regards,

Divya

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Re: [PyMOL] selection of residues in protein using plane perpendicular to Z-axis

[Jared S. <jar...@co...>]

Hi Divya - 

It's not entirely clear what you're trying to do from your description.  Are you looking to select residues near the plane, or perhaps use the plane to divide residues into "of interest" and "not of interest"?  I think PyMOL can be useful here, but the approach will likely be different depending on your end goal.

Relatedly, if you want to visualize your plane, you can try the Plane Wizard script, although that won't help with selecting atoms.

Cheers,
Jared

On April 23, 2019 at 7:46:49 PM, Divya Kaur Matta (dm...@gr...) wrote:

Hi all,

I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated.

Best Regards,
Divya 
_______________________________________________  
PyMOL-users mailing list  
Archives: http://www.mail-archive.com/pym...@li...  
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] selection of residues in protein using plane perpendicular to Z-axis

[Divya K. M. <dm...@gr...>]

Hi all,

I wanted to ask how to select a plane (perpendicular to zaxis) so that I can select all residues of interest in a protein. Any help is greatly appreciated.


Best Regards,

Divya

Re: [PyMOL] [EXTERNAL] Problem with pymol in python 3.6

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Elmira,

If you are using windows, Open Source PyMOL for python3.6 can be found here:
https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol

If you are using Mac, Open Source PyMOL via macports still depends on Python2.7 by default. 
However, you can install PyMOL built with the macports python3.6 interpreter by using the variant flag python36.
(e.g., sudo port install pymol +python36). 
See https://www.macports.org/ports.php?by=library&substr=pymol

I tested this command this morning, and it worked for me with the Mohave OS. 
It takes about twenty minutes for the dependencies to install.  
I was able to "import pymol" and run "print pymol.__path__", which returned the path to macports python3.6.
Earlier, I had made a kernel for mapcorts python3.6 so this interpreter could be used in jupyter notebook.

If you are using Linux, see the PyMOL wiki for help https://pymolwiki.org/index.php/Linux_Install.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Elmira Nazarshodeh [elm...@gm...]
Sent: Tuesday, April 23, 2019 8:35 AM
To: pym...@li...
Subject: [EXTERNAL] [PyMOL] Problem with pymol in python 3.6

Hello

I am going to work with pymol through python 3.6. When I type (from pymol import cmd) in the jupyter notebook, I get the following error:

ModuleNotFoundError: No module named 'pymol'


Could you please help me how can I fix the problem? How can I install a version of pymol that is compatible with python 3.6.?

Best Regards

[PyMOL] Problem with pymol in python 3.6

[Elmira N. <elm...@gm...>]

Hello

I am going to work with pymol through python 3.6. When I type (from pymol
import cmd) in the jupyter notebook, I get the following error:

ModuleNotFoundError: No module named 'pymol'

Could you please help me how can I fix the problem? How can I install
a version of pymol that is compatible with python 3.6.?


Best Regards

Re: [PyMOL] Ray tracing after morphing

[ahoneg <ann...@uz...>]

  1. Ray tracing after morphing (Pascal Egea)

Which version of PyMOL are you using? In the free edu version, Raytracing is suppressed.
In the incentive version, you find under the movie menu the option “ray trace frames” which you need to check.
You may also want to first set your viewport (https://pymolwiki.org/index.php/Viewport)  to a larger size to get a better resolution.

Of course, both of these actions will increase the time it takes to render your movie


____________________________________________________________

Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   hon...@bi...
phone:   +41 44 635 55 62
fax:        +41 44 635 57 12     



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>   1. Ray tracing after morphing (Pascal Egea)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Sun, 21 Apr 2019 08:58:52 -0700
> From: Pascal Egea <pa...@ms...>
> To: pym...@li...
> Subject: [PyMOL] Ray tracing after morphing
> Message-ID:
> 	<CAO...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear All,
> 
> I have been making a morph in pymol and saved the different states using
> the mpng command in the active window. However, I cannot figure out how to
> get ray-traced images to make a high quality movie in quicktime, right now
> it is quite pixelated.
> Is there a way to ray0trace each state of the morph?
> Thanks in advance.
> -- 
> Pascal F. Egea, PhD
> Assistant Professor
> UCLA, David Geffen School of Medicine
> Department of Biological Chemistry
> Boyer Hall room 356
> 611 Charles E Young Drive East
> Los Angeles CA 90095
> office (310)-983-3515
> lab      (310)-983-3516
> email     pegea at mednet.ucla.edu
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[PyMOL] 1st Call For Papers - 26th Annual Tcl/Tk Conference (Tcl'2019)

[<con...@tc...>]

Hello pymol-users, fyi ...

26th Annual Tcl/Tk Conference (Tcl'2019)
https://www.tcl-lang.org/community/tcl2019/

November 04 - 08, 2019
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

[ NEWS
 * [Submission is open](https://www.tcl-lang.org/community/tcl2019/cfp.html)
]

Important Dates:

Abstracts and proposals due   September 09, 2019
Notification to authors       September 16, 2019
WIP and BOF reservations open August 12, 2019     ** may change **
Registration opens            September 09, 2019     ** may change **
Author materials due          October 14, 2019
Tutorials Start               November 04, 2019
Conference starts             November 06, 2019

Email Contact:                tcl...@go...

Submission of Summaries

Tcl/Tk 2019 will be held in Houston, Texas, USA from November 04, 2019 to November 08, 2019.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences (Proceedings: https://www.tcl-lang.org/community/conferences.html)
have seen submissions covering a wide variety of topics including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to tcl...@go... no later than September 09, 2019. Authors of accepted
abstracts will have until October 14, 2019 to submit their final
paper for the inclusion in the conference proceedings. The proceedings
will be made available on digital media, so extra materials such as
presentation slides, code examples, code for extensions etc. are
encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com
Online proceedings will appear via
	https://www.tcl-lang.org/community/conferences.html

The authors will have 30 minutes to present their paper at
the conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 12, 2019. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 12, 2019. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (https://www.tcl-lang.org/community/tcl2019/) and will be
published on various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference, subscribe to the
tcl...@go... list. See:
https://groups.google.com/forum/#!forum/tclconference for list
information, archive, and subscription.

To keep in touch with Tcl events in general, subscribe to the
tcl-announce list. See: https://code.activestate.com/lists/tcl-announce
for list information, archive, and subscription.

Conference Committee

   * Andreas Kupries
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor - A Siemens Business
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University

Contact Information     tcl...@go...

Tcl'2019 would like to thank those who are sponsoring the conference:

   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp

[PyMOL] Ray tracing after morphing

[Pascal E. <pa...@ms...>]

Dear All,

I have been making a morph in pymol and saved the different states using
the mpng command in the active window. However, I cannot figure out how to
get ray-traced images to make a high quality movie in quicktime, right now
it is quite pixelated.
Is there a way to ray0trace each state of the morph?
Thanks in advance.
-- 
Pascal F. Egea, PhD
Assistant Professor
UCLA, David Geffen School of Medicine
Department of Biological Chemistry
Boyer Hall room 356
611 Charles E Young Drive East
Los Angeles CA 90095
office (310)-983-3515
lab      (310)-983-3516
email     pegea at mednet.ucla.edu

[PyMOL] Using Pymol for surface presentation and generating graph extremely slow

[Chao C. <bio...@gm...>]

Hello all,

Yesterday, when I installed Chimera UCSF on my computer, and found to run
Pymol become extremely slowly, particularly when generating graph using ray
function. Usually it can be done in a minute, but now takes forever. So I
uninstalled Chimera, but didn't work out.
Then I uninstalled pymol again, and reinstall a new one, but it still runs
very slowly. Have you seen this situation before? Looking forward to
receiving any feedback and comments.

Thanks,

Bio

[PyMOL] How to store primitives number in a variable

[Gianluca T. <gia...@gm...>]

Hi, I would like to store in a variable the primitives number gained
from cmd.ray(renderer=2). I am trying to redirect output using StringIO
module but seems not to work. Is there an other way to do this?

Re: [PyMOL] Greetings

[Jared S. <jar...@co...>]

Hi Shahzad - 

In your session file, these residues are part of a protein structure, so "bringing them closer together" (e.g. with the `translate` command) would distort the geometry of the protein and I would advise against it. I would recommend simply adjusting the camera position to zoom on the selected residues.

```
# create a selection for your residues of interest and zoom on them
select my_residues, resi 132+137+215+254+256+265+375
zoom my_residues

# or set the camera explicitly with the mouse (then copy using the "Get View" button and paste at command prompt)
set_view (\
     0.565557718,   -0.809213281,   -0.159118786,\
     0.178787529,   -0.068047501,    0.981527865,\
    -0.805093408,   -0.583563268,    0.106191292,\
     0.000148047,   -0.000042731,  -66.173744202,\
     0.539898396,   36.191528320,   51.672920227,\
    49.509685516,   82.788223267,  -20.000000000 )
```

If you don't want empty space between them, you could add a cartoon/ribbon/other representation, and make it some neutral color and/or semitransparent to make it unobtrusive, while providing some context for the highlighted residues.

```
show ribbon
set ribbon_color, grey90
set ribbon_as_cylinders, 1
set ribbon_transparency, 0.5
```

Hope that helps.

Cheers,
Jared

On April 12, 2019 at 8:59:33 AM, Dr Shahzad A. Pandith (drs...@uo...) wrote:

Dear all,
I am a PyMol user from past two years now. I need to know 'how can we bring two amino acid residues closer in the PyMol window' to avoid huge spacing in between.
Attached is a PyMol session file for reference.

Thanks and regards.
Shahzad

--
With best wishes
Shahzad A. Pandith, PhD
INSPIRE Faculty
Department of Botany
University of Kashmir
Voice: +91 959 660 6625, +91 941 935 4745
Email: pan...@ya...

http://bit.ly/1OzSxln |  http://bit.ly/1VIePTn  |  http://bit.ly/1IQCShp

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