pymol-users Mailing List for PyMOL Molecular Graphics System

Hi João,

1QFU has a three-fold symmetry, and only one copy of each molecule is contained in the asymmetric unit.

PyMOL (on the desktop) can load the biological assembly like this:

PyMOL> set assembly, 1
PyMOL> fetch 1qfu

Hope that helps.

Cheers,
  Thomas

On 28 Feb 2017, at 16:16, João Oliveira Jr. <joa...@gm...> wrote:

> Thank you all for your time.
> 
> Someone could please explain me why some structures aren't fully displayed?
> 
> For example, in 1QFU, I just get 01 HA attached to 01 Fab antibody arm, instead of 03 HA + 03 Fabs...
> 
> Em ter, 28 de fev de 2017 às 14:25, Thomas Holder <tho...@sc...> escreveu:
> Dear João,
> 
> The Mobile (iPad) PyMOL interface is rather limited and does not expose these options, unfortunately. The only way to display a "grid_mode=on" scene is to load a PyMOL session file (.pse) which already has the setting enabled.
> 
> Cheers,
>   Thomas
> 
> On 28 Feb 2017, at 11:57, João Oliveira Jr. <joa...@gm...> wrote:
> 
> > Dear Andreas
> >
> > Where do I find this typing command option?
> >
> > Em ter, 28 de fev de 2017 às 13:53, Andreas Forster <doc...@gm...> escreveu:
> > Dear João,
> >
> > type
> >
> > set grid_mode, on
> >
> > to see your models side by side.  You might have to align them first.  Use the command
> >
> > super model1, model2
> >
> > for that.
> >
> > All best.
> >
> >
> > Andreas
> >
> >
> > On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joa...@gm...> wrote:
> > Hi
> >
> > Please, when using PyMOL app for iPad is that possible to set up multiple structures from diffent PDB codes at the same time?
> >
> > I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB codes: 1IGY, 1IGT, 1HZH, and  5DK3) aligned side by side to save a screenshot to Photos.
> >
> > When I download two PDB codes, they appear one inside the other...
> >
> > Is that possibe using the PyMOL app?
> >
> > Best regards!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Thank you all for your time.

Someone could please explain me why some structures aren't fully displayed?

For example, in 1QFU, I just get 01 HA attached to 01 Fab antibody arm,
instead of 03 HA + 03 Fabs...

Em ter, 28 de fev de 2017 às 14:25, Thomas Holder <
tho...@sc...> escreveu:

> Dear João,
>
> The Mobile (iPad) PyMOL interface is rather limited and does not expose
> these options, unfortunately. The only way to display a "grid_mode=on"
> scene is to load a PyMOL session file (.pse) which already has the setting
> enabled.
>
> Cheers,
>   Thomas
>
> On 28 Feb 2017, at 11:57, João Oliveira Jr. <joa...@gm...> wrote:
>
> > Dear Andreas
> >
> > Where do I find this typing command option?
> >
> > Em ter, 28 de fev de 2017 às 13:53, Andreas Forster <
> doc...@gm...> escreveu:
> > Dear João,
> >
> > type
> >
> > set grid_mode, on
> >
> > to see your models side by side.  You might have to align them first.
> Use the command
> >
> > super model1, model2
> >
> > for that.
> >
> > All best.
> >
> >
> > Andreas
> >
> >
> > On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joa...@gm...>
> wrote:
> > Hi
> >
> > Please, when using PyMOL app for iPad is that possible to set up
> multiple structures from diffent PDB codes at the same time?
> >
> > I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB
> codes: 1IGY, 1IGT, 1HZH, and  5DK3) aligned side by side to save a
> screenshot to Photos.
> >
> > When I download two PDB codes, they appear one inside the other...
> >
> > Is that possibe using the PyMOL app?
> >
> > Best regards!
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Thomas,

Thanks. I re-wrote my blender scripts to accommodate both version, since 
it seems like other visualization programs generally output bonds as two 
cylinders. What I would love, though I'm not even sure its possible with 
vrml2, would be export some 'additional' info (like chain, resnum) that 
each object was associated with.

--p

On 02/28/2017 12:29 PM, Thomas Holder wrote:
> Hi Paul,
>
> Interesting observation. This change was not intentional, it's a side effect of a very low level change in the geometry generation. We should be able to optimize this for the next PyMOL release.
>
> Cheers,
>    Thomas
>
> On 24 Feb 2017, at 12:02, Paul Paukstelis <sho...@gm...> wrote:
>
>> There seem to have been some changes in how the VRML2 output is done
>> between 1.7.X and 1.8.X, though I can't find it documented in change logs.
>>
>> In 1.7.X, vrml2 output would convert sticks to cylinders that was
>> dependent on color. If a bond were split into two colors, it would
>> output as two cylinders, but if the bond were one color it would just be
>> one longer cylinder. There was also the annoying property that no matter
>> what settings you included, vrml2 would always put extra spheres at the
>> ends of cylinders to make them smooth (even though they were inside atoms)
>>
>> In 1.8.X bond cylinders are always exported as two separate cylinders,
>> even when everything is colored the same, but the annoying spheres at
>> the end of bonds are gone (yay!).
>>
>> Unfortunately, it turns out that when working with blender scripts it
>> was much easier to make everything one color so each bond was a single
>> cylinder. I can use an older version, but I was wondering if there is
>> perhaps a new setting I haven't seen yet that might let me revert this
>> behavior.
>>
>> Thanks.

Hi Paul,

Interesting observation. This change was not intentional, it's a side effect of a very low level change in the geometry generation. We should be able to optimize this for the next PyMOL release.

Cheers,
  Thomas

On 24 Feb 2017, at 12:02, Paul Paukstelis <sho...@gm...> wrote:

> There seem to have been some changes in how the VRML2 output is done 
> between 1.7.X and 1.8.X, though I can't find it documented in change logs.
> 
> In 1.7.X, vrml2 output would convert sticks to cylinders that was 
> dependent on color. If a bond were split into two colors, it would 
> output as two cylinders, but if the bond were one color it would just be 
> one longer cylinder. There was also the annoying property that no matter 
> what settings you included, vrml2 would always put extra spheres at the 
> ends of cylinders to make them smooth (even though they were inside atoms)
> 
> In 1.8.X bond cylinders are always exported as two separate cylinders, 
> even when everything is colored the same, but the annoying spheres at 
> the end of bonds are gone (yay!).
> 
> Unfortunately, it turns out that when working with blender scripts it 
> was much easier to make everything one color so each bond was a single 
> cylinder. I can use an older version, but I was wondering if there is 
> perhaps a new setting I haven't seen yet that might let me revert this 
> behavior.
> 
> Thanks.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear João,

The Mobile (iPad) PyMOL interface is rather limited and does not expose these options, unfortunately. The only way to display a "grid_mode=on" scene is to load a PyMOL session file (.pse) which already has the setting enabled.

Cheers,
  Thomas

On 28 Feb 2017, at 11:57, João Oliveira Jr. <joa...@gm...> wrote:

> Dear Andreas
> 
> Where do I find this typing command option?
> 
> Em ter, 28 de fev de 2017 às 13:53, Andreas Forster <doc...@gm...> escreveu:
> Dear João,
> 
> type
> 
> set grid_mode, on
> 
> to see your models side by side.  You might have to align them first.  Use the command
> 
> super model1, model2
> 
> for that.
> 
> All best.
> 
> 
> Andreas
> 
> 
> On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joa...@gm...> wrote:
> Hi
> 
> Please, when using PyMOL app for iPad is that possible to set up multiple structures from diffent PDB codes at the same time?
> 
> I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB codes: 1IGY, 1IGT, 1HZH, and  5DK3) aligned side by side to save a screenshot to Photos.
> 
> When I download two PDB codes, they appear one inside the other...
> 
> Is that possibe using the PyMOL app?
> 
> Best regards!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Andreas

Where do I find this typing command option?

Em ter, 28 de fev de 2017 às 13:53, Andreas Forster <doc...@gm...>
escreveu:

> Dear João,
>
> type
>
> set grid_mode, on
>
> to see your models side by side.  You might have to align them first.  Use
> the command
>
> super model1, model2
>
> for that.
>
> All best.
>
>
> Andreas
>
>
> On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joa...@gm...>
> wrote:
>
> Hi
>
> Please, when using PyMOL app for iPad is that possible to set up multiple
> structures from diffent PDB codes at the same time?
>
> I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB
> codes: 1IGY, 1IGT, 1HZH, and  5DK3) *aligned* *side by side* to save a
> screenshot to Photos.
>
> When I download two PDB codes, they appear one inside the other...
>
> Is that possibe using the PyMOL app?
>
> Best regards!
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> 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 João,

type

set grid_mode, on

to see your models side by side.  You might have to align them first.  Use
the command

super model1, model2

for that.

All best.


Andreas



On Tue, Feb 28, 2017 at 5:27 PM, João Oliveira Jr. <joa...@gm...>
wrote:

> Hi
>
> Please, when using PyMOL app for iPad is that possible to set up multiple
> structures from diffent PDB codes at the same time?
>
> I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB
> codes: 1IGY, 1IGT, 1HZH, and  5DK3) *aligned* *side by side* to save a
> screenshot to Photos.
>
> When I download two PDB codes, they appear one inside the other...
>
> Is that possibe using the PyMOL app?
>
> Best regards!
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

Hi

Please, when using PyMOL app for iPad is that possible to set up multiple
structures from diffent PDB codes at the same time?

I'm a Immunology teacher and I'd like a slide with 04 antibodies (PDB
codes: 1IGY, 1IGT, 1HZH, and  5DK3) *aligned* *side by side* to save a
screenshot to Photos.

When I download two PDB codes, they appear one inside the other...

Is that possibe using the PyMOL app?

Best regards!

Hi Leonhard,

Very interesting analysis. I'm wondering if this slowdown actually scales with number of objects or rather total number of atoms.

If your color scheme lookup by (object, resi) key is fast in Python (let's say you have it all in a dictionary), then you can use cmd.alter() with a single pass, which probably will be faster than cmd.color() in multiple passes. Example:

colors = {
  'obj1': {
    1: 0xFF0000,
    2: 0x333300,
    3: 0x000066,
  },
  'obj2': {
    1: 0x001234,
    2: 0x121212,
    3: 0x009900,
  },
}

cmd.alter('all', 'color = 0x40000000 | colors[model][resv]', space={'colors': colors})
cmd.recolor()

The magic number 040000000 is the cColor_TRGB_Bits mask which tells PyMOL that this is not a color index, but an RGB color.

Instead of a dictionary lookup, you may also use a callback function.

Check out these examples for alter with space argument:
https://pymolwiki.org/index.php/Iterate#.22space.22_argument

Cheers,
  Thomas

On 28 Feb 2017, at 09:34, Leonhard Heizinger <Leo...@ur...> wrote:

> Hi,
> coloring a certain residue in an object takes about 4 ms when only one
> object is loaded in PyMol:
> 
>  %time cmd.color("blue", "obj1of1 and resi 1")
>  CPU times: user 3.33 ms, sys: 0 ns, total: 3.33 ms
>  Wall time: 4.13 ms
> 
> Performing the same operation when a lot of other objects (~300) are
> loaded results in a highly increased execution time:
> 
>  %time cmd.color("blue", "obj1of300 and resi 1")
>  CPU times: user 243 ms, sys: 0 ns, total: 243 ms
>  Wall time: 234 ms
> 
> This is 60-fold increment compared to a PyMol Session with only one
> object loaded. All structures in this example have ~240 residues.
> 
> Consequently, coloring each residue of 300 objects in an individual
> color would take more then 4.5 hours on my machine. Of course this use
> case is pretty unlikely.
> 
> In my case I only have limited number of colors (255 colors gradient)
> which each residue could obtain. So I'm thinking about executing
> cmd.color for each color (255 times), which should be faster. However
> I'd still prefer to apply cmd.color per residue, so I don't have to
> define bulky selections per color.
> 
> Is there some way to accomplish this in a reasonable amount of time?
> Thanks!
> 
> Best,
> 
> Leonhard

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,
coloring a certain residue in an object takes about 4 ms when only one
object is loaded in PyMol:

  %time cmd.color("blue", "obj1of1 and resi 1")
  CPU times: user 3.33 ms, sys: 0 ns, total: 3.33 ms
  Wall time: 4.13 ms

Performing the same operation when a lot of other objects (~300) are
loaded results in a highly increased execution time:

  %time cmd.color("blue", "obj1of300 and resi 1")
  CPU times: user 243 ms, sys: 0 ns, total: 243 ms
  Wall time: 234 ms

This is 60-fold increment compared to a PyMol Session with only one
object loaded. All structures in this example have ~240 residues.

Consequently, coloring each residue of 300 objects in an individual
color would take more then 4.5 hours on my machine. Of course this use
case is pretty unlikely.

In my case I only have limited number of colors (255 colors gradient)
which each residue could obtain. So I'm thinking about executing
cmd.color for each color (255 times), which should be faster. However
I'd still prefer to apply cmd.color per residue, so I don't have to
define bulky selections per color.

Is there some way to accomplish this in a reasonable amount of time?
Thanks!



Best,

Leonhard

There seem to have been some changes in how the VRML2 output is done 
between 1.7.X and 1.8.X, though I can't find it documented in change logs.

In 1.7.X, vrml2 output would convert sticks to cylinders that was 
dependent on color. If a bond were split into two colors, it would 
output as two cylinders, but if the bond were one color it would just be 
one longer cylinder. There was also the annoying property that no matter 
what settings you included, vrml2 would always put extra spheres at the 
ends of cylinders to make them smooth (even though they were inside atoms)

In 1.8.X bond cylinders are always exported as two separate cylinders, 
even when everything is colored the same, but the annoying spheres at 
the end of bonds are gone (yay!).

Unfortunately, it turns out that when working with blender scripts it 
was much easier to make everything one color so each bond was a single 
cylinder. I can use an older version, but I was wondering if there is 
perhaps a new setting I haven't seen yet that might let me revert this 
behavior.

Thanks.

Dear all,

I've written a .pml script to render volumes and save png files. The script
works fine when running it from the GUI, but for some reason when I run in
command line mode with pymol -cqr myscript.pml the image saved is blank.

It appears that when running from the command line it automatically ray
traces the image, even when I set ray = 0 in the png command, and since
volumes don't work well with ray tracing, the images end up blank.

I tried setting ray_volume=1, but that still doesn't fix the problem.

My script is below, as is the output from the command line and from the
GUI.  Notice that when running from the command line there is a "Ray:
render time:" line that doesn't appear when running from the GUI.

Thanks for any insight.

Tom

*myscript.pml:*

$>cat myscript.pml:

bg white

fetch 1oky, type=2fofc, async=0

volume 1okyVol, 1oky_2fofc

set ray_volume, 1

png volume.png, ray=0


*command line output (doesn't work):*

$>pymol -cqr myscript.pml:

PyMOL>bg white

PyMOL>fetch 1oky, type=2fofc, async=0

 ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.

 BRIXStrToMap: Map Size 102 x 99 x 92

 BRIXStrToMap: Range = -0.906629 to 2.095844

 BRIXStrToMap: Calculated Mean =   -0.006, Sigma =    0.251

 BRIXStrToMap: Normalizing...

 Crystal: Unit Cell          124.162  124.162   47.300

 Crystal: Alpha Beta Gamma    90.000   90.000  120.000

 Crystal: RealToFrac Matrix

 Crystal:    0.0081    0.0046   -0.0000

 Crystal:    0.0000    0.0093   -0.0000

 Crystal:    0.0000    0.0000    0.0211

 Crystal: FracToReal Matrix

 Crystal:  124.1625  -62.0812    0.0000

 Crystal:    0.0000  107.5279    0.0000

 Crystal:    0.0000    0.0000   47.3000

 Crystal: Unit Cell Volume   631499.

 CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".

PyMOL>volume 1okyVol, 1oky_2fofc

 Executive: object "1okyVol" created.

 Volume: created "1okyVol"

PyMOL>set ray_volume, 1

 Setting: ray_volume set to on.

PyMOL>png volume.png, ray=0

 Ray: render time: 0.01 sec. = 242165.4 frames/hour (0.01 sec. accum.).

 ScenePNG: wrote 640x480 pixel image to file "volume.png".

*GUI output (works):*
$>pymol -qr myscript.pml:

 Detected OpenGL version 2.0 or greater. Shaders available.

 Detected GLSL version 1.20.

PyMOL>bg white

PyMOL>fetch 1oky, type=2fofc, async=0

 ObjectMapLoadBRIXFile: Loading from './1oky_2fofc.omap'.

 BRIXStrToMap: Map Size 102 x 99 x 92

 BRIXStrToMap: Range = -0.906629 to 2.095844

 BRIXStrToMap: Calculated Mean =   -0.006, Sigma =    0.251

 BRIXStrToMap: Normalizing...

 Crystal: Unit Cell          124.162  124.162   47.300

 Crystal: Alpha Beta Gamma    90.000   90.000  120.000

 Crystal: RealToFrac Matrix

 Crystal:    0.0081    0.0046   -0.0000

 Crystal:    0.0000    0.0093   -0.0000

 Crystal:    0.0000    0.0000    0.0211

 Crystal: FracToReal Matrix

 Crystal:  124.1625  -62.0812    0.0000

 Crystal:    0.0000  107.5279    0.0000

 Crystal:    0.0000    0.0000   47.3000

 Crystal: Unit Cell Volume   631499.

 CmdLoad: "./1oky_2fofc.omap" loaded as "1oky_2fofc".

PyMOL>volume 1okyVol, 1oky_2fofc

 Executive: object "1okyVol" created.

 Volume: created "1okyVol"

PyMOL>set ray_volume, 1

 Setting: ray_volume set to on.

PyMOL>png volume.png, ray=0

 ScenePNG: wrote 640x480 pixel image to file "volume.png".




--
Thomas D. Grant, Ph.D.
Staff Scientist
BioXFEL Science and Technology Center
Hauptman-Woodward Medical Research Institute
700 Ellicott St.
Buffalo, NY 14203

One option is to turn off shadows:

     set ray_shadow, off

Will that work for you?

_______________________________________
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 2/22/2017 11:46 AM, Vivien Schoonenberg wrote:
>
> Hi,
>
> I’m recoloring my protein in different shades of similar colors, but 
> to truly see the difference between them, I want to create a view in 
> pyMOL without any shadows.
>
> For this purpose, I want to make a half sphere behind the camera with 
> lights, which all emit the same amount of light. I have a hard time 
> figuring out how to set coordinates and changing the strength of the 
> lights. Do you maybe have a suggestion on how to solve this?
>
> Thanks,
>
> Vivien
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> 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 Vivian

If you just want to get rid of shadows in exported ray-traced images, you can specify
set ray_shadows, 0 (https://pymolwiki.org/index.php/Ray_shadow)

set depth_cue,0 (https://pymolwiki.org/index.php/Depth_cue)
will get rid of the color modulation due to dept cueing

Annemarie


------------------------------

Message: 5
Date: Wed, 22 Feb 2017 11:46:02 -0500
From: "Vivien Schoonenberg" <viv...@gm...>
Subject: [PyMOL] Getting rid of shadows
To: <pym...@li...>
Message-ID: <001201d28d2b$27a06960$76e13c20$@gmail.com>
Content-Type: text/plain; charset="us-ascii"

Hi,

 

I'm recoloring my protein in different shades of similar colors, but to
truly see the difference between them, I want to create a view in pyMOL
without any shadows.

For this purpose, I want to make a half sphere behind the camera with
lights, which all emit the same amount of light. I have a hard time figuring
out how to set coordinates and changing the strength of the lights. Do you
maybe have a suggestion on how to solve this?

 

Thanks,

Vivien

Hi Clarissa

I have just deposited the slides to my 1.5 day class on macromolecular visualization on Research Gate

https://www.researchgate.net/publication/313877004_Introduction_to_PyMOL
https://www.researchgate.net/publication/313877009_Intermediate_PyMOL
https://www.researchgate.net/publication/313877075_Advanced_PyMOL

best regards
Annemarie


Message: 1
Date: Wed, 15 Feb 2017 10:44:59 -0300
From: Clarisa Alvarez <cla...@gm...>
Subject: [PyMOL] course or tutorial to make nice pictures
To: pym...@li...
Message-ID:
<CAF...@ma...>
Content-Type: text/plain; charset="utf-8"

Hi! Do anyone know any course or tutorial to make nice images with pymol. I
have already done basic tutorials but I would like to learn a little more.
Thanks in advance.
Clarisa.
-------------- next part --------------
An HTML attachment was scrubbed...

------------------------------

Hi Rui,

 

Thank you!

I also already figured out that if I turn off the depth cue most of my
problem is solved as well ( “set depth_cue, 0”)

 

-Vivien

 

From: Rui Sousa [mailto:Rui...@un...] 
Sent: Thursday, February 23, 2017 10:02
To: pym...@li...
Subject: Re: [PyMOL] Getting rid of shadows

 

Hi Vivian,

I'm not sure if I fully understand your question, but if you want to have a
picture without shadows, by using "set light_count, 0"
(https://pymolwiki.org/index.php/Light_count) you should be able to achieve
this.

Rui

Le 22/02/2017 17:46, Vivien Schoonenberg a écrit :

Hi,

 

I’m recoloring my protein in different shades of similar colors, but to
truly see the difference between them, I want to create a view in pyMOL
without any shadows.

For this purpose, I want to make a half sphere behind the camera with
lights, which all emit the same amount of light. I have a hard time figuring
out how to set coordinates and changing the strength of the lights. Do you
maybe have a suggestion on how to solve this?

 

Thanks,

Vivien






----------------------------------------------------------------------------
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_______________________________________________
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<mailto:PyM...@li...> )
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Archives: http://www.mail-archive.com/pym...@li...

 

Hi Vivian,

I'm not sure if I fully understand your question, but if you want to 
have a picture without shadows, by using "set light_count, 0" 
(https://pymolwiki.org/index.php/Light_count) you should be able to 
achieve this.

Rui

Le 22/02/2017 17:46, Vivien Schoonenberg a écrit :
>
> Hi,
>
> I’m recoloring my protein in different shades of similar colors, but 
> to truly see the difference between them, I want to create a view in 
> pyMOL without any shadows.
>
> For this purpose, I want to make a half sphere behind the camera with 
> lights, which all emit the same amount of light. I have a hard time 
> figuring out how to set coordinates and changing the strength of the 
> lights. Do you maybe have a suggestion on how to solve this?
>
> Thanks,
>
> Vivien
>
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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Hi,

 

I'm recoloring my protein in different shades of similar colors, but to
truly see the difference between them, I want to create a view in pyMOL
without any shadows.

For this purpose, I want to make a half sphere behind the camera with
lights, which all emit the same amount of light. I have a hard time figuring
out how to set coordinates and changing the strength of the lights. Do you
maybe have a suggestion on how to solve this?

 

Thanks,

Vivien

Hi Kar Weng,

This is possible with a Python script. Save the following to a file (e.g. "mae2pdb.py") and run it with PyMOL ("File > Run Script..." or use the "run" command). This will convert all .mae files from the current directory to .pdb files.

from pymol import cmd
import glob
for filename in glob.glob('*.mae'):
    cmd.load(filename)
    cmd.save(filename[:-4] + '.pdb')
    cmd.delete('*')

Hope that helps.

Cheers,
  Thomas

On 20 Feb 2017, at 01:58, Kar Weng Ng <kar...@gm...> wrote:

> Dear Sir/Madam,
> 
> I am final year School of Pharmacy student, currently working on a homology modelling project. I am relatively new to using PyMOL. I would like to convert .mae ligand structures that were produced by glide_dock into .pdb files. I understand that I could use the: load ligand_1.mae, then go to File > Save molecule command. However I have thousands of ligand files to convert. May I know if there's a way or script that could do this in a faster way?
> 
> Thank you for your time.
> 
> Best Regards,
> Ng Kar Weng
> School of Pharmacy
> Taylor's University Lakeside Campus, Malaysia

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Sir/Madam,

I am final year School of Pharmacy student, currently working on a homology
modelling project. I am relatively new to using PyMOL. I would like to
convert .mae ligand structures that were produced by glide_dock into .pdb
files. I understand that I could use the: load ligand_1.mae, then go to
File > Save molecule command. However I have thousands of ligand files to
convert. May I know if there's a way or script that could do this in a
faster way?

Thank you for your time.

Best Regards,
Ng Kar Weng
School of Pharmacy
Taylor's University Lakeside Campus, Malaysia

have you tried using the command "ray"? also if you want to improve the
side view for a Mac you can use the two finger in trackpad, I'm not sure in
Windows (maybe it's the mouse roller)

On Wed, Feb 15, 2017 at 1:44 PM, Clarisa Alvarez <cla...@gm...
> wrote:

> Hi! Do anyone know any course or tutorial to make nice images with pymol.
> I have already done basic tutorials but I would like to learn a little more.
> Thanks in advance.
> Clarisa.
>
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>

Hi! Do anyone know any course or tutorial to make nice images with pymol. I
have already done basic tutorials but I would like to learn a little more.
Thanks in advance.
Clarisa.

Hey :)

Just as sidenote, the spectrum command takes arbitrary color schemes. Just
combine colors separated by underscores. Also fun in combination with
set_color :)

Cheers,

Tsjerk

On Feb 14, 2017 5:46 PM, "Robert Campbell" <rob...@qu...>
wrote:

Hello Peleg,

I think there are other possibilities, but my data2bfactor.py script will
do that for you.  You create a file with whitespace-separated columns
(spaces and/or tabs) in which each line contains:

chain resi resn name data

(i.e. chain, residue number, residue name, atom name and value to be
applied to the B-factor column).

The number can also be applied to the occupancy column instead if you want
to keep the B-factor intact.

Then you can use the spectrum command or my color_b.py script to colour
each atom according to the data value.  My color_b.py script has a few more
options than the spectrum command, including the ability to define a custom
colour gradient scheme.

You can find my scripts here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

On Tue, 2017-02-14 17:12  +0100,  Peleg Bar-Sapir <pe...@gm...> wrote:

> Hello,
>
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
>
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
>
> Best,
>
> Peleg




--
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

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Hello Peleg,

I think there are other possibilities, but my data2bfactor.py script will do that for you.  You create a file with whitespace-separated columns (spaces and/or tabs) in which each line contains:

chain resi resn name data 

(i.e. chain, residue number, residue name, atom name and value to be applied to the B-factor column).

The number can also be applied to the occupancy column instead if you want to keep the B-factor intact.

Then you can use the spectrum command or my color_b.py script to colour each atom according to the data value.  My color_b.py script has a few more options than the spectrum command, including the ability to define a custom colour gradient scheme.

You can find my scripts here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

On Tue, 2017-02-14 17:12  +0100,  Peleg Bar-Sapir <pe...@gm...> wrote:

> Hello,
> 
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
> 
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
> 
> Best,
> 
> Peleg




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc

Hello,

I wish to write a script that will take the molecule loaded in PyMol, and
color the molecule according to values I will calculate using the
molecules' parameters (in the end there will be one floating number per
atom). Then, I would like to display that using surface mode.

Could anyone direct me to a way of doing that? I saw scripts coloring by
atom type, but I'm not sure how to apply it for a molecule already loaded
in PyMol.

Best,

Peleg