pymol-users Mailing List for PyMOL Molecular Graphics System

Hi AC,

In PyMOL 1.8.6 we added width and height arguments to the mpng command. So this is now possible:

  set ray_trace_frames
  mpng imageprefix, width=2400

With older PyMOL versions, you have two options:

1) Run PyMOL headless (pymol -c script.pml) so that the display doesn't limit the viewport size, and put in the script:

  viewport 2400, 1800
  mpng imageprefix

2) Write your own export loop:

python
for frame in range(1, cmd.count_frames() + 1):
    cmd.frame(frame)
    cmd.png('imageprefix%04d.png' % frame, width=2400, ray=1)
python end

Cheers,
  Thomas

> On Jun 29, 2017, at 8:55 PM, Academic Research <ac....@ic...> wrote:
> 
> So far there is only info about how to "ray_trace" each frame of a movie while exporting to .png images.
> 
> My question: How can I "ray 2400" each image (regardless of my computer screen size - because I have a small computer) so i can get very high resolution images that i can combine together into a high resolution movie.
> Regards,
> 
> AC Research

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

So far there is only info about how to "ray_trace" each frame of a movie while exporting to .png images.



My question: How can I "ray 2400" each image (regardless of my computer screen size - because I have a small computer) so i can get very high resolution images that i can combine together into a high resolution movie.

Regards,

AC Research

Hi Tsjerk,

I tried two_sided_lighting but doesn't have effect. Apparently,
irrespective of the protein the surface is always a black exterior.
Now, I tried display - use display lists and that solves t but makes the
program extremely slow and heavy.
Problem in the interface? Anyone experienced this?

best
Kanika

On Wed, Jun 28, 2017 at 6:13 PM, Tsjerk Wassenaar <ts...@gm...> wrote:

> Hi Kanika,
>
> Try
>
> set two_sided_lighting
>
> Cheers,
>
> Tsjerk
>
> On Jun 28, 2017 17:14, "kanika sharma" <ksh...@gm...> wrote:
>
>> Dear PyMolers
>>
>> I want to see the cavities in my protein using the following steps:
>>
>> Setting → Surface → Cavities & Pockets Only.
>> Show surface
>> Cavity Detection Radius 5A
>>
>> But I see the surface as a black blob, if I colour it (say white), the
>> external still remains black.
>>
>> Anyone has some suggestions why this happens?
>>
>> I attached a picture of what it looks like.
>>
>> --
>> *Best,*
>>
>> *Kanika *
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> 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...
>>
>


-- 
*Best,*

*Kanika Sharma*

Hi Kanika,

Try

set two_sided_lighting

Cheers,

Tsjerk

On Jun 28, 2017 17:14, "kanika sharma" <ksh...@gm...> wrote:

> Dear PyMolers
>
> I want to see the cavities in my protein using the following steps:
>
> Setting → Surface → Cavities & Pockets Only.
> Show surface
> Cavity Detection Radius 5A
>
> But I see the surface as a black blob, if I colour it (say white), the
> external still remains black.
>
> Anyone has some suggestions why this happens?
>
> I attached a picture of what it looks like.
>
> --
> *Best,*
>
> *Kanika *
>
>
>
> ------------------------------------------------------------
> ------------------
> 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 PyMolers

I want to see the cavities in my protein using the following steps:

Setting → Surface → Cavities & Pockets Only.
Show surface
Cavity Detection Radius 5A

But I see the surface as a black blob, if I colour it (say white), the
external still remains black.

Anyone has some suggestions why this happens?

I attached a picture of what it looks like.

-- 
*Best,*

*Kanika *

Hi Mohammad -

> On Jun 22, 2017, at 4:47 PM, Mohammad Goodarzi <moh...@gm...> wrote:
> 
> Hello,
> 
> This is strange to me, 
> 
> I do this 
> 
> # get rid of all other protein chains
> remove polymer and not chain B
> 
> because I want to keep only chain A

Here, you can

remove polymer and not chain A

> # then I do this 
> remove organic and not r. 6TA
> 
> It removes I don't know what but , I still have the water and PO4 (which is few other organic)

You can select waters with 'solvent' and PO4 with 'inorganic' (it's not organic!).

> Do you know how to list all molecules or ligand coming with a PDB in PyMOL?

You can view the entire sequence by pressing the "S" button at the bottom right panel (also by Display > Sequence, and variations with Display > Sequence Mode).

To show or hide specific things, you can take advantage of the selection logic using PyMOL's Single-Word Selectors (https://pymolwiki.org/index.php/Single-word_Selectors <)" rel="nofollow">https://pymolwiki.org/index.php/Single-word_Selectors>) and Selection Algebra (https://pymolwiki.org/index.php/Selection_Algebra <)." rel="nofollow">https://pymolwiki.org/index.php/Selection_Algebra>).

Here's what I would do to address what I now understand to be your specific request:

    # keep only chain A (of protein chains)
    remove polymer and not chain A

    # remove all the solvent/ligand molecules except 6TA
    remove (all and not polymer) and not resn 6TA

Hope that helps,

Cheers,
Jared



> 
> Thanks
> Mohammad 
> 
> 
> 
> 
> 
> 
> On Thu, Jun 22, 2017 at 3:35 PM, Jared Sampson <jar...@co... <mailto:jar...@co...>> wrote:
> Hi Mohammad - 
> 
> If you click the atoms of the ligand and look at the residue name just before the back-tick character ( ` ) in the console.
> 
> e.g. should see the phrase like:
> 
>     You clicked /my_object//A/XYZ`507/C4
> 
> Hope that helps,
> 
> Cheers,
> Jared
> 
>> On Jun 22, 2017, at 4:29 PM, Mohammad Goodarzi <moh...@gm... <mailto:moh...@gm...>> wrote:
>> 
>> 
>> Mohammad 
> 
> 

Hi,

Select the one you want e.g. right click, chain select. Under the selection, Action > modify > invert > within object..

Or you can select using the sequence viewer

Hope this helps

Joel

From: Mohammad Goodarzi [mailto:moh...@gm...]
Sent: Friday, 23 June 2017 8:20 AM
To: pym...@li...
Subject: [PyMOL] Removing unwanted molecules

Hello,
    I want to know how to delete chain B and all ligands except the one that I
    want ?
    Is there any way to know all molecules which comes with a PDB and then
    remove those that you dont want?
    Thanks
    Mohammad

Hello,
    I want to know how to delete chain B and all ligands except the one
that I
    want ?
    Is there any way to know all molecules which comes with a PDB and then
    remove those that you dont want?
    Thanks
    Mohammad

Hi Gianluca,

Yes this is possible, assuming you're using PyMOL 1.8.6. Use something like this:

def read_mmtfstr(contents, oname, state=0):
    return cmd.load(contents, oname, state, cmd.loadable.mmtfstr)

Cheers,
  Thomas

> On Jun 21, 2017, at 12:07 PM, Gianluca Tomasello <gia...@gm...> wrote:
> 
> Hi, I am using read_pdbstr function to load a strucutres into pymol. Is there a way to do the same for mmtf file formats? (I mean without using temporary files)

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Leila,

You need the "CRYST1" line from the template pdb file.  That is where PyMOL gets the symmetry information from.

Cheers,
Rob

On Wed, 2017-06-21 09:29  +0200,  leila karami <kar...@gm...> wrote:

> Dear PYMOL users,
> 
> I have done a homology modelling using swiss model. Template pdb file
> contain 3 chains (A, B, C). I used only chain A for homology
> modelling as template.
> 
> There is a symmetry operator in template pdb file (temp.pdb). I want
> to use symexp to obtain dimeric structure for modeled pdb file
> (model.pdb).
> 
> I manually added following records (from temp.pdb) at the first of the
> modeled pdb file:
> ===========================================================
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
> REMARK 290
> REMARK 290      SYMOP   SYMMETRY
> REMARK 290     NNNMMM   OPERATOR
> REMARK 290       1555   X,Y,Z
> REMARK 290       2555   -X,Y,-Z
> REMARK 290       3555   X+1/2,Y+1/2,Z
> REMARK 290       4555   -X+1/2,Y+1/2,-Z
> REMARK 290
> REMARK 290     WHERE NNN -> OPERATOR NUMBER
> REMARK 290           MMM -> TRANSLATION VECTOR
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED MOLECULES.
> REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
> REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
> REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
> REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
> REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000
> REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
> REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       88.99000
> REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       28.29500
> REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
> REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       88.99000
> REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       28.29500
> REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
> REMARK 290
> CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1      12
> ORIGX1      1.000000  0.000000  0.000000        0.00000
> ORIGX2      0.000000  1.000000  0.000000        0.00000
> ORIGX3      0.000000  0.000000  1.000000        0.00000
> SCALE1      0.005619  0.000000  0.002811        0.00000
> SCALE2      0.000000  0.017671  0.000000        0.00000
> SCALE3      0.000000  0.000000  0.013436        0.00000
> 
> ===========================================================
> 
> After using symexp sym,model,(model),1 in command line, I encountered
> with:
> 
> ExecutivesSymexp-Error: No Symmetry loaded!
> 
> temp.pdb and model.pdb files are in following links:
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D&reserved=0
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D&reserved=0
> 
> Any help will be highly appreciated.
> 
> Best,
> Leila




-- 
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

Hi Leila,

I responded too quickly without reading carefully!  Adding those lines should have worked (but only the CRYST1 line is needed).  Your model.pdb file that you linked to on Dropbox does not have the CRYST1 line.  Adding that line works for me.

Cheers,
Rob

On Wed, 2017-06-21 09:29  +0200,  leila karami <kar...@gm...> wrote:

> Dear PYMOL users,
> 
> I have done a homology modelling using swiss model. Template pdb file
> contain 3 chains (A, B, C). I used only chain A for homology
> modelling as template.
> 
> There is a symmetry operator in template pdb file (temp.pdb). I want
> to use symexp to obtain dimeric structure for modeled pdb file
> (model.pdb).
> 
> I manually added following records (from temp.pdb) at the first of the
> modeled pdb file:
> ===========================================================
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
> REMARK 290
> REMARK 290      SYMOP   SYMMETRY
> REMARK 290     NNNMMM   OPERATOR
> REMARK 290       1555   X,Y,Z
> REMARK 290       2555   -X,Y,-Z
> REMARK 290       3555   X+1/2,Y+1/2,Z
> REMARK 290       4555   -X+1/2,Y+1/2,-Z
> REMARK 290
> REMARK 290     WHERE NNN -> OPERATOR NUMBER
> REMARK 290           MMM -> TRANSLATION VECTOR
> REMARK 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED MOLECULES.
> REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
> REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
> REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
> REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
> REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000
> REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
> REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       88.99000
> REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       28.29500
> REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
> REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       88.99000
> REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       28.29500
> REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
> REMARK 290
> CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1      12
> ORIGX1      1.000000  0.000000  0.000000        0.00000
> ORIGX2      0.000000  1.000000  0.000000        0.00000
> ORIGX3      0.000000  0.000000  1.000000        0.00000
> SCALE1      0.005619  0.000000  0.002811        0.00000
> SCALE2      0.000000  0.017671  0.000000        0.00000
> SCALE3      0.000000  0.000000  0.013436        0.00000
> 
> ===========================================================
> 
> After using symexp sym,model,(model),1 in command line, I encountered
> with:
> 
> ExecutivesSymexp-Error: No Symmetry loaded!
> 
> temp.pdb and model.pdb files are in following links:
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Ft8m1nrkx2s69wi9%2Fmodel.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=g6I122L2C0o%2FAObHdjC9xXwoiPUx8J9MfupIpPp07ZM%3D&reserved=0
> 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2Fmt7toc0wtenr779%2Ftemp.pdb%3Fdl%3D0&data=02%7C01%7Crobert.campbell%40queensu.ca%7C6261ebf5a5494e8b230808d4b877938b%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636336271090533556&sdata=6U5D%2BZOPnIAx3X61eeK77XLW23mroFnaM8sxiX7n1Ow%3D&reserved=0
> 
> Any help will be highly appreciated.
> 
> Best,
> Leila




-- 
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

Hi, I am using read_pdbstr function to load a strucutres into pymol. Is
there a way to do the same for mmtf file formats? (I mean without using
temporary files)

Dear PYMOL users,

I have done a homology modelling using swiss model. Template pdb file
contain 3 chains (A, B, C). I used only chain A for homology modelling as
template.

There is a symmetry operator in template pdb file (temp.pdb). I want to use
symexp to obtain dimeric structure for modeled pdb file (model.pdb).

I manually added following records (from temp.pdb) at the first of the
modeled pdb file:
===========================================================
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,Y,-Z
REMARK 290       3555   X+1/2,Y+1/2,Z
REMARK 290       4555   -X+1/2,Y+1/2,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       88.99000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       28.29500
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       88.99000
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       28.29500
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290
CRYST1  177.980   56.590   83.220  90.00 116.58  90.00 C 1 2 1      12
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.005619  0.000000  0.002811        0.00000
SCALE2      0.000000  0.017671  0.000000        0.00000
SCALE3      0.000000  0.000000  0.013436        0.00000

===========================================================

After using symexp sym,model,(model),1 in command line, I encountered with:

ExecutivesSymexp-Error: No Symmetry loaded!

temp.pdb and model.pdb files are in following links:

https://www.dropbox.com/s/t8m1nrkx2s69wi9/model.pdb?dl=0

https://www.dropbox.com/s/mt7toc0wtenr779/temp.pdb?dl=0

Any help will be highly appreciated.

Best,
Leila

Because in PDB file  1ax8.pdb, residues 25 to 38 are missing. 
Presumably, this loop was disordered in the crystal and therefore not visible.

Annemarie Honegger

> On 20 Jun 2017, at 12:10, pym...@li... wrote:
> 
> Send PyMOL-users mailing list submissions to
> 	pym...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/pymol-users
> or, via email, send a message with subject or body 'help' to
> 	pym...@li...
> 
> You can reach the person managing the list at
> 	pym...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of PyMOL-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Why does Pymol display the chain as disconnected?
>      (Ahmad Abdelzaher)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 20 Jun 2017 12:09:56 +0200
> From: Ahmad Abdelzaher <und...@gm...>
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] Why does Pymol display the chain as disconnected?
> Message-ID:
> 	<CAL...@ma...>
> Content-Type: text/plain; charset="utf-8"
> 
> http://www.rcsb.org/pdb/explore.do?structureId=1ax8
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: hfgh.png
> Type: image/png
> Size: 63891 bytes
> Desc: not available
> 
> ------------------------------
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> 
> ------------------------------
> 
> Subject: Digest Footer
> 
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> ------------------------------
> 
> End of PyMOL-users Digest, Vol 133, Issue 23
> ********************************************

PyMol doesn’t display any atoms for a region of the protein for the same reason the rcsb doesn’t for that area. The crystallographer deposited a structure without coordinates for residues 25-38.

http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1AX8 <" rel="nofollow">http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1AX8>



> On Jun 20, 2017, at 6:09 AM, Ahmad Abdelzaher <und...@gm...> wrote:
> 
> http://www.rcsb.org/pdb/explore.do?structureId=1ax8
> <hfgh.png>------------------------------------------------------------------------------
> 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...

http://www.rcsb.org/pdb/explore.do?structureId=1ax8

Dear PyMOL Users,

I am looking for a command which can determine the separation of two
atoms in terms of chemical bonds. I would like to use it in a script to
assign atom types for peptide molecules. Does any of you have an idea
for that?

Thanks in advance,

Andras Wacha

-- 
András Ferenc Wacha, PhD
research fellow, CREDO instrument responsible

Biological Nanochemistry Research Group

Institute of Materials and Environmental Chemistry
Research Centre for Natural Sciences
Hungarian Academy of Sciences (RCNS HAS)
Magyar tudósok körútja 2.
H-1117 Budapest, Hungary
Phone: +36-1-382-6427
Web: http://bionano.ttk.mta.hu, 
CREDO SAXS instrument: http://credo.ttk.mta.hu

Hi Andreas
That's the solution I was looking for. Thanks.
Cheers
Vijay

On 6/19/17, Andreas Warnecke <4nd...@gm...> wrote:
> Hej,
>
> a disabled object will not show any display, but you can easily work with
> selections, provided that a selection is defined.
>
> Try something like:
> hide everything object
> show sticks selection
>
> Cheers,
>
> Andreas
>
> On Jun 19, 2017 6:00 AM, "Vijay Masand" <vij...@gm...> wrote:
>
>> Dear All,
>> With the help of internal GUI, we can disable the appearance of an
>> object,however we can still operate on the representations of objects
>> that are disabled, even with the commands show and hide. The results
>> are apparent only when we subsequently enable the object.
>> Is there any way to enable selected atoms of disabled object? I mean
>> is there is method to visualize selected atoms even when the the
>> object is not visible in PyMOL's viewer area.
>> Cheers
>> Vijay
>>
>> --
>> Assistant Professor
>> Department of Chemistry,
>> Vidya Bharati College, Amravati, 444 602
>> Maharashtra, India.
>> Phone number- +91-9403312628
>> https://sites.google.com/site/vijaymasand/
>>
>> ------------------------------------------------------------
>> ------------------
>> 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...
>>
>


-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Hej,

a disabled object will not show any display, but you can easily work with
selections, provided that a selection is defined.

Try something like:
hide everything object
show sticks selection

Cheers,

Andreas

On Jun 19, 2017 6:00 AM, "Vijay Masand" <vij...@gm...> wrote:

> Dear All,
> With the help of internal GUI, we can disable the appearance of an
> object,however we can still operate on the representations of objects
> that are disabled, even with the commands show and hide. The results
> are apparent only when we subsequently enable the object.
> Is there any way to enable selected atoms of disabled object? I mean
> is there is method to visualize selected atoms even when the the
> object is not visible in PyMOL's viewer area.
> Cheers
> Vijay
>
> --
> Assistant Professor
> Department of Chemistry,
> Vidya Bharati College, Amravati, 444 602
> Maharashtra, India.
> Phone number- +91-9403312628
> https://sites.google.com/site/vijaymasand/
>
> ------------------------------------------------------------
> ------------------
> 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 All,
With the help of internal GUI, we can disable the appearance of an
object,however we can still operate on the representations of objects
that are disabled, even with the commands show and hide. The results
are apparent only when we subsequently enable the object.
Is there any way to enable selected atoms of disabled object? I mean
is there is method to visualize selected atoms even when the the
object is not visible in PyMOL's viewer area.
Cheers
Vijay

-- 
Assistant Professor
Department of Chemistry,
Vidya Bharati College, Amravati, 444 602
Maharashtra, India.
Phone number- +91-9403312628
https://sites.google.com/site/vijaymasand/

Oh well, if i can raytrace normally there shouldn't be problems. Thank you.

Gianluca

Il 16 giu 2017 15:45, "Thomas Holder" <tho...@sc...> ha
scritto:

> Hi Gianluca,
>
> It looks like "stick_ball" setting support never made it into the sticks
> shader of Open-Source PyMOL. It works with:
>
> - Incentive PyMOL (all rendering modes)
> - Open Source PyMOL in ray tracing and with use_shaders=0
>
> Cheers,
>   Thomas
>
>
> > On Jun 15, 2017, at 11:32 AM, Gianluca Tomasello <gia...@gm...>
> wrote:
> >
> > Hi, I am following the instructuions on https://pymolwiki.org/index.
> php/Ball_and_Stick to make a ball and stick representation. I would like
> to use only stick representation to accomplish this task, and I finded the
> last method in the page is not working properly on my version of pymol
> (1.8.4.0)
> >
> > show sticks
> > set valence, on
> > set stick_ball, on
> > set stick_ball_ratio, 3
> > set stick_radius, 0.12
> >
> > it keeps the bonds but seems to disable completly the spheres.
> >
> > I also finded that set stick_ball, on is deprecated
> >
> > "This setting is deprecated in v1.5 and later as it is always enabled."
> >
> > so i tried to use only set stick_ball_ratio, 3 without luck..
> >
> > Is there something i am missing? I would like to make something like
> this https://pymolwiki.org/index.php/File:Stick_ball_ratio_1.5.png
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Gianluca,

It looks like "stick_ball" setting support never made it into the sticks shader of Open-Source PyMOL. It works with:

- Incentive PyMOL (all rendering modes)
- Open Source PyMOL in ray tracing and with use_shaders=0

Cheers,
  Thomas


> On Jun 15, 2017, at 11:32 AM, Gianluca Tomasello <gia...@gm...> wrote:
> 
> Hi, I am following the instructuions on https://pymolwiki.org/index.php/Ball_and_Stick to make a ball and stick representation. I would like to use only stick representation to accomplish this task, and I finded the last method in the page is not working properly on my version of pymol (1.8.4.0)
> 
> show sticks
> set valence, on
> set stick_ball, on
> set stick_ball_ratio, 3
> set stick_radius, 0.12
> 
> it keeps the bonds but seems to disable completly the spheres.
> 
> I also finded that set stick_ball, on is deprecated 
> 
> "This setting is deprecated in v1.5 and later as it is always enabled."
> 
> so i tried to use only set stick_ball_ratio, 3 without luck.. 
> 
> Is there something i am missing? I would like to make something like this https://pymolwiki.org/index.php/File:Stick_ball_ratio_1.5.png

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Julian

You can also try the PDB plugin which places each chain into a selection 
automatically for you.

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


Regards

John
PDBe


On 12/06/2017 17:10, Thomas Holder wrote:
> Hi Julian,
>
> A one-liner to create chain selections looks like this:
>
> for c in cmd.get_chains(): cmd.select("chain_" + c, "chain " + c)
>
> PyMOL doesn't provide access to the PDB header fields. In principle PyMOL provides a way to access everything inside mmCIF files, see:
>
> https://pymolwiki.org/index.php/Cif_keepinmemory
>
> However, instead of doing this, I recommend to use the PDBe web API which provides the data in a friendly JSON data structure. I've attached a Python script which creates molecule (or chain) selections for 5n61 as an example. I recommend to load PDB structures from mmCIF or MMTF format, which not only have chain identifiers, but also molecule identifiers ("segi" field in PyMOL).
>
> Hope that helps.
>
> Cheers,
>    Thomas
>
>> On Jun 12, 2017, at 12:21 PM, Julian Reitz <jul...@gm...> wrote:
>>
>> Dear all,
>>
>> I have a pdb-file with multiple chains (5N61).
>>
>> Is there an easy way to create selections for all the chains that are defined in the pdb-header (A to U) without doing it manually for every chain (select A, chain A)?
>> Is it also possible to use the MOLECULE information from the header to name the selections?
>>
>> Thank you in advance,
>>
>> Julian
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>
> ------------------------------------------------------------------------------
> 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...

-- 
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

http://www.pdbe.org
http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

Hi, I am following the instructuions on
https://pymolwiki.org/index.php/Ball_and_Stick to make a ball and stick
representation. I would like to use only stick representation to accomplish
this task, and I finded the last method in the page is not working properly
on my version of pymol (1.8.4.0)

show sticksset valence, onset stick_ball, onset stick_ball_ratio, 3set
stick_radius, 0.12


it keeps the bonds but seems to disable completly the spheres.

I also finded that set stick_ball, on is deprecated

*"This setting is deprecated in v1.5 and later as it is always enabled."*

so i tried to use only set stick_ball_ratio, 3 without luck..

Is there something i am missing? I would like to make something like this
https://pymolwiki.org/index.php/File:Stick_ball_ratio_1.5.png

Dear PyMOL Users,

I serve as the 2016-2017 chair of the Stanford Synchrotron Radiation Lightsource (SSRL) Users Executive Committee (UEC). This is a volunteer group that is independent of SSRL.

You probably have heard that the proposed DOE budget absorbs a large cut in part by shutting down SSRL. SSRL is one of four DOE synchrotron radiation labs in the US. SSRL has a very efficient mail-in crystallography program. It is so successful that only 3% of crystallographers show up at SSRL to collect data manually. Usually, this latter group has very challenging crystals that require manual intervention. The closure of SSRL will shift a massive workload onto the remaining three synchrotron radiation labs that are run by DOE. This will reduce access to synchrotron radiation for all crystallographers and other users of synchrotron radiation (SAXS, XFAS, and so on). One lab, (APS), is scheduled to be shutdown for several years for a major upgrade, thereby further reducing access to synchrotron radiation. This situation will further reduce the productivity and world standing of US science. The SSRL UEC is asking all concerned scientists to go to the SSRL UEC facebook page for more information about what they can do. Please follow this link to a infographic (https://drive.google.com/drive/folders/0B1zncsHsyAevUGpWQkJzeG9mN1k) and to the SSRL UEC Facebook page (https://www.facebook.com/ssrluec).

If you are not a US citizen, please do not contact the US Congress. Instead, please ask your US colleagues that use or rely on the products of synchrotron radiation to contact Congress.

The above are my opinions as a private citizen and do not necessarily reflect those of my employer nor of SSRL.

Best regards,

Blaine

Blaine Mooers, Ph.D.
201-2017 Chair SSRL UEC
Assistant Professor
Department of Biochemistry and Molecular Biology, College of Medicine
University of Oklahoma Health Sciences Center
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
Faculty webpage<" rel="nofollow">http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d->   X-ray lab (LBSF)<http://" rel="nofollow">http://research.ouhsc.edu/CoreFacilities/LaboratoryofBiomolecularStructureandFunction.aspx>   Molecular Graphics<" rel="nofollow">https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/moleculargraphicslinks.html> Links <" rel="nofollow">https://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/MolecularGraphicsLinks.html>  Small Angle Scattering <" rel="nofollow">http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links-27aug2014.html?sfvrsn=0>
office: (405) 271-8300   lab: (405) 271-8313   e-mail:  bla...@ou...