pymol-users Mailing List for PyMOL Molecular Graphics System

You can use the partial argument of the load command to get two sessions together.

load session1.pse
load session2.pse, partial=1

> On Dec 28, 2017, at 6:03 PM, david gae <dd...@uc...> wrote:
> 
> Dear Maria, 
> 
> I don’t think there is a direct way to connect two sessions together. One thought I had is that you could save coordinates from one session and then same coordinates from the other session.
> 
> lastly, open an another session and do the following:
> 
> load state1.pdb 
> load state2.pdb, state1
> 
> cheers,
> David 
> 
>  
>> On Dec 28, 2017, at 10:16 AM, COSTA Maria <mar...@i2... <mailto:mar...@i2...>> wrote:
>> 
>>  
>> Dear PyMOL users,
>>  
>> I would like to do a movie showing a conformational change of my molecule. I guess that for that purpose I need to store the views of the two states but the problem is that my two states are in two different pymol sessions. Is there a way to combine the two views in the same pymol file ? or I need to redo the views in the same pymol session from the beginning ?
>> I hope I’m being clear enough….
>>  
>> Thank you so much for any help !
>>  
>> Maria Costa
>>  
>> I2BC – UMR9198
>> 91198 Gif-sur-Yvette cedex
>> France  
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Dear Maria, 

I don’t think there is a direct way to connect two sessions together. One thought I had is that you could save coordinates from one session and then same coordinates from the other session.

lastly, open an another session and do the following:

load state1.pdb 
load state2.pdb, state1

cheers,
David 

 
> On Dec 28, 2017, at 10:16 AM, COSTA Maria <mar...@i2...> wrote:
> 
>  
> Dear PyMOL users,
>  
> I would like to do a movie showing a conformational change of my molecule. I guess that for that purpose I need to store the views of the two states but the problem is that my two states are in two different pymol sessions. Is there a way to combine the two views in the same pymol file ? or I need to redo the views in the same pymol session from the beginning ?
> I hope I’m being clear enough….
>  
> Thank you so much for any help !
>  
> Maria Costa
>  
> I2BC – UMR9198
> 91198 Gif-sur-Yvette cedex
> France  
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org <!" rel="nofollow">http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <" rel="nofollow">http://sdm.link/slashdot_______________________________________________>
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Dear PyMOL users,

I would like to do a movie showing a conformational change of my molecule. I guess that for that purpose I need to store the views of the two states but the problem is that my two states are in two different pymol sessions. Is there a way to combine the two views in the same pymol file ? or I need to redo the views in the same pymol session from the beginning ?
I hope I'm being clear enough....

Thank you so much for any help !

Maria Costa

I2BC - UMR9198
91198 Gif-sur-Yvette cedex
France

and that was it. renamed the file so it doenst start with _ and worked.

Thank you Jared

On Wed, Dec 27, 2017 at 3:38 PM, Jared Sampson <jar...@co...>
wrote:

> Hi Ricardo -
>
> I believe this actually has to do with the name of your PDB file.  If you
> give an object a name with a leading underscore (as in "_sphere" which
> would be the default name created for a file called "_sphere.pdb"), it will
> be hidden from the object list.  Renaming your file to "sphere.pdb" gives
> me the object in the list.  (I'm not sure if this is documented, but might
> make a good addition to the set_name
> <" rel="nofollow">https://pymolwiki.org/index.php/Set_name> or load
> <" rel="nofollow">https://pymolwiki.org/index.php/Load> PyMOL Wiki pages.)
>
> You can also specify an object name if you're loading from a script or the
> command line:
>
> load _sphere.pdb, my_sphere
>
> Hope that helps,
>
> Cheers,
> Jared
>
>
> On December 27, 2017 at 2:08:04 PM, ric...@ku... (
> ric...@ku...) wrote:
>
>
> Hi Jared. This is what i mean. I have opened in the image i attach a PDB
> file (which i also have attached) and as you can see, there is no object on
> the right. Im using PyMol 2.0.6.
>
>
> On Wed, Dec 27, 2017 at 10:45 AM, Jared Sampson <
> jar...@co...> wrote:
>
>> Hi Ricardo -
>>
>> On recent versions of PyMOL, there should be a scroll bar associated with
>> the object list.  What version of PyMOL are you using?  If it is older,
>> might I suggest trying out the recently released PyMOL 2?
>> https://pymol.org/2/
>>
>> Alternatively, if you know the name of the PDB file, the object name
>> should be the part of the file name before the extension (e.g. 1abc.pdb
>> becomes '1abc'), so you can color via entering commands at either the
>> internal command prompt (at the bottom of the graphics window), or the one
>> in the Tcl/Tk window, like this:
>>
>> color red, 1abc
>>
>> Hope that helps,
>>
>> Cheers,
>> Jared
>>
>> On December 27, 2017 at 12:49:49 AM, ric...@ku... (
>> ric...@ku...) wrote:
>>
>> Hello.
>>
>> I load some PDB files for visualization which is just fine, but some of
>> the files are not shown in the object list on the right of the GUI, so I
>> can't change colors or display types.
>>
>> How can I fix that?
>>
>> Thanks.
>> ------------------------------------------------------------
>> ------------------
>> 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 Ricardo - 

I believe this actually has to do with the name of your PDB file.  If you give an object a name with a leading underscore (as in "_sphere" which would be the default name created for a file called "_sphere.pdb"), it will be hidden from the object list.  Renaming your file to "sphere.pdb" gives me the object in the list.  (I'm not sure if this is documented, but might make a good addition to the set_name or load PyMOL Wiki pages.)

You can also specify an object name if you're loading from a script or the command line:

	load _sphere.pdb, my_sphere

Hope that helps,

Cheers,
Jared


On December 27, 2017 at 2:08:04 PM, ric...@ku... (ric...@ku...) wrote:

Hi Jared. This is what i mean. I have opened in the image i attach a PDB file (which i also have attached) and as you can see, there is no object on the right. Im using PyMol 2.0.6.


On Wed, Dec 27, 2017 at 10:45 AM, Jared Sampson <jar...@co...> wrote:
Hi Ricardo - 

On recent versions of PyMOL, there should be a scroll bar associated with the object list.  What version of PyMOL are you using?  If it is older, might I suggest trying out the recently released PyMOL 2?  https://pymol.org/2/

Alternatively, if you know the name of the PDB file, the object name should be the part of the file name before the extension (e.g. 1abc.pdb becomes '1abc'), so you can color via entering commands at either the internal command prompt (at the bottom of the graphics window), or the one in the Tcl/Tk window, like this:

color red, 1abc

Hope that helps,

Cheers,
Jared

On December 27, 2017 at 12:49:49 AM, ric...@ku... (ric...@ku...) wrote:

Hello.

I load some PDB files for visualization which is just fine, but some of the files are not shown in the object list on the right of the GUI, so I can't change colors or display types.

How can I fix that?

Thanks.
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Hi Jared. This is what i mean. I have opened in the image i attach a PDB
file (which i also have attached) and as you can see, there is no object on
the right. Im using PyMol 2.0.6.






[image: Inline image 2]


On Wed, Dec 27, 2017 at 10:45 AM, Jared Sampson <jar...@co...>
wrote:

> Hi Ricardo -
>
> On recent versions of PyMOL, there should be a scroll bar associated with
> the object list.  What version of PyMOL are you using?  If it is older,
> might I suggest trying out the recently released PyMOL 2?
> https://pymol.org/2/
>
> Alternatively, if you know the name of the PDB file, the object name
> should be the part of the file name before the extension (e.g. 1abc.pdb
> becomes '1abc'), so you can color via entering commands at either the
> internal command prompt (at the bottom of the graphics window), or the one
> in the Tcl/Tk window, like this:
>
> color red, 1abc
>
> Hope that helps,
>
> Cheers,
> Jared
>
> On December 27, 2017 at 12:49:49 AM, ric...@ku... (
> ric...@ku...) wrote:
>
> Hello.
>
> I load some PDB files for visualization which is just fine, but some of
> the files are not shown in the object list on the right of the GUI, so I
> can't change colors or display types.
>
> How can I fix that?
>
> Thanks.
> ------------------------------------------------------------------------------
>
> 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 Ricardo - 

On recent versions of PyMOL, there should be a scroll bar associated with the object list.  What version of PyMOL are you using?  If it is older, might I suggest trying out the recently released PyMOL 2?  https://pymol.org/2/

Alternatively, if you know the name of the PDB file, the object name should be the part of the file name before the extension (e.g. 1abc.pdb becomes '1abc'), so you can color via entering commands at either the internal command prompt (at the bottom of the graphics window), or the one in the Tcl/Tk window, like this:

	color red, 1abc

Hope that helps,

Cheers,
Jared

On December 27, 2017 at 12:49:49 AM, ric...@ku... (ric...@ku...) wrote:

Hello.

I load some PDB files for visualization which is just fine, but some of the files are not shown in the object list on the right of the GUI, so I can't change colors or display types.

How can I fix that?

Thanks.
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Hello.

I load some PDB files for visualization which is just fine, but some of the
files are not shown in the object list on the right of the GUI, so I can't
change colors or display types.

How can I fix that?

Thanks.

Hi,

I am trying to make a plugin that updates some information in a separate window on mouseover or select atom event. Is there any way to register a plugin method as listener for mouse events in the main gui?

Thanks!

Igor Petrik, PhD

Structural Biologist I

Hi Cavi - 

This should do it:

	select delta, resi 11 and resn ARG and name CD and state 76

or, using a selection macro:

	select delta, ARG`11/CD and state 76

If you want to show all the states simultaneously to highlight differences from state 76, you can also use:

	set all_states, 1

Hope that helps,

Cheers,
Jared


On December 20, 2017 at 7:52:46 PM, Cavi via PyMOL-users (pym...@li...) wrote:

Hello everyone!

I have a pdb file of a protein structure solved by NMR. It consists of 120 states/models/conformations depending on which term you prefer. Pymol refers to them as states.

My question is, if I want to select atom 'CD' of residue number 11 (which is an arginine) of state 76, how can I go about it?
I have been able to select the CD atoms of all arginine residues shown in their various states using these commands:
select delta, (r;arg) and (n;CD)   #selects all the CD atoms of arginine residues in their various states
show dots, delta                   #show them as dots
color red, delta                   #color the dots as red
Now I want to further refine my selection by highlighting one of these states as a sphere and of a different color. Please how can I do this?
My question again, how can I select all the CD atoms of arginine residues, choose only the CD atoms of one of the arginines (e.g arginine 11) and highlight one of the states (e.g. state 76) as a blue sphere.
Thank you in advance!

Best regards,
Cavi

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pse is a pymol session file which includes all the information that you see
in your python window, like hidden residues, selections, distance
measurements, coloring, surfaces, cartoons, alignments, etc. PDB is the
protein data bank file format which is usually simply the XYZ coordinates
and B-factors of each atom in your molecule, perhaps with meta information
from the experiment that generated it. In other words, pse will save your
work, but pdb will just save your molecule.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431

On Fri, Dec 22, 2017 at 5:54 PM, Inbal Dagan <inb...@gm...> wrote:

> Hi.
> I'm new to PyMol and can't seem to find an answer online about the
> differences between saving in pdb format and saving in pse format.
>
> Thanks very much,
> Inbal
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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> Archives: http://www.mail-archive.com/pym...@li...
>

Hi.
I'm new to PyMol and can't seem to find an answer online about the
differences between saving in pdb format and saving in pse format.

Thanks very much,
Inbal

Seasonal greetings to all PyMOL users!

If you are curious what the next PyMOL release will bring and you enjoy checking out experimental software, have a look at this:

https://pymol.org/alpha/

This version adds support for the 3Dconnexion SpaceNavigator on all platforms - a formerly MacPyMOL exclusive feature. It also brings back the "auto_copy_images" setting, now on all platforms (formerly Windows and Mac only).

Happy Holidays!
The PyMOL team at Schrödinger

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hello everyone!
I have a pdb file of a protein structure solved by NMR. It consists of 120 states/models/conformations depending on which term you prefer. Pymol refers to them as states.

My question is, if I want to select atom 'CD' of residue number 11 (which is an arginine) of state 76, how can I go about it?I have been able to select the CD atoms of all arginine residues shown in their various states using these commands:select delta, (r;arg) and (n;CD)   #selects all the CD atoms of arginine residues in their various states
show dots, delta                   #show them as dots
color red, delta                   #color the dots as redNow I want to further refine my selection by highlighting one of these states as a sphere and of a different color. Please how can I do this?My question again, how can I select all the CD atoms of arginine residues, choose only the CD atoms of one of the arginines (e.g arginine 11) and highlight one of the states (e.g. state 76) as a blue sphere.Thank you in advance!
Best regards,Cavi

Hi Wolfram,

That reminds me that I compiled a (very incomplete) selection language comparison table a long time ago. Finally managed to upload it to the PyMOLWiki:

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

Phenix's and PyMOL's language are actually pretty close.

Cheers,
  Thomas

> On Dec 18, 2017, at 7:57 PM, wtempel <wt...@gm...> wrote:
> 
> Speaking of atom selection, I wonder how many pymol and phenix users would benefit from a fully "standardized" selection syntax. Would this be a worthwhile design goal?
> Wolfram Tempel

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Speaking of atom selection, I wonder how many pymol and phenix users would
benefit from a fully "standardized" selection syntax. Would this be a
worthwhile design goal?
Wolfram Tempel

On Mon, Dec 18, 2017 at 1:41 PM, Thomas Holder <
tho...@sc...> wrote:

> We'd like to know your thoughts!
>
> How should we name the new selectors for protein and nucleic acid?
>
> Link to poll:
> https://goo.gl/forms/r0Ck03VTytZQxN4A2
>
> We will enhance the PyMOL selection language by adding a new selector for
> protein, and a new one for nucleic acid. They will be subsets of the
> already existing "polymer" selector.
>
> The obvious keyword choices seem to be "nucleic" and "protein". However,
> this would likely introduce conflicts with existing workflows where e.g.
> files are named "nucleic.pdb" or "protein.pdb", and PyMOL would load them
> as named objects of the same name.
>
> We are looking for new keywords that minimize the chance of such naming
> conflicts.
>
> For an overview of the current selection language, see
> https://pymolwiki.org/index.php/Selection_Algebra
>
> --
> 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
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...

We'd like to know your thoughts!

How should we name the new selectors for protein and nucleic acid?

Link to poll:
https://goo.gl/forms/r0Ck03VTytZQxN4A2

We will enhance the PyMOL selection language by adding a new selector for protein, and a new one for nucleic acid. They will be subsets of the already existing "polymer" selector.

The obvious keyword choices seem to be "nucleic" and "protein". However, this would likely introduce conflicts with existing workflows where e.g. files are named "nucleic.pdb" or "protein.pdb", and PyMOL would load them as named objects of the same name.

We are looking for new keywords that minimize the chance of such naming conflicts.

For an overview of the current selection language, see
https://pymolwiki.org/index.php/Selection_Algebra

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear PyMOL people,

Please can anyone tell me if there's any way to draw/ray so that a
selection exactly fills the frame?

At the moment, I'm using `zoom complete=1` (restricted to the protein) and
then I'm auto cropping the resulting image (with `convert -trim`). This is
solution is good enough but please can anyone tell me if there's a better
way I could be doing it?

Many thanks for any help.

Tony Lewis



On 30 November 2017 at 12:00, Tony Lewis <ton...@gm...> wrote:

> Dear PyMOL people,
>
> Please can anyone tell me if there's a standard way to select either of
> nucleic / protein separately?
>
> I can use `polymer` to get both together but I can't see a standard way
> to distinguish nucleic / protein within that.
>
> I'm currently using something like `resn A+C+G+U+DA+DC+DG+DT` to identify
> nucleic but that's inadequate because it misses out various resn values (eg
> BRU, OMG etc) that are part of modified DNA/RNA.
>
> The thing is: PyMOL clearly *knows* which bits are protein versus nucleic
> because it draws the cartoons accordingly. So it feels like I should be
> accessing this info from PyMOL rather than trying to hack together a list
> of resn values.
>
>

Hi Thomas,

To have same stick size for hydrogens, set stick_h_scale to 1.0, see:
https://pymolwiki.org/index.php/stick_h_scale

I don't think that PyMOL's behavior for loading multi-entry .sdf files has changed. If get the same behavior in 1.7.2.1 and any other version. The entries are loaded into one object as discrete states, with the same (carbon) color. Adding hydrogens to discrete objects was never supported.

Are you sure you didn't load .sdf files "multiplexed" in the past? This would split the states into individual objects.

load targets.sdf, multiplex=1

If your example really behaves different in 1.9 and 1.7, then it would be great if you could send me the input files.

Thanks,
  Thomas

> On Dec 14, 2017, at 9:18 AM, Thomas Strunz <beg...@ho...> wrote:
> 
> I've upgraded some of the users to version 1.9.0.0 due to moving to windows 10. It's the build from Christoph Gohlke.
> 
> We use it mainly for one purpose and to make it easier I created a short pml script to load the data and apply settings. However pymol doesn't behave the same anymore. 
> 
> The script:
> 
> reference.sdf
> targets.sdf
> preset.pretty(selection='all')
> set valence, 1
> set stick_radius, 0.2
> 
> In version 1.7.2.1 this would load the 2 files and all mols in file 2 had a different coloring than in file 1. Also hydrogen hat the same stick size as the other bonds. I could go to hide/show to remove/add the hydrogens.
> 
> In Version 1.9.0.0 this is different:
> 
> 	• all molecules have the same color. Changing color isn't applied automatically anymore
> 	• The hydrogen sticks are tiny. how do I make them the same size again? (least important issue)
> 	• If I hide all the hydrogens I can't make them appear again.
> For 3: there is no options unde rshow menu to show the hydrogens again. If I go to Action menu and add hyrodgens I get an error:
>  AddHydrogens-Error: can't modify a discrete object.
> 
> So how can i show hide hydrogens?
> 
> Thanks for the help.
> 
> Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear list subscribers,

we are very happy to announce next year’s “32nd Molecular Modelling 
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The MMWS has a long history of giving young scientists (especially 
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####### Pre-conference workshop #######
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-- 
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  Zentralinstitut fuer Scientific Computing (ZISC)
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I've upgraded some of the users to version 1.9.0.0 due to moving to windows 10. It's the build from Christoph Gohlke.


We use it mainly for one purpose and to make it easier I created a short pml script to load the data and apply settings. However pymol doesn't behave the same anymore.


The script:


reference.sdf
targets.sdf
preset.pretty(selection='all')
set valence, 1
set stick_radius, 0.2

In version 1.7.2.1 this would load the 2 files and all mols in file 2 had a different coloring than in file 1. Also hydrogen hat the same stick size as the other bonds. I could go to hide/show to remove/add the hydrogens.

In Version 1.9.0.0 this is different:


  1.  all molecules have the same color. Changing color isn't applied automatically anymore
  2.  The hydrogen sticks are tiny. how do I make them the same size again? (least important issue)
  3.  If I hide all the hydrogens I can't make them appear again.

For 3: there is no options unde rshow menu to show the hydrogens again. If I go to Action menu and add hyrodgens I get an error:
 AddHydrogens-Error: can't modify a discrete object.

So how can i show hide hydrogens?

Thanks for the help.

Thomas

Hi Wolfram,

Yes, mmCIF has been suggested to PDB2PQR developers, see:
https://github.com/Electrostatics/apbs-pdb2pqr/issues/471

Cheers,
  Thomas

> On Dec 7, 2017, at 8:06 PM, wtempel <wt...@gm...> wrote:
> 
> Thomas,
> how did you know? I removed the --whitespace switch, and get a meaningful model displayed in PyMOL. Has the mmcif format been suggested to the PDB2PQR developers?
> Many thanks.
> Wolfram
> 
> On Thu, Dec 7, 2017 at 3:01 AM, Thomas Holder <tho...@sc...> wrote:
> Hi Wolfram,
> 
> Do you run pdb2pqr with the --whitespace option? If yes, remove that and see if PyMOL is happy with the output.
> 
> Some versions of PyMOL's APBS Tools plugin have the --whitespace option by default (first page, "pdb2pqr command line options") but it seems that this flag creates about as many problems as it solves. The correct solution would be to retire the PQR format and replace it with mmCIF, which is not a fixed column format.
> 
> Cheers,
>   Thomas
> 
> > On Dec 7, 2017, at 1:14 AM, wtempel <wt...@gm...> wrote:
> >
> > Hello,
> > loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles the model in some systematic way, whereas PDB2PQR version 1.8 output appears to be displayed correctly. After superficial inspection I concluded that in 2.1.1 output, columns from (and including) the atom number appear to be shifted to the right by one position. Indeed, when I apply
> > sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be displayed correctly in PyMOL. My question to those familiar with pqr models and the pymol source: is the sed hack safe as in that it would not distort any subsequently calculated APBS surfaces?
> > Best regards.
> > Wolfram Tempel

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Paul,

Put this line in your pymolrc file (File > Edit pymolrc):

set auto_show_classified, 0

See also
https://pymolwiki.org/index.php/auto_show_classified

Cheers,
  Thomas

> On Dec 12, 2017, at 7:22 PM, Paul Paukstelis <sho...@gm...> wrote:
> 
> Forgive me  if this is answered somewhere else. I couldn't find the answer.
> 
> How does one change the default view on startup/load (now cartoon in 2.0) to lines or sticks?
> 
> Thanks,
> 
> --paul

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Forgive me  if this is answered somewhere else. I couldn't find the answer.

How does one change the default view on startup/load (now cartoon in 
2.0) to lines or sticks?

Thanks,

--paul

Thomas,
how did you know? I removed the --whitespace switch, and get a meaningful
model displayed in PyMOL. Has the mmcif format been suggested to the
PDB2PQR developers?
Many thanks.
Wolfram

On Thu, Dec 7, 2017 at 3:01 AM, Thomas Holder <tho...@sc...
> wrote:

> Hi Wolfram,
>
> Do you run pdb2pqr with the --whitespace option? If yes, remove that and
> see if PyMOL is happy with the output.
>
> Some versions of PyMOL's APBS Tools plugin have the --whitespace option by
> default (first page, "pdb2pqr command line options") but it seems that this
> flag creates about as many problems as it solves. The correct solution
> would be to retire the PQR format and replace it with mmCIF, which is not a
> fixed column format.
>
> Cheers,
>   Thomas
>
> > On Dec 7, 2017, at 1:14 AM, wtempel <wt...@gm...> wrote:
> >
> > Hello,
> > loading a pqr (PDB2PQR version 2.1.1) file into pymol 1.7 … 1.9 garbles
> the model in some systematic way, whereas PDB2PQR version 1.8 output
> appears to be displayed correctly. After superficial inspection I concluded
> that in 2.1.1 output, columns from (and including) the atom number appear
> to be shifted to the right by one position. Indeed, when I apply
> > sed 's/^ATOM /ATOM/', the so modified 2.1.1 output appears to be
> displayed correctly in PyMOL. My question to those familiar with pqr models
> and the pymol source: is the sed hack safe as in that it would not distort
> any subsequently calculated APBS surfaces?
> > Best regards.
> > Wolfram Tempel
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>