pymol-users Mailing List for PyMOL Molecular Graphics System

My pymolrc file contains a line: viewport 1350,950
which nicely fills my screen when I start pymol 1.8. However in pymol2 the
screen has the correct dimensions but the whole thing is offest to the
right and down. What should be the top left corner of the window is placed
about a quarter of the way from the left hand side and about one sixth of
the way down from the top.

Is it a bug or is there a new viewport command?



-- 

Prof. Gary J. Hunter,

Laboratory of Biochemistry and Protein Science,

Department of Physiology and Biochemistry,

University of Malta, Msida, MSD 2080, Malta.

phone: +356 2340 2917

phone: +356 21316655 (secretary),  Fax: +356 21310577

http://www.um.edu.mt/ms/physbiochem

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Hi Mohammad - 

The `align` function (https://pymolwiki.org/index.php/Align) does a sequence-based (as opposed to structural-based) alignment of different objects.  If you need to use a specific alignment from an external program, see Thomas Holder's post to this mailing list from last week:

https://sourceforge.net/p/pymol/mailman/message/36193233/

Hope that helps,

Cheers,
Jared

On January 26, 2018 at 6:12:25 PM, Mohammad Goodarzi (moh...@gm...) wrote:

Jared, 

Thanks for your message. Do you know how to align several proteins based on their similar domain ? I mean overlap them based on their similar sequence that I know the read ? 

Thanks
Mohammad 

On Fri, Jan 26, 2018 at 3:53 PM, Jared Sampson <jar...@co...> wrote:
Hi Mohammad - 

If you know the residue numbers at the domain boundaries, you can do this at the command line with, e.g.:

color red, chain A and resi 1-100
color cyan, chain A and resi 101-200
etc.

Hope that helps.

Cheers,
Jared


On January 26, 2018 at 4:48:43 PM, Mohammad Goodarzi (moh...@gm...) wrote:

Hello,

I have a sequence and I obtain various domains. I want to show them with various colors.
How can one do that? for example can one of you show it on SIRT1

Thanks
Mohammad
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Jared,

Thanks for your message. Do you know how to align several proteins based on
their similar domain ? I mean overlap them based on their similar sequence
that I know the read ?

Thanks
Mohammad

On Fri, Jan 26, 2018 at 3:53 PM, Jared Sampson <jar...@co...>
wrote:

> Hi Mohammad -
>
> If you know the residue numbers at the domain boundaries, you can do this
> at the command line with, e.g.:
>
> color red, chain A and resi 1-100
> color cyan, chain A and resi 101-200
> etc.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On January 26, 2018 at 4:48:43 PM, Mohammad Goodarzi (
> moh...@gm...) wrote:
>
> Hello,
>
> I have a sequence and I obtain various domains. I want to show them with
> various colors.
> How can one do that? for example can one of you show it on SIRT1
>
> Thanks
> Mohammad
> ------------------------------------------------------------
> ------------------
> 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 Mohammad - 

If you know the residue numbers at the domain boundaries, you can do this at the command line with, e.g.:

color red, chain A and resi 1-100
color cyan, chain A and resi 101-200
etc.

Hope that helps.

Cheers,
Jared


On January 26, 2018 at 4:48:43 PM, Mohammad Goodarzi (moh...@gm...) wrote:

Hello,

I have a sequence and I obtain various domains. I want to show them with various colors.
How can one do that? for example can one of you show it on SIRT1

Thanks
Mohammad
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Hello,

I have a sequence and I obtain various domains. I want to show them with
various colors.
How can one do that? for example can one of you show it on SIRT1

Thanks
Mohammad

Hi Thomas,

In my use-case, I'd like to distribute .pml scripts to my PyMOL-using
users, which display the alignment correctly out-of-the-box, without the
users having to install anything. AFAIU, it doesn't sound as though I'd be
able to do that with this solution.

Please may I add 1 vote for supporting this feature out-of-the-box. :)

Anyway, thanks very much for your help - much appreciated.

Kind regards,

Tony


On 17 January 2018 at 10:04, Thomas Holder <tho...@sc...>
wrote:

> Hi Tony,
>
> It's possible, but not out of the box. I wrote a script for this some time
> ago which uses biopython and emboss. If you're using Linux or MacOS,
> everything is prepackaged for you in Anaconda Cloud. For installation
> instructions and examples, see:
> https://pymolwiki.org/index.php/Load_aln
>
> Cheers,
>   Thomas
>
> > On Jan 11, 2018, at 11:40 AM, Tony Lewis <ton...@gm...> wrote:
> >
> > Dear PyMOL people,
> >
> > Please can anyone tell me whether there's an easy way to use an
> alignment of the residues in the displayed structures (say, from a FASTA
> file) to align the residues shown in the sequence display?
> >
> > I would find this a very powerful feature.
> >
> > Many thanks for any help.
> >
> > Tony Lewis
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Tony,

It's possible, but not out of the box. I wrote a script for this some time ago which uses biopython and emboss. If you're using Linux or MacOS, everything is prepackaged for you in Anaconda Cloud. For installation instructions and examples, see:
https://pymolwiki.org/index.php/Load_aln

Cheers,
  Thomas

> On Jan 11, 2018, at 11:40 AM, Tony Lewis <ton...@gm...> wrote:
> 
> Dear PyMOL people,
> 
> Please can anyone tell me whether there's an easy way to use an alignment of the residues in the displayed structures (say, from a FASTA file) to align the residues shown in the sequence display?
> 
> I would find this a very powerful feature.
> 
> Many thanks for any help.
> 
> Tony Lewis

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

The source of 1.9.0.0 is likely the subversion repository, which also has
the history that shows the changes.

https://sourceforge.net/p/pymol/code/4184/log/?path=/trunk

As for pymol 2.0 coming to open source, the announcement for 2.0 said the
improvements would be pushed to the open source repository in early 2018.

On Fri, Jan 12, 2018 at 4:48 PM, CAS IT Services <ca...@al...> wrote:

> Disclaimer:  I am not a chemist, nor a PyMol user.  I am an IT guy trying
> to assist students and educators with installing PyMol.
>
> I am pretty sure I can figure out how to get PyMol working from the
> compiled source that Christoph Gohlke offers for download, but I thought I
> should try to compile it myself.
>
> Does anyone know why there is a discrepancy between the version of the
> downloadable source tarball found here (v1.8.6.0) and the version Christoph
> offers (v1.9.0.0)?
>
> Assuming that I trust Christoph's offering, what changed between 1.8.6.0
> and 1.9.0.0?
>
> Also, does anyone know if 1.9.0.0 is the end for open source PyMol?  Has
> Schrodinger completed a conversion to a fully commercial (and likely
> profitable) version with v2.0?
>
> 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...
>

Disclaimer:  I am not a chemist, nor a PyMol user.  I am an IT guy trying to assist students and educators with installing PyMol.

I am pretty sure I can figure out how to get PyMol working from the compiled source that Christoph Gohlke offers for download, but I thought I should try to compile it myself.

Does anyone know why there is a discrepancy between the version of the downloadable source tarball found here (v1.8.6.0) and the version Christoph offers (v1.9.0.0)?  

Assuming that I trust Christoph's offering, what changed between 1.8.6.0 and 1.9.0.0?

Also, does anyone know if 1.9.0.0 is the end for open source PyMol?  Has Schrodinger completed a conversion to a fully commercial (and likely profitable) version with v2.0?

Thanks.

The transform matrix you’re using is the identity matrix, so it won’t have any effect.

-David

> On Jan 11, 2018, at 6:54 PM, Benjamin Bailly <bb...@gm...> wrote:
> 
> Hi Thomas,
> 
> Thanks for your reply.
> 
> So if I am correct, for my protein get_coords fetches a very large matrix of thousands and thousands of rows. This could prove very impractical if I want to stores those coordinates in a script.
> 
> To circumvent this issue I tried the following but it did not seem to work:
> 
> print cmd.get_object_matrix('%prot')   # to obtain my coordinates in a 4X4 format
> 
> PyMOL>cmd.transform_selection("su", [[1.0,0.0,0.0,0.0], [0.0,1.0,0.0,0.0], [0.0,0.0,1.0,0.0], [0.0,0.0,0.0,1.0]], homogenous=1)
> CmdTransformSelection-DEBUG: bad matrix
> 
> PyMOL>cmd.transform_selection("su", [1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0], homogenous=1)  # In that case nothing happens
> 
> What do you think I am doing wrong?
> 
> Many thanks,
> 
> Ben
> 
> --
> 
> Dr Benjamin Bailly | Research Scientist – von Itzstein group
> 
> Institute for Glycomics
> Griffith University | Gold Coast campus | QLD 4222 | Institute for Glycomics (G26) Room 4.30
> 
> 
> 
> _______________________
> 
> Benjamin Bailly 
> +61 479 17 66 34 (Australia)
> 
>> On 11 January 2018 at 17:26, Thomas Holder <tho...@sc...> wrote:
>> Hi Ben,
>> 
>> The coordinates argument must have a Nx3 shape, that means:
>> len(coordinates) = number of atoms
>> len(coordinates[0]) = 3
>> 
>> You can use numpy's reshape() function:
>> 
>> import numpy
>> coordinates = numpy.asfarray(coordinates).reshape((-1,3))
>> cmd.load_coords(coordinates, '%prot')
>> 
>> I recommend to prefix the object name with "%" to unambiguously address a named object or selection. I mention this because I just ran into a common selection language ambiguity problem myself: I named my object "obj01" and then pasted your code without changing the object name. The error message was "atom count mismatch" instead of "invalid selection name". Why? Because "prot" was evaluated as the selection keyword "protected", so it was a valid (but empty) selection expression.
>> 
>> Cheers,
>>   Thomas
>> 
>> > On Jan 11, 2018, at 7:43 AM, Benjamin Bailly <bb...@gm...> wrote:
>> >
>> > Hi everyone,
>> >
>> > I have been scratching my head quite a bit on this one, I am sure there must be a simple solution but I can't seem to figure it out.
>> >
>> > In short, I would like to record the spacial coordinates of a protein so that when I run my script I can fetch it from the PDB and place it exactly where I would like it to be.
>> >
>> > I used this command to obtain the coordinates, and here is the output I get:
>> >
>> > PyMOL>print cmd.get_coords('prot')
>> > [[159.402 258.709 204.556]
>> >  [159.932 259.514 204.223]
>> >  [158.951 258.206 203.792]
>> >  ...
>> >  [117.662 263.108 309.314]
>> >  [115.591 265.038 307.88 ]
>> >  [116.386 259.713 306.195]]
>> >
>> > To load the position in my script I know that I should be able to use the following command however I can not figure out the format required:
>> >
>> > cmd.load_coords(coordinates, 'prot')
>> >
>> > I tried to use all the floats the ones after the other like [1.1, 2.2, 3.3,...] and I was close to making it work, but it said the numbers of atoms did not match. I read that I should probably used a numpy array but I am not sure of its format.
>> >
>> > Your help would be much appreciated,
>> >
>> > Many thanks
>> >
>> > Ben
>> 
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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> _______________________________________________
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Hi Thomas,

Thanks for your reply.

So if I am correct, for my protein get_coords fetches a very large matrix
of thousands and thousands of rows. This could prove very impractical if I
want to stores those coordinates in a script.

To circumvent this issue I tried the following but it did not seem to work:

print cmd.get_object_matrix('%prot')   # to obtain my coordinates in a 4X4
format

PyMOL>cmd.transform_selection("su", [[1.0,0.0,0.0,0.0], [0.0,1.0,0.0,0.0],
[0.0,0.0,1.0,0.0], [0.0,0.0,0.0,1.0]], homogenous=1)
CmdTransformSelection-DEBUG: bad matrix

PyMOL>cmd.transform_selection("su", [1.0,0.0,0.0,0.0,0.0,1.0,0.0,
0.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,1.0], homogenous=1)  # In that case nothing
happens

What do you think I am doing wrong?

Many thanks,

Ben

--

Dr Benjamin Bailly | Research Scientist – von Itzstein group

Institute for Glycomics
Griffith University | Gold Coast campus | QLD 4222 | Institute for
Glycomics (G26) Room 4.30



_______________________

*Benjamin Bailly*
+61 479 17 66 34 (Australia)

On 11 January 2018 at 17:26, Thomas Holder <tho...@sc...>
wrote:

> Hi Ben,
>
> The coordinates argument must have a Nx3 shape, that means:
> len(coordinates) = number of atoms
> len(coordinates[0]) = 3
>
> You can use numpy's reshape() function:
>
> import numpy
> coordinates = numpy.asfarray(coordinates).reshape((-1,3))
> cmd.load_coords(coordinates, '%prot')
>
> I recommend to prefix the object name with "%" to unambiguously address a
> named object or selection. I mention this because I just ran into a common
> selection language ambiguity problem myself: I named my object "obj01" and
> then pasted your code without changing the object name. The error message
> was "atom count mismatch" instead of "invalid selection name". Why? Because
> "prot" was evaluated as the selection keyword "protected", so it was a
> valid (but empty) selection expression.
>
> Cheers,
>   Thomas
>
> > On Jan 11, 2018, at 7:43 AM, Benjamin Bailly <bb...@gm...> wrote:
> >
> > Hi everyone,
> >
> > I have been scratching my head quite a bit on this one, I am sure there
> must be a simple solution but I can't seem to figure it out.
> >
> > In short, I would like to record the spacial coordinates of a protein so
> that when I run my script I can fetch it from the PDB and place it exactly
> where I would like it to be.
> >
> > I used this command to obtain the coordinates, and here is the output I
> get:
> >
> > PyMOL>print cmd.get_coords('prot')
> > [[159.402 258.709 204.556]
> >  [159.932 259.514 204.223]
> >  [158.951 258.206 203.792]
> >  ...
> >  [117.662 263.108 309.314]
> >  [115.591 265.038 307.88 ]
> >  [116.386 259.713 306.195]]
> >
> > To load the position in my script I know that I should be able to use
> the following command however I can not figure out the format required:
> >
> > cmd.load_coords(coordinates, 'prot')
> >
> > I tried to use all the floats the ones after the other like [1.1, 2.2,
> 3.3,...] and I was close to making it work, but it said the numbers of
> atoms did not match. I read that I should probably used a numpy array but I
> am not sure of its format.
> >
> > Your help would be much appreciated,
> >
> > Many thanks
> >
> > Ben
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

When I attempt to run Caver3.01 as a plugin in Pymol 2.0.6 , I get Java error messages: 1) Testing if Java is installed, FAIL; 2) Can't execute ['java", 'version'] Error 6] The handle is invalid.

Java version 8 Update 151 is installed on my 64 bit PC running under Win7

Has anyone encountered this problem?

Marilyn Jorns
****************************************
Marilyn Jorns, PhD
Professor
Department of Biochemistry and Molecular Biology
Drexel University College of Medicine
245 N. 15th Street
Philadelphia PA 19102
Phone: (215) 762 7495
FAX: (215) 762 4452

Dear PyMOL people,

Please can anyone tell me whether there's an easy way to use an alignment
of the residues in the displayed structures (say, from a FASTA file) to
align the residues shown in the sequence display?

I would find this a very powerful feature.

Many thanks for any help.

Tony Lewis

Hi Ben,

The coordinates argument must have a Nx3 shape, that means:
len(coordinates) = number of atoms
len(coordinates[0]) = 3

You can use numpy's reshape() function:

import numpy
coordinates = numpy.asfarray(coordinates).reshape((-1,3))
cmd.load_coords(coordinates, '%prot')

I recommend to prefix the object name with "%" to unambiguously address a named object or selection. I mention this because I just ran into a common selection language ambiguity problem myself: I named my object "obj01" and then pasted your code without changing the object name. The error message was "atom count mismatch" instead of "invalid selection name". Why? Because "prot" was evaluated as the selection keyword "protected", so it was a valid (but empty) selection expression.

Cheers,
  Thomas

> On Jan 11, 2018, at 7:43 AM, Benjamin Bailly <bb...@gm...> wrote:
> 
> Hi everyone,
> 
> I have been scratching my head quite a bit on this one, I am sure there must be a simple solution but I can't seem to figure it out.
> 
> In short, I would like to record the spacial coordinates of a protein so that when I run my script I can fetch it from the PDB and place it exactly where I would like it to be.
> 
> I used this command to obtain the coordinates, and here is the output I get:
> 
> PyMOL>print cmd.get_coords('prot')
> [[159.402 258.709 204.556]
>  [159.932 259.514 204.223]
>  [158.951 258.206 203.792]
>  ...
>  [117.662 263.108 309.314]
>  [115.591 265.038 307.88 ]
>  [116.386 259.713 306.195]]
> 
> To load the position in my script I know that I should be able to use the following command however I can not figure out the format required:
> 
> cmd.load_coords(coordinates, 'prot')
> 
> I tried to use all the floats the ones after the other like [1.1, 2.2, 3.3,...] and I was close to making it work, but it said the numbers of atoms did not match. I read that I should probably used a numpy array but I am not sure of its format.
> 
> Your help would be much appreciated,
> 
> Many thanks
> 
> Ben

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi everyone,

I have been scratching my head quite a bit on this one, I am sure there
must be a simple solution but I can't seem to figure it out.

In short, I would like to record the spacial coordinates of a protein so
that when I run my script I can fetch it from the PDB and place it exactly
where I would like it to be.

I used this command to obtain the coordinates, and here is the output I get:

PyMOL>print cmd.get_coords('prot')
[[159.402 258.709 204.556]
 [159.932 259.514 204.223]
 [158.951 258.206 203.792]
 ...
 [117.662 263.108 309.314]
 [115.591 265.038 307.88 ]
 [116.386 259.713 306.195]]

To load the position in my script I know that I should be able to use the
following command however I can not figure out the format required:

cmd.load_coords(coordinates, 'prot')

I tried to use all the floats the ones after the other like [1.1, 2.2,
3.3,...] and I was close to making it work, but it said the numbers of
atoms did not match. I read that I should probably used a numpy array but I
am not sure of its format.

Your help would be much appreciated,

Many thanks

Ben

Hi Rex -

Open-Source PyMOL is freely available.  You can find installation instructions on the PyMOL Wiki: 

https://pymolwiki.org/index.php/Linux_Install 
https://pymolwiki.org/index.php/MAC_Install 
https://pymolwiki.org/index.php/Windows_Install

Hope that helps,

Cheers,
Jared

On January 10, 2018 at 12:13:26 PM, Rex Palmer (rex...@bt...) wrote:

As a retired member of academic staff (Birlbeck College, London) I would like to know
if it is possible for me to obtain a free copy of the Pymol software.
This would be of great help in my research on high resolution protein structures.
I have recently published a 0.9A X-ray study of Human Recombinant Insulin.
Best wishes 
 
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://www.springer.com/978-1-4641-3954-7
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As a retired member of academic staff (Birlbeck College, London) I would like to knowif it is possible for me to obtain a free copy of the Pymol software.This would be of great help in my research on high resolution protein structures.I have recently published a 0.9A X-ray study of Human Recombinant Insulin.Best wishes  Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://www.springer.com/978-1-4641-3954-7