Re: [PyMOL] Logging the sculpt wizard

[Jed Goldstone]

You might want to try using Modeller instead.
http://www.salilab.org/modeller/wiki/Mutate%20model
It does higher level modelling.

Jed

Martin Hediger wrote:
> Dear List
> I'm trying to automate the following sequence of steps in a PyMOL python 
> script:
> 1. Start the mutagenesis wizard
> 2. Mutate a reside according to an input from the script (some integer 
> to specify the id)
> 3. "Apply" and close the mutagenesis wizard
> 4. Start the Sculpt Wizard
> 5. Fix all coordinates but the residue just mutated
> 6. Start the sculpt algorithm to get a rough optimization of the side chain
> 7. End the sculpt algorithm and close the sculpt wizard.
> 8. Save the structure to a new file.
>
> I have the steps up to 3. ready in a script for generation of variants.
> However, when running a log file while performing steps 4. onwards, 
> there are no commands written into the log file for the sculpting 
> functions. Pressing the "Sculpt" button in the PyMOLX11Hybrid does not 
> lead to a command I can see in the log file.
> What would be the Python code to start the sculpt process?
>
> Any hints are welcome.
>
> Thanks a lot.
>
>
>
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[PyMOL] Logging the sculpt wizard

[Martin Hediger]

Dear List
I'm trying to automate the following sequence of steps in a PyMOL python 
script:
1. Start the mutagenesis wizard
2. Mutate a reside according to an input from the script (some integer 
to specify the id)
3. "Apply" and close the mutagenesis wizard
4. Start the Sculpt Wizard
5. Fix all coordinates but the residue just mutated
6. Start the sculpt algorithm to get a rough optimization of the side chain
7. End the sculpt algorithm and close the sculpt wizard.
8. Save the structure to a new file.

I have the steps up to 3. ready in a script for generation of variants.
However, when running a log file while performing steps 4. onwards, 
there are no commands written into the log file for the sculpting 
functions. Pressing the "Sculpt" button in the PyMOLX11Hybrid does not 
lead to a command I can see in the log file.
What would be the Python code to start the sculpt process?

Any hints are welcome.

Thanks a lot.



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Re: [PyMOL] How to get pymol 1.4

[Stephen P Molnar]

Thank you for your reply.

I was too much in a hurry to write.  I shall curb my impatience and wait for
your announcement.

Stephen P. Molnar, Ph.D.  Life is a
fuzzy set
Foundation for Chemistry Stochastic
and multivriate
http://www.FoundationForChemistry.com


-Original Message-
From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] 
Sent: Wednesday, March 23, 2011 3:07 PM
To: Stephen P Molnar
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to get pymol 1.4

Hi Stephen,

> I would like to know if, and when, 1.4 will be available for downloading.

Yes, PyMOL v1.4 will be released to the open-source.  I will prepare
the v1.4 release file soon (hopefully less than two weeks' time).

As Michael noted, it's nothing insidious: within hours of releasing
the v1.4 to the incentive users, I had to get in a plane and fly to
the west coast to present and support PyMOL.  I'm at the
crystallographic WCPCW meeting this week, and ACS next week.  When I
return home, I'll merge the volumes code and make the release file.

I'll announce it when I finish and it's posted.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120


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Re: [PyMOL] How to get pymol 1.4

[Jason Vertrees]

Hi Stephen,

> I would like to know if, and when, 1.4 will be available for downloading.

Yes, PyMOL v1.4 will be released to the open-source.  I will prepare
the v1.4 release file soon (hopefully less than two weeks' time).

As Michael noted, it's nothing insidious: within hours of releasing
the v1.4 to the incentive users, I had to get in a plane and fly to
the west coast to present and support PyMOL.  I'm at the
crystallographic WCPCW meeting this week, and ACS next week.  When I
return home, I'll merge the volumes code and make the release file.

I'll announce it when I finish and it's posted.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] How to get pymol 1.4

[Mark J van Raaij]

read Jasons mail:

Greetings,

I'm delighted to announce that the Incentive build of PyMOL v1.4
has been released. Current subscribers can download the binaries
for Windows, Mac and Linux from http://pymol.org/dsc/ip and
access documentation and videos from
http://pymol.org/dsc/dokuwiki/doku.php?id=media:new14.

As you will see, the PyMOL builds are much larger. This is
because we're shipping a newer and much fuller version of Python,
optimized libraries for map generation, and chemistry libraries
for the new stereochemical labeling and atom typing.

Here's the Incentive PyMOL v1.4 feature list:

• New 64-bit MacPyMOL allows Mac users to access more than 4 GB
of memory

• Volume visualization for unique display of volumetric data and
simultaneous visualization of multiple iso-surfaces (see
http://pymol.org/volume)

• Electron density map generation from reflection data (Mac and
Linux only, Windows coming soon)

• Stereochemical labeling

• Improved Atom Typing; SYBYL/MOL2 and MacroModel support

• OpenGL Shaders (GLSL) for improved on-screen rendering
(cartoons, sticks, surfaces, volumes).

• Dynamic measurements (distances, bond angles and dihedral
angles)

• File > Save Molecule now allows saving of multiple files,
multi-state PDBs to a single file, and multi-state PDBs to
multiple files

• Improved State Handling makes operations on multi-state objects
easier

• Built using updated and Schrödinger-compatible distribution of
Python (v2.7).

• PyMOL Web GUI (PWG)

• Several bug fixes

Many of these features are already in the open-source code.
Within the next few weeks, we will put the volume visualization and
shaders into the open-source code. Stereochemical labeling and map
generation are not in the open-source project, but we are working on
adding them to the open-source project.

I will send an update soon when the volume visualization is in the
open-source code.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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On 23 Mar 2011, at 19:50, Stephen P Molnar wrote:

> Going to www.pymol.org, clicking on OpenSource and then 
> sf.net/projects/pymol/develop followed by Download PyMOL Molecular Graphics 
> System will download pumol-1.3r2-src.tar.bz2.
>  
> I would like to know if, and when, 1.4 will be available for downloading.
>  
> Stephen P. Molnar, Ph.D.  Life is a 
> fuzzy set
> Foundation for Chemistry Stochastic 
> and multivriate
> http://www.FoundationForChemistry.com
>  
> From: Michael Lerner [mailto:mgler...@gmail.com] 
> Sent: Wednesday, March 23, 2011 2:22 PM
> To: li...@cowsandmilk.net
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] How to get pymol 1.4
>  
> In addition to David's excellent email, I would like to point out that Jason 
> is extremely dedicated to the open-source future of PyMOL, so much so that I 
> don't think a better PyMOL maintainer could have been chosen. 
>  
> I think that, for people who have been using/contributing to PyMOL for a long 
> time, there's a natural inclination to say "Oh no! A more commercial entity 
> is now in charge!" and assume that things are both worse than they are and 
> likely to get even worse. I certainly had some of those thoughts myself, but 
> I've talked with Jason many times (sometimes initiated by me and sometimes 
> initiated by him) and I'm convinced that things are in excellent hands.
>  
> Just as an example of how it's easy to assume the worst, there have been 
> quite a few complaints about the way in which PyMOL is hosted on Sourceforge. 
> People went to download the source and, instead of a source tarball, found a 
> link to a text file. Outrage at the fact that the actual source had somehow 
> been hidden was then expressed. First of all, that text file contained very 
> clear instructions on how to actually download the source. Second, and this 
> will likely come as a complete shock to the people who complained, the text 
> file is EXACTLY the system that Warren put in place. You may want to read 
> that again, because, as far as I know, nobody complained about the system 
> when Warren was in charge, but many people lept to the conclusion that 
> nefarious forces were at work when they saw the exact same system under 
> Schrodinger. Third, and perhaps most important, Jason's reaction upon hearing 
> these complaints was to add a source tarball to the Sour

Re: [PyMOL] How to get pymol 1.4

[Stephen P Molnar]

Going to www.pymol.org, clicking on OpenSource and then
sf.net/projects/pymol/develop followed by Download PyMOL Molecular Graphics
System will download pumol-1.3r2-src.tar.bz2.

 

I would like to know if, and when, 1.4 will be available for downloading.

 

Stephen P. Molnar, Ph.D.  Life is a
fuzzy set

Foundation for Chemistry Stochastic
and multivriate

http://www.FoundationForChemistry.com

 

From: Michael Lerner [mailto:mgler...@gmail.com] 
Sent: Wednesday, March 23, 2011 2:22 PM
To: li...@cowsandmilk.net
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to get pymol 1.4

 

In addition to David's excellent email, I would like to point out that Jason
is extremely dedicated to the open-source future of PyMOL, so much so that I
don't think a better PyMOL maintainer could have been chosen. 

 

I think that, for people who have been using/contributing to PyMOL for a
long time, there's a natural inclination to say "Oh no! A more commercial
entity is now in charge!" and assume that things are both worse than they
are and likely to get even worse. I certainly had some of those thoughts
myself, but I've talked with Jason many times (sometimes initiated by me and
sometimes initiated by him) and I'm convinced that things are in excellent
hands.

 

Just as an example of how it's easy to assume the worst, there have been
quite a few complaints about the way in which PyMOL is hosted on
Sourceforge. People went to download the source and, instead of a source
tarball, found a link to a text file. Outrage at the fact that the actual
source had somehow been hidden was then expressed. First of all, that text
file contained very clear instructions on how to actually download the
source. Second, and this will likely come as a complete shock to the people
who complained, the text file is EXACTLY the system that Warren put in
place. You may want to read that again, because, as far as I know, nobody
complained about the system when Warren was in charge, but many people lept
to the conclusion that nefarious forces were at work when they saw the exact
same system under Schrodinger. Third, and perhaps most important, Jason's
reaction upon hearing these complaints was to add a source tarball to the
Sourceforge download page. If you go to pymol.org and click on "open
source", you go directly to the Sourceforge page from which you can download
that tarball. So, if anything, PyMOL's open-source nature is *more*
accessible now.

 

I would say the the creation of the Warren L. DeLano Memorial PyMOL
Open-Source Fellowship also clearly demonstrates Schrodinger's commitment to
both open source and the PyMOL community, although I should mention in the
interest of full disclosure that I have the great honor of receiving the
2010-2011 fellowship.

 

I'm sure there are several other examples like this, but the main thing I'd
like to say is that Jason is very accessible (both via email and through
this list) and extremely responsive. If you're worried about something,
especially something as important as the continuing open-source nature of
PyMOL, try sending a collegial email to the list. PyMOL's userbase is huge,
and I'm sure that many other people have the same concern. I'm also sure
that Jason (or someone else on the list) will give you a surprisingly good
answer. Open-source code thrives on community and trust, and I've really
seen no signs to indicate that those aren't still to be had in top-notch
form with PyMOL.

 

Cheers,

 

-Michael

On Wed, Mar 23, 2011 at 7:12 AM,  wrote:

a) you're mistaken, Warren's incentive builds had extra features.  Also,
Warren had announced pretty clear plans of adding more features to the
incentive builds and not releasing them open source for several years

b) if you've been following the list, Jason has stated that many of the 1.4
features are on their way to the open source repository.

 

Sure, I am of the type that wishes all features were open source and that
Jason did all development directly against a repository we could all see,
but I think he's done a good job communicating the way development is
happening to the list and schrodinger's model for the incentive builds seems
to be hardly different from what Warren had started doing.


-David


On Mar 23, 2011, at 6:33 AM, Abhinav Verma  wrote:

And why would that be? I thought that pymol is open source and till Warren
was there all updates were available in the open source domain and incentive
builds were limited to windows executable and involving support!! 





On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij 
wrote:

> Is the 1.4 version restricted to incentive downloads only??

Yes

>
> Thanks,
>

--
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking adv

Re: [PyMOL] How to get pymol 1.4

[Michael Lerner]

In addition to David's excellent email, I would like to point out that Jason
is extremely dedicated to the open-source future of PyMOL, so much so that I
don't think a better PyMOL maintainer could have been chosen.

I think that, for people who have been using/contributing to PyMOL for a
long time, there's a natural inclination to say "Oh no! A more commercial
entity is now in charge!" and assume that things are both worse than they
are and likely to get even worse. I certainly had some of those thoughts
myself, but I've talked with Jason many times (sometimes initiated by me and
sometimes initiated by him) and I'm convinced that things are in excellent
hands.

Just as an example of how it's easy to assume the worst, there have been
quite a few complaints about the way in which PyMOL is hosted on
Sourceforge. People went to download the source and, instead of a source
tarball, found a link to a text file. Outrage at the fact that the actual
source had somehow been hidden was then expressed. First of all, that text
file contained very clear instructions on how to actually download the
source. Second, and this will likely come as a complete shock to the people
who complained, the text file is EXACTLY the system that Warren put in
place. You may want to read that again, because, as far as I know, nobody
complained about the system when Warren was in charge, but many people lept
to the conclusion that nefarious forces were at work when they saw the exact
same system under Schrodinger. Third, and perhaps most important, Jason's
reaction upon hearing these complaints was to add a source tarball to the
Sourceforge download page. If you go to pymol.org and click on "open
source", you go directly to the Sourceforge page from which you can download
that tarball. So, if anything, PyMOL's open-source nature is *more*
accessible now.

I would say the the creation of the Warren L. DeLano Memorial PyMOL
Open-Source Fellowship also clearly demonstrates Schrodinger's commitment to
both open source and the PyMOL community, although I should mention in the
interest of full disclosure that I have the great honor of receiving the
2010-2011 fellowship.

I'm sure there are several other examples like this, but the main thing I'd
like to say is that Jason is very accessible (both via email and through
this list) and extremely responsive. If you're worried about something,
especially something as important as the continuing open-source nature of
PyMOL, try sending a collegial email to the list. PyMOL's userbase is huge,
and I'm sure that many other people have the same concern. I'm also sure
that Jason (or someone else on the list) will give you a surprisingly good
answer. Open-source code thrives on community and trust, and I've really
seen no signs to indicate that those aren't still to be had in top-notch
form with PyMOL.

Cheers,

-Michael

On Wed, Mar 23, 2011 at 7:12 AM,  wrote:

> a) you're mistaken, Warren's incentive builds had extra features.  Also,
> Warren had announced pretty clear plans of adding more features to the
> incentive builds and not releasing them open source for several years
> b) if you've been following the list, Jason has stated that many of the 1.4
> features are on their way to the open source repository.
>
> Sure, I am of the type that wishes all features were open source and that
> Jason did all development directly against a repository we could all see,
> but I think he's done a good job communicating the way development is
> happening to the list and schrodinger's model for the incentive builds seems
> to be hardly different from what Warren had started doing.
>
> -David
>
> On Mar 23, 2011, at 6:33 AM, Abhinav Verma  wrote:
>
> And why would that be? I thought that pymol is open source and till Warren
> was there all updates were available in the open source domain and incentive
> builds were limited to windows executable and involving support!!
>
>
>
>
> On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij <
> mjvanra...@cnb.csic.es> wrote:
>
>> > Is the 1.4 version restricted to incentive downloads only??
>>
>> Yes
>>
>> >
>> > Thanks,
>> >
>> --
>> > Enable your software for Intel(R) Active Management Technology to meet
>> the
>> > growing manageability and security demands of your customers. Businesses
>> > are taking advantage of Intel(R) vPro (TM) technology - will your
>> software
>> > be a part of the solution? Download the Intel(R) Manageability Checker
>> > today!
>> 
>> http://p.sf.net/sfu/intel-dev2devmar___
>> > PyMOL-users mailing list ( 
>> PyMOL-users@lists.sourceforge.net)
>> > Info Page: 
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives:
>> 

Re: [PyMOL] How to get pymol 1.4

[Abhinav Verma]

Thanks for pointing out Jason's email. I missed that.
And at the same time I shall learn to read and understand the fine-print
under "open source".

On Wed, Mar 23, 2011 at 12:12 PM,  wrote:

> a) you're mistaken, Warren's incentive builds had extra features.  Also,
> Warren had announced pretty clear plans of adding more features to the
> incentive builds and not releasing them open source for several years
> b) if you've been following the list, Jason has stated that many of the 1.4
> features are on their way to the open source repository.
>
> Sure, I am of the type that wishes all features were open source and that
> Jason did all development directly against a repository we could all see,
> but I think he's done a good job communicating the way development is
> happening to the list and schrodinger's model for the incentive builds seems
> to be hardly different from what Warren had started doing.
>
> -David
>
> On Mar 23, 2011, at 6:33 AM, Abhinav Verma  wrote:
>
> And why would that be? I thought that pymol is open source and till Warren
> was there all updates were available in the open source domain and incentive
> builds were limited to windows executable and involving support!!
>
>
>
>
> On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij <
> mjvanra...@cnb.csic.es> wrote:
>
>> > Is the 1.4 version restricted to incentive downloads only??
>>
>> Yes
>>
>> >
>> > Thanks,
>> >
>> --
>> > Enable your software for Intel(R) Active Management Technology to meet
>> the
>> > growing manageability and security demands of your customers. Businesses
>> > are taking advantage of Intel(R) vPro (TM) technology - will your
>> software
>> > be a part of the solution? Download the Intel(R) Manageability Checker
>> > today!
>> 
>> http://p.sf.net/sfu/intel-dev2devmar___
>> > PyMOL-users mailing list ( 
>> PyMOL-users@lists.sourceforge.net)
>> > Info Page: 
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives:
>> 
>> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>>
>
> --
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Re: [PyMOL] alter_state

[Thomas Holder]

Hello kanika,

your multiplication and your python syntax for multiplication are
wrong, it must be:
alter_state 1, 3m8v_a, (x,y,z)=((-0.5*x+0.866025*y), (0.866025*x+0.5*y),-z)

For REMARK 350, check these scripts:
http://www.pymolwiki.org/index.php/BiologicalUnit
http://www.pymolwiki.org/index.php/BiologicalUnit/Quat

Cheers,
  Thomas

On Wed, Mar 23, 2011 at 12:09 PM, kanika sharma  wrote:
> for protein 3m8v, the alter_state command I am using for REM350 is:
> create 3m8v_a, 3m8v
> alter_state 1, 3m8v_a, (x,y,z)=((-0.5+0.866025)x+(0.866025+0.5)y,-z)
> But it gives error at x saying invalid syntax..According to
> BIOMT transformations i think this should be the correct equation..
> I shall be thankful if anyone can let me know the bug..
> PDB file shot is:
> 3M8V
> REMARK 350 BIOMOLECULE: 1
>
> REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
>
> REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
>
> REMARK 350 SOFTWARE USED: PISA
>
> REMARK 350 TOTAL BURIED SURFACE AREA: 3410 ANGSTROM**2
>
> REMARK 350 SURFACE AREA OF THE COMPLEX: 12290 ANGSTROM**2
>
> REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
>
> REMARK 350   BIOMT1   1  1.00  0.00  0.00        0.0
>
> REMARK 350   BIOMT2   1  0.00  1.00  0.00        0.0
>
> REMARK 350   BIOMT3   1  0.00  0.00  1.00        0.0
>
> REMARK 350   BIOMT1   2 -0.50  0.866025  0.00        0.0
>
> REMARK 350   BIOMT2   2  0.866025  0.50  0.00        0.0
>
> REMARK 350   BIOMT3   2  0.00  0.00 -1.00        0.0
>
>
>
> Regards,
> kanika


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Spemannstr. 35
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Re: [PyMOL] alter_state

[kanika sharma]

I get the mistake..
Thanks all..
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Re: [PyMOL] How to get pymol 1.4

[lists]

a) you're mistaken, Warren's incentive builds had extra features.  Also, Warren 
had announced pretty clear plans of adding more features to the incentive 
builds and not releasing them open source for several years
b) if you've been following the list, Jason has stated that many of the 1.4 
features are on their way to the open source repository.

Sure, I am of the type that wishes all features were open source and that Jason 
did all development directly against a repository we could all see, but I think 
he's done a good job communicating the way development is happening to the list 
and schrodinger's model for the incentive builds seems to be hardly different 
from what Warren had started doing.

-David

On Mar 23, 2011, at 6:33 AM, Abhinav Verma  wrote:

> And why would that be? I thought that pymol is open source and till Warren 
> was there all updates were available in the open source domain and incentive 
> builds were limited to windows executable and involving support!! 
> 
> 
> 
> 
> On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij  
> wrote:
> > Is the 1.4 version restricted to incentive downloads only??
> 
> Yes
> 
> >
> > Thanks,
> > --
> > Enable your software for Intel(R) Active Management Technology to meet the
> > growing manageability and security demands of your customers. Businesses
> > are taking advantage of Intel(R) vPro (TM) technology - will your software
> > be a part of the solution? Download the Intel(R) Manageability Checker
> > today! 
> > http://p.sf.net/sfu/intel-dev2devmar___
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> 
> 
> --
> Enable your software for Intel(R) Active Management Technology to meet the
> growing manageability and security demands of your customers. Businesses
> are taking advantage of Intel(R) vPro (TM) technology - will your software 
> be a part of the solution? Download the Intel(R) Manageability Checker 
> today! http://p.sf.net/sfu/intel-dev2devmar
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Re: [PyMOL] How to get pymol 1.4

[Abhinav Verma]

And why would that be? I thought that pymol is open source and till Warren
was there all updates were available in the open source domain and incentive
builds were limited to windows executable and involving support!!




On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij
wrote:

> > Is the 1.4 version restricted to incentive downloads only??
>
> Yes
>
> >
> > Thanks,
> >
> --
> > Enable your software for Intel(R) Active Management Technology to meet
> the
> > growing manageability and security demands of your customers. Businesses
> > are taking advantage of Intel(R) vPro (TM) technology - will your
> software
> > be a part of the solution? Download the Intel(R) Manageability Checker
> > today!
> http://p.sf.net/sfu/intel-dev2devmar___
> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
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[PyMOL] How to get pymol 1.4

[Abhinav Verma]

How do I download pymol 1.4 from the svn.

I used
svn co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol

but i still got the 1.3 version.

Is the 1.4 version restricted to incentive downloads only??

Thanks,
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