pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Sena,

PyMOL does not yet have such functionality.  The built in rotamer
libraries are only for amino acids not nucleic.

Cheers,

-- Jason

On Fri, May 27, 2011 at 4:27 PM, Rajagopalan, Senapathy
<SRa...@tm...> wrote:
> Hi Everyone,
> Sorry if this is a dumb question, but can you use the mutagenesis tool
> mutate a DNA base…say make a A->G mutation? Coot can do it and I can see
> pymol does it easily for protein residues, but what about for DNA/RNA?
> Thanks
> Sena
>
> Methodist. Leading Medicine.
>
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> With the market-leading solution for virtual backup and recovery,
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Everyone,

Sorry if this is a dumb question, but can you use the mutagenesis tool mutate a DNA base…say make a A->G mutation? Coot can do it and I can see pymol does it easily for protein residues, but what about for DNA/RNA?

Thanks
Sena

Methodist. Leading Medicine. Recognized by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at  methodisthealth.com Follow us at  twitter.com/MethodistHosp and  www.facebook.com/MethodistHospital  ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

Hi all,

Thanks to Michael and Jason for their suggestions. I apologise for starting a
new thread; I had inadvertently deleted the email conversation.

I looked into hollow, but since the binding pocket is large and very
irregularly shaped, it seemed as though it would be tricky to include the
whole binding pocket without also including areas I didn't want, such as nearby
cavities and pockets. Also, the surface carving was slow because my system is
very large (the protein is roughly 35,000 atoms). So in the end I devised some
aliases and constructed the binding pocket's surface piecemeal. Painstaking,
but it got the job done :-)

Thanks again,
Ben
-- 
For greater security, I support S/MIME encryption.

Dear Michael,

Thank you for updating the script.
Now it does not give any error, however, I have a new issue.

The logfile from NCONT looks like this:


 LIST OF CONTACTS :
 ==================


   source atoms     target atoms       distance angle      symmetry operation

 Lys    24A  CA  Asp   263D  CG   ...  4.94    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Lys    24A  C   Asp   263D  O    ...  4.98    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CB   ...  4.60    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CG   ...  5.00    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Lys    24A  CB  Asp   263D  CB   ...  4.21    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  OD1  ...  4.24    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CG   ...  3.87    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  OD2  ...  3.78    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Lys    24A  CG  Asp   263D  OD1  ...  4.85    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CG   ...  4.60    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  OD2  ...  4.21    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Lys    24A  CD  Asp   263D  OD1  ...  4.64    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CG   ...  4.29    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  OD2  ...  3.55    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Lys    24A  CE  Asp   263D  OD1  ...  3.92    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CG   ...  3.90    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  OD2  ...  3.25    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Lys    24A  NZ  Asp   263D  OD1  ...  4.97 *  [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  CG   ...  4.95    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  OD2  ...  4.13 *  [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
 Ala    25A  N   Asp   263D  CA   ...  4.92    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  C    ...  4.98    [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
                 Asp   263D  O    ...  4.22 *  [   -1B   ]   3: -X,  Y+1/2,  -Z+1/2
  

......ETC.......


Therefore, I do not know how to define in PYMOL  the protein in the asymmetric unit (selName1) and the symmetry related molecule (selName2).
As it is a long list of contacts and I would like to compare many structures in several crystal forms, manual selection is not really feasible.

Thank you in advance for your help,

Ivan Campeotto




________________________________________
From: Michael Lerner [mgl...@gm...]
Sent: 26 May 2011 14:50
To: Campeotto, Ivan
Cc: Tsjerk Wassenaar; pym...@li...
Subject: Re: [PyMOL] ContactsNCONT script error

The webpage is now indented correctly.

Oddly enough, it was only mis-indented for top-level lines (def, def, cmd.extend). Everything else was consistent.

On Thu, May 26, 2011 at 5:34 AM, Campeotto, Ivan <i.c...@im...<mailto:i.c...@im...>> wrote:
Dear Tsjerk and Michael,

Thank you for your quick reply.
The script is now working.

Thank you again,

Ivan Campeotto

________________________________________
From: Tsjerk Wassenaar [ts...@gm...<mailto:ts...@gm...>]
Sent: 26 May 2011 07:18
To: Michael Lerner
Cc: Campeotto, Ivan; pym...@li...<mailto:pym...@li...>
Subject: Re: [PyMOL] ContactsNCONT script error

Hi,

The first line is okay, but the rest seems to have an extra space,
indeed. You can remove it from the script using:

sed -i 's/^ //' script.py

Hope it helps,

Tsjerk

On Thu, May 26, 2011 at 4:33 AM, Michael Lerner <mgl...@gm...<mailto:mgl...@gm...>> wrote:
> Hi Ivan,
> There's definitely a bug in that script. It looks like most of the file has
> one extra space of indentation. I don't feel comfortable changing it at the
> moment, as I'm not on a machine that has ccp4, but perhaps someone else can
> fix and test it. If not, I'll fix it tomorrow.
> Cheers,
> -Michael
> On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan
> <i.c...@im...<mailto:i.c...@im...>> wrote:
>>
>> Dear All,
>>
>>
>> I would like to compare the intermolecular crystal contacts in seven
>> crystal forms of the same enzyme.
>>  I produced a list of contacts for each crystal form using the program
>>  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki
>> (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a
>> lot of time.
>>  Unfortunately, when I run the ContactsNCONT script,  I always have the
>> following message with different PCs running  different OS (Windows, RedHat
>> or Mac):
>>
>> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
>> line 338, in parse
>>    parsing.run_file(path,self.pymol_names,self.pymol_names)
>>  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py",
>> line 455, in run_file
>>    execfile(file,global_ns,local_ns)
>>  File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3
>>     def parseContacts( f ):
>>    ^
>>  IndentationError: unexpected indent
>>
>>
>> Any suggestion will be more than appreciated.
>>
>>
>> Thank you in advance,
>>
>> Regards
>>
>> Ivan Campeotto
>> Centre for Molecular Microbiology and Infection
>> Imperial College London
>>
>>
>> ------------------------------------------------------------------------------
>> vRanger cuts backup time in half-while increasing security.
>> With the market-leading solution for virtual backup and recovery,
>> you get blazing-fast, flexible, and affordable data protection.
>> Download your free trial now.
>> http://p.sf.net/sfu/quest-d2dcopy1
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands



--
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

The webpage is now indented correctly.

Oddly enough, it was only mis-indented for top-level lines (def, def,
cmd.extend). Everything else was consistent.

On Thu, May 26, 2011 at 5:34 AM, Campeotto, Ivan <i.c...@im...
> wrote:

> Dear Tsjerk and Michael,
>
> Thank you for your quick reply.
> The script is now working.
>
> Thank you again,
>
> Ivan Campeotto
>
> ________________________________________
> From: Tsjerk Wassenaar [ts...@gm...]
> Sent: 26 May 2011 07:18
> To: Michael Lerner
> Cc: Campeotto, Ivan; pym...@li...
> Subject: Re: [PyMOL] ContactsNCONT script error
>
> Hi,
>
> The first line is okay, but the rest seems to have an extra space,
> indeed. You can remove it from the script using:
>
> sed -i 's/^ //' script.py
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, May 26, 2011 at 4:33 AM, Michael Lerner <mgl...@gm...>
> wrote:
> > Hi Ivan,
> > There's definitely a bug in that script. It looks like most of the file
> has
> > one extra space of indentation. I don't feel comfortable changing it at
> the
> > moment, as I'm not on a machine that has ccp4, but perhaps someone else
> can
> > fix and test it. If not, I'll fix it tomorrow.
> > Cheers,
> > -Michael
> > On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan
> > <i.c...@im...> wrote:
> >>
> >> Dear All,
> >>
> >>
> >> I would like to compare the intermolecular crystal contacts in seven
> >> crystal forms of the same enzyme.
> >>  I produced a list of contacts for each crystal form using the program
> >>  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki
> >> (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me
> a
> >> lot of time.
> >>  Unfortunately, when I run the ContactsNCONT script,  I always have the
> >> following message with different PCs running  different OS (Windows,
> RedHat
> >> or Mac):
> >>
> >> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
> >> line 338, in parse
> >>    parsing.run_file(path,self.pymol_names,self.pymol_names)
> >>  File "C:\Program Files\DeLano
> Scientific\PyMOL/modules\pymol\parsing.py",
> >> line 455, in run_file
> >>    execfile(file,global_ns,local_ns)
> >>  File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3
> >>     def parseContacts( f ):
> >>    ^
> >>  IndentationError: unexpected indent
> >>
> >>
> >> Any suggestion will be more than appreciated.
> >>
> >>
> >> Thank you in advance,
> >>
> >> Regards
> >>
> >> Ivan Campeotto
> >> Centre for Molecular Microbiology and Infection
> >> Imperial College London
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> vRanger cuts backup time in half-while increasing security.
> >> With the market-leading solution for virtual backup and recovery,
> >> you get blazing-fast, flexible, and affordable data protection.
> >> Download your free trial now.
> >> http://p.sf.net/sfu/quest-d2dcopy1
> >> _______________________________________________
> >> PyMOL-users mailing list (PyM...@li...)
> >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >> Archives: http://www.mail-archive.com/pym...@li...
> >
> >
> >
> > --
> > Michael Lerner, Ph.D.
> > IRTA Postdoctoral Fellow
> > Laboratory of Computational Biology NIH/NHLBI
> > 5635 Fishers Lane, Room T909, MSC 9314
> > Rockville, MD 20852 (UPS/FedEx/Reality)
> > Bethesda MD 20892-9314 (USPS)
> >
> >
> ------------------------------------------------------------------------------
> > vRanger cuts backup time in half-while increasing security.
> > With the market-leading solution for virtual backup and recovery,
> > you get blazing-fast, flexible, and affordable data protection.
> > Download your free trial now.
> > http://p.sf.net/sfu/quest-d2dcopy1
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Dear Tsjerk and Michael,

Thank you for your quick reply.
The script is now working.

Thank you again,

Ivan Campeotto

________________________________________
From: Tsjerk Wassenaar [ts...@gm...]
Sent: 26 May 2011 07:18
To: Michael Lerner
Cc: Campeotto, Ivan; pym...@li...
Subject: Re: [PyMOL] ContactsNCONT script error

Hi,

The first line is okay, but the rest seems to have an extra space,
indeed. You can remove it from the script using:

sed -i 's/^ //' script.py

Hope it helps,

Tsjerk

On Thu, May 26, 2011 at 4:33 AM, Michael Lerner <mgl...@gm...> wrote:
> Hi Ivan,
> There's definitely a bug in that script. It looks like most of the file has
> one extra space of indentation. I don't feel comfortable changing it at the
> moment, as I'm not on a machine that has ccp4, but perhaps someone else can
> fix and test it. If not, I'll fix it tomorrow.
> Cheers,
> -Michael
> On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan
> <i.c...@im...> wrote:
>>
>> Dear All,
>>
>>
>> I would like to compare the intermolecular crystal contacts in seven
>> crystal forms of the same enzyme.
>>  I produced a list of contacts for each crystal form using the program
>>  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki
>> (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a
>> lot of time.
>>  Unfortunately, when I run the ContactsNCONT script,  I always have the
>> following message with different PCs running  different OS (Windows, RedHat
>> or Mac):
>>
>> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
>> line 338, in parse
>>    parsing.run_file(path,self.pymol_names,self.pymol_names)
>>  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py",
>> line 455, in run_file
>>    execfile(file,global_ns,local_ns)
>>  File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3
>>     def parseContacts( f ):
>>    ^
>>  IndentationError: unexpected indent
>>
>>
>> Any suggestion will be more than appreciated.
>>
>>
>> Thank you in advance,
>>
>> Regards
>>
>> Ivan Campeotto
>> Centre for Molecular Microbiology and Infection
>> Imperial College London
>>
>>
>> ------------------------------------------------------------------------------
>> vRanger cuts backup time in half-while increasing security.
>> With the market-leading solution for virtual backup and recovery,
>> you get blazing-fast, flexible, and affordable data protection.
>> Download your free trial now.
>> http://p.sf.net/sfu/quest-d2dcopy1
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi,

The first line is okay, but the rest seems to have an extra space,
indeed. You can remove it from the script using:

sed -i 's/^ //' script.py

Hope it helps,

Tsjerk

On Thu, May 26, 2011 at 4:33 AM, Michael Lerner <mgl...@gm...> wrote:
> Hi Ivan,
> There's definitely a bug in that script. It looks like most of the file has
> one extra space of indentation. I don't feel comfortable changing it at the
> moment, as I'm not on a machine that has ccp4, but perhaps someone else can
> fix and test it. If not, I'll fix it tomorrow.
> Cheers,
> -Michael
> On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan
> <i.c...@im...> wrote:
>>
>> Dear All,
>>
>>
>> I would like to compare the intermolecular crystal contacts in seven
>> crystal forms of the same enzyme.
>>  I produced a list of contacts for each crystal form using the program
>>  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki
>> (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a
>> lot of time.
>>  Unfortunately, when I run the ContactsNCONT script,  I always have the
>> following message with different PCs running  different OS (Windows, RedHat
>> or Mac):
>>
>> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
>> line 338, in parse
>>    parsing.run_file(path,self.pymol_names,self.pymol_names)
>>  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py",
>> line 455, in run_file
>>    execfile(file,global_ns,local_ns)
>>  File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3
>>     def parseContacts( f ):
>>    ^
>>  IndentationError: unexpected indent
>>
>>
>> Any suggestion will be more than appreciated.
>>
>>
>> Thank you in advance,
>>
>> Regards
>>
>> Ivan Campeotto
>> Centre for Molecular Microbiology and Infection
>> Imperial College London
>>
>>
>> ------------------------------------------------------------------------------
>> vRanger cuts backup time in half-while increasing security.
>> With the market-leading solution for virtual backup and recovery,
>> you get blazing-fast, flexible, and affordable data protection.
>> Download your free trial now.
>> http://p.sf.net/sfu/quest-d2dcopy1
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Hi Ivan,

There's definitely a bug in that script. It looks like most of the file has
one extra space of indentation. I don't feel comfortable changing it at the
moment, as I'm not on a machine that has ccp4, but perhaps someone else can
fix and test it. If not, I'll fix it tomorrow.

Cheers,

-Michael

On Wed, May 25, 2011 at 7:35 PM, Campeotto, Ivan <i.c...@im...
> wrote:

> Dear All,
>
>
> I would like to compare the intermolecular crystal contacts in seven
> crystal forms of the same enzyme.
>  I produced a list of contacts for each crystal form using the program
>  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki (
> http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a
> lot of time.
>  Unfortunately, when I run the ContactsNCONT script,  I always have the
> following message with different PCs running  different OS (Windows, RedHat
> or Mac):
>
> File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py",
> line 338, in parse
>    parsing.run_file(path,self.pymol_names,self.pymol_names)
>  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py",
> line 455, in run_file
>    execfile(file,global_ns,local_ns)
>  File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3
>     def parseContacts( f ):
>    ^
>  IndentationError: unexpected indent
>
>
> Any suggestion will be more than appreciated.
>
>
> Thank you in advance,
>
> Regards
>
> Ivan Campeotto
> Centre for Molecular Microbiology and Infection
> Imperial College London
>
>
> ------------------------------------------------------------------------------
> vRanger cuts backup time in half-while increasing security.
> With the market-leading solution for virtual backup and recovery,
> you get blazing-fast, flexible, and affordable data protection.
> Download your free trial now.
> http://p.sf.net/sfu/quest-d2dcopy1
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Dear All,


I would like to compare the intermolecular crystal contacts in seven crystal forms of the same enzyme.
 I produced a list of contacts for each crystal form using the program  NCONT from CCP4 and I  found the ContactsNCONT script in the PyMOL Wiki (http://www.pymolwiki.org/index.php/ContactsNCONT), which would save me a lot of time.
 Unfortunately, when I run the ContactsNCONT script,  I always have the following message with different PCs running  different OS (Windows, RedHat or Mac):

File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 338, in parse
    parsing.run_file(path,self.pymol_names,self.pymol_names)
  File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", line 455, in run_file
    execfile(file,global_ns,local_ns)
  File "C:/Documents and Settings/Ivan/Desktop/ContactsNCONT.py", line 3
     def parseContacts( f ):
    ^
 IndentationError: unexpected indent


Any suggestion will be more than appreciated.


Thank you in advance,

Regards

Ivan Campeotto
Centre for Molecular Microbiology and Infection
Imperial College London

Greetings,

I'm happy to announce that JyMOL v1.1 has been released.  JyMOL is a
Java-based component for embedding PyMOL graphics into
web browsers and standalone Java applications.

Even though JyMOL is not open-source, we provide no-cost access for
academic researchers.  To get JyMOL for your academic project, please
read the directions for requesting a license at
http://pymol.org/buy#jymol and then submit a request.  Current JyMOL
license holders may download the new version from http://pymol.org/dsc/ip.

Here are some of the new features for this release:
 * -- 3D Stereo support (even inside the browser!)
 * -- over a dozen new functions
 * -- improved documentation and demos
 * -- updated third party components

Cheers,

-- Jason

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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Vivek,

In Editing Mode, just click the vertex atom and then move the mobile
end of the angle by pressing shift while dragging with the left mouse
button.

Cheers,

-- Jason

On Mon, May 23, 2011 at 6:01 PM, Vivek Ranjan <vr...@gm...> wrote:
> Hello,
> I have an xyz file with coordinates of atoms in a molecule. I want to change
> some of the bond angles ? I wonder if its doable in pymol ? I can easily
> change dihedral, but I could not figure out the same for the angles ? Please
> let me know.
>
> --
> Thank you and Regards,
>
> Vivek Ranjan
>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hello,

I have an xyz file with coordinates of atoms in a molecule. I want to change
some of the bond angles ? I wonder if its doable in pymol ? I can easily
change dihedral, but I could not figure out the same for the angles ? Please
let me know.

-- 
Thank you and Regards,

Vivek Ranjan

Greetings,

I am delighted to announce that Schrӧdinger is offering a second PyMOL
Open-Source Fellowship position.  The Fellowship is awarded by
Schrӧdinger to an outstanding member of the PyMOL open-source
community so that s/he can develop free resources to help scientific
progress and the community as a whole.

With this fellowship, the recipient will have the autonomy to
participate in a PyMOL project or an open-source-related software or
research activity that the recipient believes is most interesting and
will have the greatest impact. Recipients are also expected to help
maintain the PyMOLWiki and support the open-source community via the
pymol-users mailing list.  Furthermore, all content created under
these fellowships will be open-source and freely available.

We will be releasing detailed fellowship information and application
instructions soon.  If you're thinking of applying, you might want to
start planning a project that will benefit PyMOL and the open-source
project in general.

Cheers,

-- Jason

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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Jonathan,

>   I am trying to model the flexing about the elbow angle
>   of 2 Fabs, that are in close proximity
>   to each other on a viral capsid.

This sounds pretty cool.  Any chance you could share the final movie with us?


>   i have created the 2 nmr like pdbs (that contain the morphs)
>   , that have 30 sets of coordinates in each of them.  The models
>   go from model 1, angle x to model 30 angle y.
>
>   i would like to animate both fabs simultaneously
>   but stagger the looping so that
>
>   pdb1 the states go from 1 to 30, whilst at the same time
>   for pdb2 the states go from 30 to 1.

This is possible from the movie timeline (right-click store with
state, for a given object) or the command API using the 'mview'
command:

# make a blank movie over 110 frames
mset 1x110

# goto frame ten and set obj1 and ob2
frame 10
mview store, object=obj1, state=1
mview store, object=obj2, state=100

# goto frame 110 and set obj1 and obj2 in their final states
# pymol will interpolate everything else for you
frame 110
mview store, object=obj1, state=100
mview store, object=obj2, state=1

This creates a 110 frame movie where in frame 10, object one
transitions from state 1 to state 100 over 100 frames.  Likewise,
object 2 transitions from state 100 down to state 1 over 100 frames.

See also,
  * -- http://www.pymolwiki.org/index.php/MovieSchool

Hope this helps.

Cheers,

-- Jason

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

(e) Jas...@sc...
(o) +1 (603) 374-7120

  apologies for the incoherence of the description
  but its a reflection of my mind at the moment......

   I am trying to model the flexing about the elbow angle 
   of 2 Fabs, that are in close proximity
   to each other on a viral capsid.

   i have created the 2 nmr like pdbs (that contain the morphs)
   , that have 30 sets of coordinates in each of them.  The models 
   go from model 1, angle x to model 30 angle y.

   i would like to animate both fabs simultaneously
   but stagger the looping so that 

   pdb1 the states go from 1 to 30, whilst at the same time
   for pdb2 the states go from 30 to 1.

   ie  i cant see how to for each frame assign a particular state from
    pdb1 and a different state from pdb2.

    the mset command doesnt seem to allow you to select for objects.

   many thanks
   jon

  


   
Dr. Jonathan M. Grimes, 
NDM Senior Reseach Fellow
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK

Email: Jon...@st..., Web: www.strubi.ox.ac.uk 
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547       

Hi Ben,

Michael's advice is pretty solid--I would start there.

Having said that, PyMOL does have a few tricks to allow you to find
and highlight such pockets, but it could get tricky.

# fetch a protein with a buried ligand
fetch 1qkt, async=0

# pull out the ligand to its own object
extract ligand, org

# make a real selection
select lig, org

# set the selection
set surface_carve_selection, lig

# set the cutoff; hide surface >4.5 Ang from lig
set surface_carve_cutoff, 5.5

# let PyMOL consider surfacing everything
flag ignore, none

# show surface (using above constraints)
show surface

# hide the ligand surface
hide surface, lig

# set up the view/reps
set surface_color, 0x778899
set transparency, 0.5
orient org
zoom org, 5

set two_sided_lighting

rebuild

ray

See:
* -- http://www.pymolwiki.org/index.php/Surface_carve_selection
* -- http://www.pymolwiki.org/index.php/Surface_carve_cutoff

Hope this helps.

Cheers,

-- Jason



On Fri, May 20, 2011 at 7:38 PM, Michael Lerner <mgl...@gm...> wrote:
> The last time I tried to do something similar, I found HOLLOW
> (http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial
> for showing a binding site, rather than an interior cavity,
> here: http://hollow.sourceforge.net/binding.html .
> Cheers,
> -Michael
>
> On Fri, May 20, 2011 at 7:11 PM, Ben Roberts <be...@ro...> wrote:
>>
>> Hi list,
>>
>> I'm trying to use PyMOL to construct an image of the total contiguous
>> contact
>> surface that starts at a particular place on the surface of a protein,
>> without
>> all the visual distraction and clutter that comes from other regions of
>> the
>> protein surface (not to mention internal cavities).
>>
>> I started by rendering up the whole protein as "Contact surface" with
>> "Cavities and pockets only" shown. Unfortunately, this displays a large
>> number
>> of bubbles, some of which, despite being far away in space from the region
>> of
>> interest, manage to effectively obscure bits and pieces of it.
>>
>> So my next thought was to try removing the extraneous bits, however, I
>> can't
>> seem to select atoms in surface view; I have to display everything as
>> lines or
>> similar. Removing things that way gets very unwieldy, not least because of
>> all
>> the atoms that don't contribute anything to the surface but appear in
>> front
>> of, behind, or otherwise near to the atoms that do so.
>>
>> A third option I tried was to build the surface up, starting from the
>> known
>> points of interest, but this too is painstaking because of the need to
>> guess
>> where I should next expand the selection to in order to fill in the gaps.
>>
>> A remaining method of getting only the cavity of interest would, I guess,
>> be
>> to create a selection consisting only of those atoms that contribute
>> something
>> to the currently rendered surface (in this case, cavities and voids). I
>> could
>> then render those as spheres or something and hide unwanted contributors.
>> Is
>> there a way of specifying such a selection? Alternatively, is there some
>> other
>> smart way to achieve what I want (and by smart, I mean a way that isn't
>> time-
>> consuming and unusually error-prone)? I've already tried Googling, to no
>> avail; I got, mostly, instructions about how to display surfaces in
>> general.
>>
>> I should mention that I'm using a recent version of MacPyMol, on Mac OS X
>> 10.6.7.
>>
>> Any tips are welcome. Thanks!
>>
>> Best regards,
>> Ben
>> --
>> For greater security, I support S/MIME encryption.
>>
>>
>>
>> ------------------------------------------------------------------------------
>> What Every C/C++ and Fortran developer Should Know!
>> Read this article and learn how Intel has extended the reach of its
>> next-generation tools to help Windows* and Linux* C/C++ and Fortran
>> developers boost performance applications - including clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>
>
>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

The last time I tried to do something similar, I found HOLLOW (
http://hollow.sourceforge.net/) to be very useful. There's a nice tutorial
for showing a binding site, rather than an interior cavity, here:
http://hollow.sourceforge.net/binding.html .

Cheers,

-Michael

On Fri, May 20, 2011 at 7:11 PM, Ben Roberts <be...@ro...> wrote:

> Hi list,
>
> I'm trying to use PyMOL to construct an image of the total contiguous
> contact
> surface that starts at a particular place on the surface of a protein,
> without
> all the visual distraction and clutter that comes from other regions of the
> protein surface (not to mention internal cavities).
>
> I started by rendering up the whole protein as "Contact surface" with
> "Cavities and pockets only" shown. Unfortunately, this displays a large
> number
> of bubbles, some of which, despite being far away in space from the region
> of
> interest, manage to effectively obscure bits and pieces of it.
>
> So my next thought was to try removing the extraneous bits, however, I
> can't
> seem to select atoms in surface view; I have to display everything as lines
> or
> similar. Removing things that way gets very unwieldy, not least because of
> all
> the atoms that don't contribute anything to the surface but appear in front
> of, behind, or otherwise near to the atoms that do so.
>
> A third option I tried was to build the surface up, starting from the known
> points of interest, but this too is painstaking because of the need to
> guess
> where I should next expand the selection to in order to fill in the gaps.
>
> A remaining method of getting only the cavity of interest would, I guess,
> be
> to create a selection consisting only of those atoms that contribute
> something
> to the currently rendered surface (in this case, cavities and voids). I
> could
> then render those as spheres or something and hide unwanted contributors.
> Is
> there a way of specifying such a selection? Alternatively, is there some
> other
> smart way to achieve what I want (and by smart, I mean a way that isn't
> time-
> consuming and unusually error-prone)? I've already tried Googling, to no
> avail; I got, mostly, instructions about how to display surfaces in
> general.
>
> I should mention that I'm using a recent version of MacPyMol, on Mac OS X
> 10.6.7.
>
> Any tips are welcome. Thanks!
>
> Best regards,
> Ben
> --
> For greater security, I support S/MIME encryption.
>
>
>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)

Hi list,

I'm trying to use PyMOL to construct an image of the total contiguous contact
surface that starts at a particular place on the surface of a protein, without
all the visual distraction and clutter that comes from other regions of the
protein surface (not to mention internal cavities).

I started by rendering up the whole protein as "Contact surface" with
"Cavities and pockets only" shown. Unfortunately, this displays a large number
of bubbles, some of which, despite being far away in space from the region of
interest, manage to effectively obscure bits and pieces of it.

So my next thought was to try removing the extraneous bits, however, I can't
seem to select atoms in surface view; I have to display everything as lines or
similar. Removing things that way gets very unwieldy, not least because of all
the atoms that don't contribute anything to the surface but appear in front
of, behind, or otherwise near to the atoms that do so.

A third option I tried was to build the surface up, starting from the known
points of interest, but this too is painstaking because of the need to guess
where I should next expand the selection to in order to fill in the gaps.

A remaining method of getting only the cavity of interest would, I guess, be
to create a selection consisting only of those atoms that contribute something
to the currently rendered surface (in this case, cavities and voids). I could
then render those as spheres or something and hide unwanted contributors. Is
there a way of specifying such a selection? Alternatively, is there some other
smart way to achieve what I want (and by smart, I mean a way that isn't time-
consuming and unusually error-prone)? I've already tried Googling, to no
avail; I got, mostly, instructions about how to display surfaces in general.

I should mention that I'm using a recent version of MacPyMol, on Mac OS X
10.6.7.

Any tips are welcome. Thanks!

Best regards,
Ben
-- 
For greater security, I support S/MIME encryption.

Hi Nick,

Thanks, I'll update the code.

Cheers,

-- Jason

On Fri, May 20, 2011 at 1:13 PM, Nicolas Bock <nic...@gm...> wrote:
> I realized that the "mdo" command can be used to change the
> stick_transparency setting.
>
> mdo 1: set_bond stick_transparency, 0, all
> mdo 100: set_bond stick_transparency, 0.8, all
>
> and so on. I noticed that the example section in the help text for the
> mdo command is incorrect. It states:
>
>> EXAMPLE
>>
>>     // Creates a single frame movie involving a rotation about X and Y
>>
>>     load test.pdb
>>     mset 1
>>     mdo 1, turn x,5; turn y,5;
>>     mplay
>
> however, it should read:
>
> mdo 1: turn x,5; turn y,5;
>
> nick
>
>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

Thanks.

On 05/20/11 11:13, Jason Vertrees wrote:
> Hi Nick,
> 
> This is something Robert Campbell alluded to a few days ago.  To get
> what you want, the "python block" and "mdo" are you friends:
> 
> # create an ala fragment and setup the view
> 
> frag ala
> as sticks
> orient
> 
> # 60-frame movie
> 
> mset 1x60
> 
> # start a Python block that fades out the fragment
> 
> python
> for x in range(60):
>   cmd.mdo(x, "set_bond stick_transparency, %f, ala" % (x/60.))
> python end
> 
> # play the movie
> 
> mplay
> 
> See:
> * -- http://www.pymolwiki.org/index.php/Mdo
> * -- http://www.pymolwiki.org/index.php/Python
> 
> Cheers,
> 
> -- Jason
> 
> 
> On Fri, May 20, 2011 at 12:54 PM, Nicolas Bock <nic...@gm...> wrote:
>> When I do the following
>>
>> hide all
>> show sticks, all
>> scene 001, store
>>
>> set_bond stick_transparency, 0.5, all
>> scene 002, store
>>
>> scene 001
>>
>> the stick_transparency setting is not restored. I was hoping I could use
>> scenes to slowly fade out a part of a molecule by adding several scenes
>> with increasing stick_transparency values.
>>
>> Thanks, nick
>>
>>
>> ------------------------------------------------------------------------------
>> What Every C/C++ and Fortran developer Should Know!
>> Read this article and learn how Intel has extended the reach of its
>> next-generation tools to help Windows* and Linux* C/C++ and Fortran
>> developers boost performance applications - including clusters.
>> http://p.sf.net/sfu/intel-dev2devmay
>> _______________________________________________
>> 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 Nick,

This is something Robert Campbell alluded to a few days ago.  To get
what you want, the "python block" and "mdo" are you friends:

# create an ala fragment and setup the view

frag ala
as sticks
orient

# 60-frame movie

mset 1x60

# start a Python block that fades out the fragment

python
for x in range(60):
  cmd.mdo(x, "set_bond stick_transparency, %f, ala" % (x/60.))
python end

# play the movie

mplay

See:
* -- http://www.pymolwiki.org/index.php/Mdo
* -- http://www.pymolwiki.org/index.php/Python

Cheers,

-- Jason


On Fri, May 20, 2011 at 12:54 PM, Nicolas Bock <nic...@gm...> wrote:
> When I do the following
>
> hide all
> show sticks, all
> scene 001, store
>
> set_bond stick_transparency, 0.5, all
> scene 002, store
>
> scene 001
>
> the stick_transparency setting is not restored. I was hoping I could use
> scenes to slowly fade out a part of a molecule by adding several scenes
> with increasing stick_transparency values.
>
> Thanks, nick
>
>
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

I realized that the "mdo" command can be used to change the
stick_transparency setting.

mdo 1: set_bond stick_transparency, 0, all
mdo 100: set_bond stick_transparency, 0.8, all

and so on. I noticed that the example section in the help text for the
mdo command is incorrect. It states:

> EXAMPLE
> 
>     // Creates a single frame movie involving a rotation about X and Y
> 
>     load test.pdb
>     mset 1
>     mdo 1, turn x,5; turn y,5;
>     mplay

however, it should read:

mdo 1: turn x,5; turn y,5;

nick

When I do the following

hide all
show sticks, all
scene 001, store

set_bond stick_transparency, 0.5, all
scene 002, store

scene 001

the stick_transparency setting is not restored. I was hoping I could use
scenes to slowly fade out a part of a molecule by adding several scenes
with increasing stick_transparency values.

Thanks, nick

Hi Carsten,

> thanks for the follow-up. Let us know when the issue is fixed.

The bug is now fixed.  I have pushed the changes to the open-source
project and can release an updated build for incentive supporters.

Cheers,

-- Jason

On Thu, May 19, 2011 at 12:20 PM, Schubert, Carsten [PRDUS]
<CSC...@it...> wrote:
> Hi Jason,
>
> thanks for the follow-up. Let us know when the issue is fixed.
>
> Cheers,
>
>        Carsten
>
>> -----Original Message-----
>> From: Jason Vertrees [mailto:jas...@sc...]
>> Sent: Thursday, May 19, 2011 12:11 PM
>> To: Schubert, Carsten [PRDUS]
>> Cc: pym...@li...; he...@sc...
>> Subject: Re: [PyMOL] New 16 char length restriction of object names in
>> menu?
>>
>> Hi Carsten,
>>
>> I'd like to follow up on this.  There is no character limit, but there
>> is a bug.  PyMOL is inappropriately clipping names in groups if the
>> internal GUI cuts off the end of the name.  The current workaround for
>> your sessions is to expand the internal_gui to show the names, and
>> then save your session.
>>
>> I'll look into fixing this ASAP.
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Thu, May 19, 2011 at 11:33 AM, Jason Vertrees
>> <jas...@sc...> wrote:
>> > Hi Carsten,
>> >
>> >> Has the length of the object name entry in the right hand menu been
>> >> restricted to 16 characters in v1.4.x? Prior to 1.4.x there seemed
>> to have
>> >> been no limit on the length of the entry.
>> >
>> > There is no such limit on the length of names.
>> >
>> >> For instance
>> >> cmd.load("reallylongmapnamehere",
>> >> format="ccp4",object="reallylongmapnamehere") would truncate the
>> display of
>> >> the object to "reallylongmapna". I suppose that would be fine for
>> some
>> >> applications, but in my case I am distributing sessions, which
>> contain
>> >> fairly long object names to be self-explanatory, so I am dependent
>> on this
>> >> feature to work. Could this be reverted back to unlimited or at
>> least
>> >> implement a setting controlling the length of the entry?
>> >
>> > You have a few options.
>> >
>> > If you want to hide the state-counter to get a few more characters on
>> > the line just "set state_counter_mode, 0".  Alternatively, you could
>> > just increase the internal_gui_width--eg
>> >
>> > set internal_gui_width, 300
>> >
>> > Cheers,
>> >
>> > -- Jason
>> >
>> > --
>> > Jason Vertrees, PhD
>> > PyMOL Product Manager
>> > Schrodinger, LLC
>> >
>> > (e) Jas...@sc...
>> > (o) +1 (603) 374-7120
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jas...@sc...
>> (o) +1 (603) 374-7120
>
>



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

(e) Jas...@sc...
(o) +1 (603) 374-7120

hi "pymol"

> > I always get a segmentation fault, when I click "help"->"about" to see the
> > version details of pymol. The respective entry in /var/log/messages is:
...
> Indeed on a few Linux distros, there is a crash when selecting Help >
> About.  We're trying to track down the cause.  The error happens in
> our pure Python code and the segfault happens in the libtcl8.5 shared
> library.

i compiled 1.4.1 from sources on freebsd-7.4 and 8.2 ... 
help->about works fine ... it also has tk/tcl-8.5.9

i didn't compile/install on centos/suse/slackware

let me know if you guys want me to try poking around with
those boxes

i tend to run "online updates" regularly, freebsd are updated daily

---

latest rasmol-2.7.2.1.1.13/jmol-11.8.24 also works nicely on
freebsd-7.4 .. 8.2 is little whacky

c ya
alvin
http://Linux-1U.net/BioChem