pymol-users

Re: [PyMOL] APBS plugin woes

[Michael L. <mgl...@gm...>]

Can you go to the "Program Locations" tab and find out which version of APBS
you're using? There's a problem with the one in
/Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.

I've added instructions for fixing this problem to
http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
top of the page, under "APBS Plugin FAQ". Could you try them out and see if
they work for you?

Thanks,

-Michael

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dga...@ni...>wrote:

> I download and install macpymol-1_2r2.tgz.
>
> I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
> up.
>
> Load a pdb file after removing HETATM lines.
>
> Open APBS Tools and set grid:
> Log:
> Maximum number of grid points exceeded.  Old grid dimensions were
> [129, 97, 129]
> Fine grid points rounded down from [117, 87, 117]
> New grid dimensions are [97, 65, 97]
>  APBS Tools: coarse grid: (76.908,61.259,77.489)
>  APBS Tools: fine grid: (65.240,56.035,65.582)
>  APBS Tools: center: (-22.620,-1.106,-3.967)
>  APBS Tools: fine grid points (97,65,97)
>
> Click "Run APBS", see hydrogens appear, see residues being selected
> and unselected, then the display says:
>
> Log:
> ObjectMapLoadDXFile-Error: Unable to open file!
> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>
>
> Help?
> PowerBook, PPC, 10.4.11
>
> Dave
>
>
> --
> David N. Garboczi, PhD
> Phone: 301-496-4773
> Head, Structural Biology Section (SBS)
> Research Technologies Branch (RTB)
> National Institute of Allergy and Infectious Diseases (NIAID)
> National Institutes of Health (NIH)
> Twinbrook 2/Room 110
> 12441 Parklawn Drive
> Rockville, Maryland 20852-1742
> Fax:    301-402-0284
> Email: dga...@ni...
>
>
> The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be
> used by anyone who is not the original intended recipient.  If you have
> received this e-mail in error please inform the sender and delete it
> from your mailbox or any other storage devices.  The National Institute
> of Allergy and Infectious Diseases (NIAID) shall not accept liability
> for any statement made that are the sender's own and not expressly made
> on behalf of the NIAID by one of its representatives.
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> 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)

Re: [PyMOL] APBS plugin woes

[Michael L. <mgl...@gm...>]

We solved the problem this afternoon. The version of APBS that comes with
PyMOL does not work on Tiger (10.4). Neither does the universal binary of
apbs-1.2.1b available on sourceforge.

An older version of apbs (0.5) worked. We are in the middle of installing
APBS via MacPorts, as it seems like that should work too.

I've added some troubleshooting instructions to both

http://pymolwiki.org/index.php/APBS
and
http://pymolwiki.org/index.php/User:Mglerner

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dga...@ni...>wrote:

> I download and install macpymol-1_2r2.tgz.
>
> I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
> up.
>
> Load a pdb file after removing HETATM lines.
>
> Open APBS Tools and set grid:
> Log:
> Maximum number of grid points exceeded.  Old grid dimensions were
> [129, 97, 129]
> Fine grid points rounded down from [117, 87, 117]
> New grid dimensions are [97, 65, 97]
>  APBS Tools: coarse grid: (76.908,61.259,77.489)
>  APBS Tools: fine grid: (65.240,56.035,65.582)
>  APBS Tools: center: (-22.620,-1.106,-3.967)
>  APBS Tools: fine grid points (97,65,97)
>
> Click "Run APBS", see hydrogens appear, see residues being selected
> and unselected, then the display says:
>
> Log:
> ObjectMapLoadDXFile-Error: Unable to open file!
> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>
>
> Help?
> PowerBook, PPC, 10.4.11
>
> Dave
>
>
> --
> David N. Garboczi, PhD
> Phone: 301-496-4773
> Head, Structural Biology Section (SBS)
> Research Technologies Branch (RTB)
> National Institute of Allergy and Infectious Diseases (NIAID)
> National Institutes of Health (NIH)
> Twinbrook 2/Room 110
> 12441 Parklawn Drive
> Rockville, Maryland 20852-1742
> Fax:    301-402-0284
> Email: dga...@ni...
>
>
> The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be
> used by anyone who is not the original intended recipient.  If you have
> received this e-mail in error please inform the sender and delete it
> from your mailbox or any other storage devices.  The National Institute
> of Allergy and Infectious Diseases (NIAID) shall not accept liability
> for any statement made that are the sender's own and not expressly made
> on behalf of the NIAID by one of its representatives.
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> 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)

Re: [PyMOL] APBS plugin woes

[Jason V. <jas...@gm...>]

FYI, that worked for me.  I just copied the binary to /usr/local/lib.

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner <mgl...@gm...> wrote:
> Can you go to the "Program Locations" tab and find out which version of APBS
> you're using? There's a problem with the one in
> /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.
>
> I've added instructions for fixing this problem to
> http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
> top of the page, under "APBS Plugin FAQ". Could you try them out and see if
> they work for you?
>
> Thanks,
>
> -Michael
>
> On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi <dga...@ni...>
> wrote:
>>
>> I download and install macpymol-1_2r2.tgz.
>>
>> I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
>> up.
>>
>> Load a pdb file after removing HETATM lines.
>>
>> Open APBS Tools and set grid:
>> Log:
>> Maximum number of grid points exceeded.  Old grid dimensions were
>> [129, 97, 129]
>> Fine grid points rounded down from [117, 87, 117]
>> New grid dimensions are [97, 65, 97]
>>  APBS Tools: coarse grid: (76.908,61.259,77.489)
>>  APBS Tools: fine grid: (65.240,56.035,65.582)
>>  APBS Tools: center: (-22.620,-1.106,-3.967)
>>  APBS Tools: fine grid points (97,65,97)
>>
>> Click "Run APBS", see hydrogens appear, see residues being selected
>> and unselected, then the display says:
>>
>> Log:
>> ObjectMapLoadDXFile-Error: Unable to open file!
>> ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
>>
>>
>> Help?
>> PowerBook, PPC, 10.4.11
>>
>> Dave
>>
>>
>> --
>> David N. Garboczi, PhD
>> Phone: 301-496-4773
>> Head, Structural Biology Section (SBS)
>> Research Technologies Branch (RTB)
>> National Institute of Allergy and Infectious Diseases (NIAID)
>> National Institutes of Health (NIH)
>> Twinbrook 2/Room 110
>> 12441 Parklawn Drive
>> Rockville, Maryland 20852-1742
>> Fax:    301-402-0284
>> Email: dga...@ni...
>>
>>
>> The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be
>> used by anyone who is not the original intended recipient.  If you have
>> received this e-mail in error please inform the sender and delete it
>> from your mailbox or any other storage devices.  The National Institute
>> of Allergy and Infectious Diseases (NIAID) shall not accept liability
>> for any statement made that are the sender's own and not expressly made
>> on behalf of the NIAID by one of its representatives.
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> 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)
>
> ------------------------------------------------------------------------------
> Join us December 9, 2009 for the Red Hat Virtual Experience,
> a free event focused on virtualization and cloud computing.
> Attend in-depth sessions from your desk. Your couch. Anywhere.
> http://p.sf.net/sfu/redhat-sfdev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>