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Re: [PyMOL] ContactsNCONT script error
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From: Campeotto, I. <i.c...@im...> - 2011-05-26 14:22:44
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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
>>
>>
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>
>
>
> --
> 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)
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