Re: [PyMOL] ContactsNCONT script error

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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)

Re: [PyMOL] ContactsNCONT script error

PyMOL is an OpenGL based molecular visualization system

Re: [PyMOL] ContactsNCONT script error