This definitely seems like a bug… even when I change the chain IDs beforehand, coot is still changing all the chain IDs back to A and renumbering when I merge the molecules.
I can get around that by doing PDB manipulations elsewhere, but it used to work very well in coot.
Oliver.
On Mar 18, 2014, at 7:27 PM, Oliver Clarke <[log in to unmask]> wrote:
> Thanks Tim - yes, that is what I have been doing subsequently also
> On Mar 18, 2014, at 7:10 PM, Tim Gruene <[log in to unmask]> wrote:
> Thanks Tim - yes, that is what I have been doing subsequently. This seems to be different to Coot’s behavior in the past though, or am I misremembering?
>
> I seem to recall that in the past, when merging two chains of the same name, the chains would always be renamed to avoid renumbering issues - the current behavior is better in some situations, for sure, but not in all situations, I think.
>
> Also coot seems to be sometimes creating “dummy molecules” for want of a better word when I copy molecules - additional molecules that are present in the display manager but do not seem to exist otherwise.
>
> Oliver.
>
>> Dear Oliver,
>>
>> there is a simple work-around: first merge, then renumber. I learned
>> this the hard way, too, and learned it quickly ;-)
>>
>> Cheers,
>> Tim
>>
>> On 03/18/2014 12:30 AM, Oliver Clarke wrote:
>>> Hi all,
>>>
>>> Coot seems to be renumbering residues when I merge chains, even when the numbering of the chains does not overlap. This seems like a bug?
>>>
>>> It only seems to happen when I am merging helices placed with coot (which incidentally seem to lack chain IDs by default now). It is a little dismaying to find after having carefully renumbered many individual helices that all the numbers have changed after merging the helices together in a single molecule.
>>>
>>> I am running Coot 0.8-pre r4966 on Ubuntu 13.10.
>>>
>>> Oliver.
>>> On Mar 14, 2014, at 8:00 PM, COOT automatic digest system <[log in to unmask]> wrote:
>>>
>>>> There are 7 messages totaling 427 lines in this issue.
>>>>
>>>> Topics of the day:
>>>>
>>>> 1. Per chain ramachandran? (2)
>>>> 2. Delete chain
>>>> 3. unable to launch coot (4)
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Date: Thu, 13 Mar 2014 22:59:49 -0400
>>>> From: Oliver Clarke <[log in to unmask]>
>>>> Subject: Per chain ramachandran?
>>>>
>>>> Hi all, is there anyway to access/modify the Ramachandran plot display via a python or scheme function?
>>>>
>>>> I would like to display a Ramachandran plot calculated just for the currently selected protein chain. do_ramachandran() only seems to take a molecule number, not chain ID.
>>>>
>>>> In cases where there many chains in the asymmetric unit, I think this would be useful while building.
>>>>
>>>> Cheers,
>>>> Oliver.
>>>>
>>>> ------------------------------
>>>>
>>>> Date: Fri, 14 Mar 2014 04:00:50 +0000
>>>> From: Oliver Clarke <[log in to unmask]>
>>>> Subject: Re: Delete chain
>>>>
>>>> I realised the script I posted previously to delete a chain doesn't take account of insertion codes etc.
>>>>
>>>> The attached script hopefully fixes that and adds a couple of other widgets that I find useful into a "Custom" menu (when placed in the ~/.coot-preferences directory).
>>>>
>>>> Oliver.
>>>>
>>>> ------------------------------
>>>>
>>>> Date: Fri, 14 Mar 2014 09:21:31 +0000
>>>> From: Andreas Förster <[log in to unmask]>
>>>> Subject: Re: Per chain ramachandran?
>>>>
>>>> I second that.
>>>>
>>>>
>>>> Andreas
>>>>
>>>>
>>>>
>>>> On 14/03/2014 2:59, Oliver Clarke wrote:
>>>>> Hi all, is there anyway to access/modify the Ramachandran plot display via a python or scheme function?
>>>>>
>>>>> I would like to display a Ramachandran plot calculated just for the currently selected protein chain. do_ramachandran() only seems to take a molecule number, not chain ID.
>>>>>
>>>>> In cases where there many chains in the asymmetric unit, I think this would be useful while building.
>>>>>
>>>>> Cheers,
>>>>> Oliver.
>>>>>
>>>>
>>>> --
>>>> Andreas Förster
>>>> Crystallization and X-ray Facility Manager
>>>> Centre for Structural Biology
>>>> Imperial College London
>>>>
>>>> ------------------------------
>>>>
>>>> Date: Fri, 14 Mar 2014 17:23:42 +0000
>>>> From: Ignacio Mir Sanchis <[log in to unmask]>
>>>> Subject: unable to launch coot
>>>>
>>>> Dear cooters,
>>>> I installed fink and packages (in OS X 10.9.2) following directions from Scott lab web page (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up)
>>>> When I try to launch coot this message appears:
>>>>
>>>> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_
>>>> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib
>>>> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib
>>>> in /sw/lib/libcoot-lidia-core.0.dylib
>>>> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@"
>>>>
>>>> Can anyone tell me what I'm doing wrong?
>>>> Thank you so much in advance.
>>>>
>>>> Nacho
>>>>
>>>> ------------------------------
>>>>
>>>> Date: Fri, 14 Mar 2014 13:47:17 -0400
>>>> From: Scott Horowitz <[log in to unmask]>
>>>> Subject: Re: unable to launch coot
>>>>
>>>> On that note, I actually recently assigned 60 students to do an assignment
>>>> for class using Coot to solve the structure of a protein using maps
>>>> downloaded from EDS. And almost every student who had mavericks on their
>>>> mac had major issues getting it to work. Older versions of OS X were fine.
>>>>
>>>> Scott
>>>>
>>>> PS The students loved the assignment- I highly recommend trying it
>>>>
>>>>
>>>> On Fri, Mar 14, 2014 at 1:23 PM, Ignacio Mir Sanchis <
>>>> [log in to unmask]> wrote:
>>>>
>>>>> Dear cooters,
>>>>> I installed fink and packages (in OS X 10.9.2) following directions from
>>>>> Scott lab web page (
>>>>> http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up
>>>>> )
>>>>> When I try to launch coot this message appears:
>>>>>
>>>>> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_
>>>>> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib
>>>>> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib
>>>>> in /sw/lib/libcoot-lidia-core.0.dylib
>>>>> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@"
>>>>>
>>>>> Can anyone tell me what I'm doing wrong?
>>>>> Thank you so much in advance.
>>>>>
>>>>> Nacho
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Scott Horowitz, Ph.D.
>>>> Research Associate
>>>> Howard Hughes Medical Institute
>>>>
>>>> University of Michigan
>>>> Department of Molecular, Cellular, and Developmental Biology
>>>> Bardwell lab
>>>> 830 N. University Ave, Room 4007
>>>> Ann Arbor, MI 48109
>>>> phone: 734-647-6683
>>>> fax: 734-615-4226
>>>>
>>>> ------------------------------
>>>>
>>>> Date: Fri, 14 Mar 2014 11:11:28 -0700
>>>> From: "William G. Scott" <[log in to unmask]>
>>>> Subject: Re: unable to launch coot
>>>>
>>>> Dear Nacho:
>>>>
>>>> The “coot-pre” package should work. In updating that, I think I probably broke the “stable” coot package.
>>>>
>>>> Also, the stand-alone ones all work (just tested).
>>>>
>>>> http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
>>>>
>>>> Sorry,
>>>>
>>>> Bill
>>>>
>>>>
>>>>
>>>> On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis <[log in to unmask]> wrote:
>>>>
>>>>> Dear cooters,
>>>>> I installed fink and packages (in OS X 10.9.2) following directions from Scott lab web page (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up)
>>>>> When I try to launch coot this message appears:
>>>>>
>>>>> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_
>>>>> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib
>>>>> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib
>>>>> in /sw/lib/libcoot-lidia-core.0.dylib
>>>>> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@"
>>>>>
>>>>> Can anyone tell me what I'm doing wrong?
>>>>> Thank you so much in advance.
>>>>>
>>>>> Nacho
>>>>
>>>> William G. Scott
>>>> Professor
>>>> Department of Chemistry and Biochemistry
>>>> and The Center for the Molecular Biology of RNA
>>>> University of California at Santa Cruz
>>>> Santa Cruz, California 95064
>>>> USA
>>>> http://scottlab.ucsc.edu/scottlab/
>>>>
>>>> ------------------------------
>>>>
>>>> Date: Fri, 14 Mar 2014 11:40:42 -0700
>>>> From: "William G. Scott" <[log in to unmask]>
>>>> Subject: Re: unable to launch coot
>>>>
>>>> I am updating the “stable” coot in fink to rev. 4965 which should work fine with the latest rkdit.
>>>>
>>>>
>>>> On Mar 14, 2014, at 11:11 AM, William G. Scott <[log in to unmask]> wrote:
>>>>
>>>>> Dear Nacho:
>>>>>
>>>>> The “coot-pre” package should work. In updating that, I think I probably broke the “stable” coot package.
>>>>>
>>>>> Also, the stand-alone ones all work (just tested).
>>>>>
>>>>> http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot
>>>>>
>>>>> Sorry,
>>>>>
>>>>> Bill
>>>>>
>>>>>
>>>>>
>>>>> On Mar 14, 2014, at 10:23 AM, Ignacio Mir Sanchis <[log in to unmask]> wrote:
>>>>>
>>>>>> Dear cooters,
>>>>>> I installed fink and packages (in OS X 10.9.2) following directions from Scott lab web page (http://scottlab.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start#Unix_Shell_Environment_Set_Up)
>>>>>> When I try to launch coot this message appears:
>>>>>>
>>>>>> dyld: Symbol not found: __ZNK5RDKit4Dict5toanyISsEEN5boost3anyET_
>>>>>> Referenced from: /sw/lib/libcoot-lidia-core.0.dylib
>>>>>> Expected in: /sw/lib/rdkit/libRDGeneral.1.dylib
>>>>>> in /sw/lib/libcoot-lidia-core.0.dylib
>>>>>> /sw/bin/coot: line 9: 9411 Trace/BPT trap: 5 /sw/bin/coot-real "$@"
>>>>>>
>>>>>> Can anyone tell me what I'm doing wrong?
>>>>>> Thank you so much in advance.
>>>>>>
>>>>>> Nacho
>>>>>
>>>>> William G. Scott
>>>>> Professor
>>>>> Department of Chemistry and Biochemistry
>>>>> and The Center for the Molecular Biology of RNA
>>>>> University of California at Santa Cruz
>>>>> Santa Cruz, California 95064
>>>>> USA
>>>>> http://scottlab.ucsc.edu/scottlab/
>>>>>
>>>>>
>>>>>
>>>>
>>>> ------------------------------
>>>>
>>>> End of COOT Digest - 13 Mar 2014 to 14 Mar 2014 (#2014-40)
>>>> **********************************************************
>>>
>>
>> --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>
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