Re: [ccp4bb] Coot (OS X) unable to read CRYST1 line

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Subject: Re: Coot (OS X) unable to read CRYST1 line
From: Pavan p {- dot -} vaidyanathan {- at -} UMIAMI {- dot -} EDU
Date: 2008-03-17

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Subject: Re: Coot (OS X) unable to read CRYST1 line
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-03-17

Hi,

It may just be a typo in your letter, but there should only be
a single space between the last zero and the "P". Spacing matters
in PDB files.

Dale Tronrud

Pavan wrote:
> Thanks for all those quick replies! Im sorry my post didnt carry the
> CRYST1 line.
> It should have read:
>
> CRYST1 86.316 86.316 279.245 90.00 90.00 120.00 P 65
>
> I tried all your suggestions but I still cannot get coot to read the SG.
>
> What is strange is that when coot starts up (coot --pdb ABCD.pdb) it
> gives these information messages in terminal:
>
> <...snip>
> Reading coordinate file: /sw/share/coot/standard-residues.pdb
> PDB file /sw/share/coot/standard-residues.pdb has been read.
> No Spacegroup found for this PDB file
> Cell: 40.631 109.18 93.243 90 90 90
>
> art_render_invoke: no image source given
> art_render_invoke: no image source given
> initalize graphics molecules...initializing molecules...done
> done.
>
> (handle-read-draw-molecule-with-recentre "ABCD.pdb" 1)
> Reading coordinate file: ABCD.pdb
> PDB file ABCD.pdb has been read.
> No Spacegroup found for this PDB file
> Cell: 86.316 86.316 279.245 90 90 120
> !! Warning:: No symmetry available for this molecule
> No Symmetry for this model
> INFO:: NCS chain comparison 0/644
> Molecule 0 read successfully
>
>
> It apparently cannot read the space group info from the
> standard-residues.pdb either. The CRYST1 line from that pdb reads as
> follows:
>
> CRYST1 40.631 109.180 93.243 90.00 90.00 90.00 P 1
>
> This pdb seems to be part of the coot install. I haven't touched this
> file before.
>
> Any thoughts? And thanks for your time.
> Pavan
>
> On Mon, Mar 17, 2008 at 5:47 PM, Tim Gruene wrote:
>> your CRYST1 card is most likely missing the actual space group name. You
>> can fix this with e.g. pdbset:
>>
>> pdbset xyzin your.pdb xyzout pdb-with-spacegroup-name.pdb << eof
>> spac P21212
>> end
>> eof
>>
>> where you replace P21212 with your actual space group name.
>> Tim
>>
>> --

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CCP4bb <-- 2008 <-- March 2008 <-- 17 March 2008

Previous message:
Subject: Re: Coot (OS X) unable to read CRYST1 line
From: Pavan p {- dot -} vaidyanathan {- at -} UMIAMI {- dot -} EDU
Date: 2008-03-17