Re: [COOT] Export HOLE-coot atoms as pdb
Not sure what you guys are trying to accomplish, but I used the "hollow" package which generates probe atoms in PDB format suitable for loading into PyMol or coot. (Have not worked with this for a while hopefully I don't have to eat my words (-: ) http://hollow.sourceforge.net/ HTH Carsten -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Oliver Clarke Sent: Tuesday, March 31, 2015 2:58 PM To: COOT@JISCMAIL.AC.UK Subject: Re: [COOT] Export HOLE-coot atoms as pdb Hi Alex, I don't believe there is a way to do this at present (the probe dots are not atoms and as such cannot be manipulated in the same way), but I would also find this useful, for exactly this purpose. Cheers, Oliver. On Mon, 30 Mar 2015 14:00:03 -0700, Alexander Kintzer wrote: >Hello all, > >I am looking to export the probe atoms generated by HOLE in coot as a >pdb or equivalent to make a figure in pymol or chimera. The probes are >visible in coot and I can make plots of probe radius vs coordinate, but >haven't found a way to export the probe coordinates in the documentation. > >any suggestions would be appreciated. > >best, >Alex >
Re: [COOT] Export HOLE-coot atoms as pdb
Hi Alex, I don't believe there is a way to do this at present (the probe dots are not atoms and as such cannot be manipulated in the same way), but I would also find this useful, for exactly this purpose. Cheers, Oliver. On Mon, 30 Mar 2015 14:00:03 -0700, Alexander Kintzer wrote: >Hello all, > >I am looking to export the probe atoms generated by HOLE in coot as a pdb >or equivalent to make a figure in pymol or chimera. The probes are visible >in coot and I can make plots of probe radius vs coordinate, but haven't >found a way to export the probe coordinates in the documentation. > >any suggestions would be appreciated. > >best, >Alex >
[COOT] Export HOLE-coot atoms as pdb
Hello all, I am looking to export the probe atoms generated by HOLE in coot as a pdb or equivalent to make a figure in pymol or chimera. The probes are visible in coot and I can make plots of probe radius vs coordinate, but haven't found a way to export the probe coordinates in the documentation. any suggestions would be appreciated. best, Alex
Re: [COOT] Atoms with zero occupancy
in 0.72: Extensions->Modeling->Atoms with Zero Occupancies That should do the trick, or not? Cheers, -C. -Original Message- From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Tuesday, January 14, 2014 10:13 AM To: COOT@JISCMAIL.AC.UK Subject: [COOT] Atoms with zero occupancy I would like the coot option - find residues with missing atoms to at least have the option to pick those residues where there are atoms with occupancy set to 0.00. Do others feel this would be helpful? Eleanor Dodson
Re: [COOT] Atoms with zero occupancy
Yes, it would certainly be helpful. Sent from my Galaxy S®III Original message From: Eleanor Dodson Date:01/14/2014 10:12 AM (GMT-05:00) To: COOT@JISCMAIL.AC.UK Subject: Atoms with zero occupancy I would like the coot option - find residues with missing atoms to at least have the option to pick those residues where there are atoms with occupancy set to 0.00. Do others feel this would be helpful? Eleanor Dodson
Re: [COOT] Atoms with zero occupancy
I have added this in the python Extensions. For now you can start this for your "imol" in the python scripting window: zero_occ_atoms_gui(imol) NB There may be better way in the future and to make this a more permanent feature. B > I would like the coot option - find residues with missing atoms to at > least have the option to pick those residues where there are atoms > with occupancy set to 0.00. > > Do others feel this would be helpful? > > Eleanor Dodson > -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
[COOT] Atoms with zero occupancy
I would like the coot option - find residues with missing atoms to at least have the option to pick those residues where there are atoms with occupancy set to 0.00. Do others feel this would be helpful? Eleanor Dodson
Re: [COOT] atoms used for SSM rmsd
Per SUPERPOSE manual, they are. I believe the distances for individual residues are for Ca atoms too. On Fri, 2010-07-02 at 14:17 +0200, Tim Gruene wrote: > Dear all, > > which atoms are used for the calculation of an SSM superposition in coot? I > suppose they are only the C-alpha atoms but would like to have a confirmation. > > Ta, Tim > -- Coot verendus est
[COOT] atoms used for SSM rmsd
Dear all, which atoms are used for the calculation of an SSM superposition in coot? I suppose they are only the C-alpha atoms but would like to have a confirmation. Ta, Tim -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [COOT] Atoms
It would seem sensible to do this if the element column is not present (which of course it should be ...) Phil On 3 Oct 2008, at 10:33, Paul Emsley wrote: It turns out that Eugine Krissinel is way ahead of me - in mmdb he provides a flag to fix up the missing elements. This is non-optionally done now in 0.5.1-pre-1 and following versions. Paul Charlie Bond wrote: How straightforward would it be to modify coot to automatically 'run pdbset' on loaded pdb files to overcome this issue? Cheers, Charlie Lynn F. Ten Eyck wrote: On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay --Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz .
Re: [COOT] Atoms
It turns out that Eugine Krissinel is way ahead of me - in mmdb he provides a flag to fix up the missing elements. This is non-optionally done now in 0.5.1-pre-1 and following versions. Paul Charlie Bond wrote: How straightforward would it be to modify coot to automatically 'run pdbset' on loaded pdb files to overcome this issue? Cheers, Charlie Lynn F. Ten Eyck wrote: On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay --Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz .
Re: [COOT] Atoms
All un-fsck options should be non-default optional, lest they create other problems. On Oct 2, 2008, at 6:27 PM, Charlie Bond wrote: How straightforward would it be to modify coot to automatically 'run pdbset' on loaded pdb files to overcome this issue? Cheers, Charlie Lynn F. Ten Eyck wrote: On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay --Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz . -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
Re: [COOT] Atoms
How straightforward would it be to modify coot to automatically 'run pdbset' on loaded pdb files to overcome this issue? Cheers, Charlie Lynn F. Ten Eyck wrote: On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay --Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz . -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia [EMAIL PROTECTED] +61 8 6488 4406
Re: [COOT] Atoms
On 2 Oct 2008, at 09:11, Kay Diederichs wrote: Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). The 4-character atom name did not allow well enough for unique identification of the element type, especially with H atoms. Overloading the atom name with element type causes a lot of problems. Separating the atom type to another column allows for both atom type and ionization state -- i.e. correct identification of the scattering factor needed. Example: Atom type Fe -- is it ferrous, ferric, or ferryl? You need to know for both refinement and modeling. Lynn Ten Eyck running through pdbset fixes this easily. best, Kay -- Kay Diederichs http://strucbio.biologie.uni- konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz
Re: [COOT] Atoms
Phil Evans schrieb: In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil Yes I think so - I found that PDB files that behave like that lack the atom type in the last column (which might be req'd by the new PDB format convention - no idea why). running through pdbset fixes this easily. best, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
[COOT] Atoms
In the new coot, lots of my PDB files have all atoms coloured white. Is this a consequence of the new PDB format conventions Phil
