Re: [Chimera-users] failing to open saved PDBs
Hi Elaine, OK, that is what I had expected to happen yes - and that NMR ensemble looks to be what I was anticipating. I've attached the PDB chimera created here. I'm no expert on PDB internal formatting but it at least looks to me like there are coordinates, sequence information etc etc. I had thought that I had taken care to make sure whole models were saved (not just sel atoms), but I'll replicate it to make sure. Applying the preset in any event didn't work. Maybe you can spot what's wrong with it? Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey>
Hi Joe, Not sure what you are looking at, but when I look in the file I see there are no atom coordinates whatsoever! I.e., no ATOM or HETATM lines between the MODEL and ENDMDL lines. Intro to PDB format: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2016, at 3:00 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi Elaine,
OK, that is what I had expected to happen yes - and that NMR ensemble looks to be what I was anticipating. I've attached the PDB chimera created here. I'm no expert on PDB internal formatting but it at least looks to me like there are coordinates, sequence information etc etc. I had thought that I had taken care to make sure whole models were saved (not just sel atoms), but I'll replicate it to make sure.
Applying the preset in any event didn't work.
Maybe you can spot what's wrong with it?
Joe Healey
M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk
Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry)
Twitter: @JRJHealey | Website: MOAC Page <inner_outer_fits.pdb>
Thanks Elaine, I think you were right and it was just my unfamiliarity with the format so I hadn't noticed it being empty. I resolved my issue anyway by selecting the models I wanted and ensuring that 'save selected' was ticked; so I now have the file I would have expected to have generated in the first place. Joe Healey M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk Jointly working in: Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit) and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry) Twitter: @JRJHealey<https://twitter.com/JRJHealey> | Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 30 November 2016 17:44:42 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu Subject: Re: failing to open saved PDBs Hi Joe, Not sure what you are looking at, but when I look in the file I see there are no atom coordinates whatsoever! I.e., no ATOM or HETATM lines between the MODEL and ENDMDL lines. Intro to PDB format: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2016, at 3:00 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:
Hi Elaine,
OK, that is what I had expected to happen yes - and that NMR ensemble looks to be what I was anticipating. I've attached the PDB chimera created here. I'm no expert on PDB internal formatting but it at least looks to me like there are coordinates, sequence information etc etc. I had thought that I had taken care to make sure whole models were saved (not just sel atoms), but I'll replicate it to make sure.
Applying the preset in any event didn't work.
Maybe you can spot what's wrong with it?
Joe Healey
M.Sc. B.Sc. (Hons) PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk
Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry)
Twitter: @JRJHealey | Website: MOAC Page <inner_outer_fits.pdb>
participants (2)
-
Elaine Meng -
Healey, Joe