[phenixbb] secondary structure presentation in VMD

Tristan Croll tic20 at cam.ac.uk
Sun Jan 21 10:23:42 PST 2018

I’m guessing this structure is on the large side? Unless something has changed since I last used it, VMD ignores secondary structure annotations in the PDB file. It calculates them instead using an old version of STRIDE, which fails beyond 9,999 residues (or possibly atoms? Can’t remember now). One can hack together a quick-fix solution fairly easily (basically split the structure into smaller pieces, calculate for each of those then copy the results back to the master structure). If you really want the secondary structure in VMD to match what Pymol sees, you could do it fairly easily with a little scripting in both packages. VMD gets/sets secondary structure as a simple Tcl array of characters, one per residue. So all you’d need to do in Pymol is a simple loop over all residues to get their secondary structure designation and write the corresponding character to a text file. Then load the text file in VMD, convert the string to a character array, and apply it to your model. A mite fiddly, but doable.

Alternatively, have you tried ChimeraX? It’s really rather nice in what it can do.

Hope this helps,


Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY


> On 21 Jan 2018, at 15:44, Paul Emsley <pemsley at mrc-lmb.cam.ac.uk> wrote:
> Hi Charles,
>> On 21/01/2018 15:04, CPMAS Chen wrote:
>> This may be a little off-topic. I have posted this in VMD users mail list. I want to try here too to see
>> if anyone experienced similar issue.
>> VMD and pymol gave different presentation on the secondary structure of a protein.
>> I correctly labelled all helices and sheets.
> I wonder what that means. How did you label all helices and sheets and how did you know that you did it correctly?
> Paul
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