[Chimera-users] Delete Bug?

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 27 11:47:56 PDT 2015

Hi Korbin,
	Your deletion command leaves only a handful of residues in chains near the H chain.  This results in a pathological behavior in the algorithm that tries to match the residues in a chain to their corresponding SEQRES records [used in deciding if a residue is actually a bound ligand].  So if you had waited long enough (~15 minutes) the command would have actually finished.
	There are two possible workarounds until I can fix this.  One is to just hide the atoms/ribbons instead of deleting them.  The other is to make Chimera "forget" about the SEQRES records before you delete things.  The following Python code will do that:

from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
	headers = m.pdbHeaders
	del headers["SEQRES"]

If you put the above in a file ending in ".py" (e.g. forget-seqres.py) then you can execute the code with the "open" command (e.g. open ~/forget-seqres.py).


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Apr 27, 2015, at 10:28 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Oh sorry, I failed to try the deletion step at which you observed the problem!  Now I can reproduce the hang, even when bypassing selection.  We are looking into it...
> Elaine
>> On Apr 27, 2015, at 9:19 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Korbin,
>> I didn’t have trouble executing these commands.  The result after
>> open 1CT1
>> zonesel :.h 3.5 extend true
>> select invert
>> was 3452 atoms 3381 bonds selected.  However, assuming you are not working with surface pieces or trying to select surface pieces, you could more simply just use the atom zone specifiers.  Then inversion isn’t necessary.  For example,
>> sel :.h za>3.5
>> also selects 3452 atoms and 3381 bonds.  You could also be daring and bypass selection entirely:
>> del :.h za>3.5 
>> I tested both selection methods in the current daily build and in release version 1.10.1.  The “za” is for an atom-based cutoff, whereas “z” or “zr” would be residue-based; see the “zones” section of the atomspec docs:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>
>> Best,
>> 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 Apr 27, 2015, at 7:34 AM, Korbin West <khwest16 at wabash.edu> wrote:
>>> Hi all,
>>> I'm running some code on Chimera to select only certain chains and nearby aspects, but when I try to delete the extraneous information, Chimera freezes up. I'll detail the commands I use below, and for reference I'm interested in the H chain of 1CT1, but it doesn't seem to work with any of its chains.
>>> open 1CT1
>>> zonesel :.h 3.5 extend true
>>> select invert
>>> del sel
>>> It then freezes on del sel. I've tried this with other pdb files and it works fine, but for some reason it stops on this one.  For example, it works fine on 1PZ3 for its A and B chains.
>>> Is this some kind of bug or is there a work-around to this issue? We looked at the residues and couldn't find anything out of place, so we are not sure what is happening. Much thanks in advance.
>>> Best,
>>> Korbin West​
>>> Wabash College
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