Re: [PyMOL] symexp eats chain ID

Hi Andreas, good find! The most recent changes in SVN introduce multi-letter chain support. This required a non-trivial refactoring of the internal data structure. You found a reference counting bug, I'll fix that. Cheers, Thomas On 09 Sep 2014, at 06:24, Andreas Förster wrote: > Dear all,

Re: [PyMOL] symexp eats chain ID

Should be a bug of your particular version. I cannot reproduce it following your instructions on MacOSX Good luck! Gian On 9/9/14 12:24 PM, Andreas Förster wrote: > Dear all, > > I've noticed that chain IDs disappear after creating symmetry-related > copies: > > fetch 1ubq > -> You clicked /1ubq/

[PyMOL] symexp eats chain ID

Dear all, I've noticed that chain IDs disappear after creating symmetry-related copies: fetch 1ubq -> You clicked /1ubq//A/LEU`73/CG symexp symm1, 1ubq, 1ubq and i. 30, 10 -> You clicked /1ubq//(null)/LEU`73/CG -> You clicked /symm100-1//(null)/LEU`73/CG Chain A turns into chain (null). Wh

Re: [PyMOL] symexp

Hi Kanika, They should. The CRYST1 record holds all the information required to build the crystal. Do note that the symexp command generates neighbouring symmetry mates, given a cut off distance. It does not build the filled unit cell. Thomas put a script on the wiki last year to build you that: h

Re: [PyMOL] symexp

You are right, Thomas! The information is redundant in REMARK 290. I just performed a small test which confirms your conclusion: remove CRYST1 will make symexp to complain "ExecutiveSymExp-Error: No symmetry loaded!" even if REMARK 290 is present, while removing REMARK 290 does not have any effe

Re: [PyMOL] symexp

Should not the positions of ASU's generated by REMARK290 be same as the symmetry mates generated? -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of y

Re: [PyMOL] symexp

> It seems REMARK 290 that contains crystallographic symmetry > transformations is used for computing the positions of neighboring ASUs. the CRYST1 record is sufficient for generating symmetry mates, so pymol most likely does not read REMARK 290. Cheers, Thomas -- Thomas Holder MPI for Develo

Re: [PyMOL] symexp

Hi, Kanika, The source code can be found at function ExecutiveSymExp() in the file ./trunk/pymol/layer3/Executive.c Normally, a PDB is equivalent to an ASU (except for some cases like capsid). "Symexp is used to reconstruct neighboring ASUs." ( http://pymolwiki.org/index.php/Symexp ) It seems RE

[PyMOL] symexp

I used symexp command for 3QK9 using distance of 2.75 to generate ASU(asymmetric unit). Does symexp generate these symmetry mates from the remark290 of PDB file? I couldnot find the code for symexp in pymolwiki. Can anyone help out? Regards, Kanika --

[PyMOL] symexp in scripts

Warren, I am able to create symmetry-related molecules by typing the symexp command into the PyMol window interactively, but including the identical command in my script (see below) does not work. This is frustrating, as I need to create H-bonds to the symmetry molecules, and now must type a