Hi Tristan, Thank you very much!! I will continue with my exploration and I am grateful for all the assistance.
Best regards, Orly On Sun, Jan 12, 2020 at 11:18 PM Tristan Croll <[email protected]> wrote: > (sending again because it seems the message board server gets a little > confused by Python files as attachments). > > Hi Orly, > > Turns out I didn't have a pre-baked method for this specific task, but > the method defined in the attached file works - although you'll > undoubtedly want to adapt it to your specific purposes. To play around > with it, download and install ChimeraX 0.91, then install Clipper with > "toolshed install clipper" on its command line. Then, you can open the > ChimeraX interactive Python shell with Tools/General/Shell. This comes > with the top-level ChimeraX session object pre-loaded with the variable > name "session". Copy-paste the method definition in to that, and you'll > be ready to explore. You can also run Python files with "open xxx.py" on > the command line or on starting ChimeraX with "chimerax xxx.py" - in > either case, these will also have the session object automatically > available. > > Best regards, > > Tristan > > On 2020-01-12 19:54, orly avraham wrote: > > Hi Tristan, > > > > I am looking into all the options listed, yet would still highly > > appreciate any additional resources! > > If you would be kind enough to share an example script that would be > > great. > > > > Best, > > Orly > > > > On Sun, Jan 12, 2020 at 9:12 PM Tristan Croll <[email protected]> wrote: > > > >> Just to add to the already-excellent list of replies, this can also > >> be done quite straightforwardly with the Clipper plugin in ChimeraX. > >> I’d be happy to provide an example script if you want one. > >> > >> Best regards, > >> > >> Tristan > >> > >> On 12 Jan 2020, at 18:54, orly avraham > >> <[email protected]> wrote: > >> > >> Hi Marcin, > >> > >> Thank you very much for your detailed reply! > >> You pointed out many special cases that I wouldn't have thought of. > >> Indeed an existing solution is highly preferred, and I appreciate > >> you pointing out several available libraries. I came across Gemmi > >> and I will give it another look, and I will examine the additional > >> resources you mentioned as well. > >> > >> Best regards, > >> Orly Avraham > >> > >> On Sun, Jan 12, 2020 at 5:59 PM Marcin Wojdyr <[email protected]> > >> wrote: > >> Hi Zhijie, > >> > >> it's good and instructive to implement such things from the ground > >> up, > >> but there are many special cases that one would be discovering while > >> testing this procedure, so if the time is limited it may be better > >> to > >> use an existing solution. > >> > >> For instance, here one may find out that using the SCALE1 record > >> doesn't give the sufficient accuracy. In the example in your script > >> you have 6 significant digits in the unit cell lengths in CRYST1, > >> but > >> only 4 significant digits in SCALE1. (The accuracy of SCALE1 is > >> problematic in general; sometimes it needs to be manually removed > >> when > >> a program reads it in preference to CRYST1.) > >> > >> Then one may find out that the 3x3x3 supercell is not sufficient. If > >> the molecule is far from the origin, symmetry operations send it far > >> away. For example, 5M3H annotates (in the mmCIF format) hydrogen > >> bond > >> between 1_555 and 2_11516 - the symmetry mate is shifted 16 unit > >> cells > >> in the z direction. Since you already use fractional coordinates in > >> your script you could tell directly from the center-of-mass > >> coordinates how many unit cells it should be shifted. Say, you have > >> x=3.1, so to shift it near the origin you shift it by 3 unit cells > >> along x. > >> > >> But even if all the molecules are shifted near the origin, the 3x3x3 > >> cell is still not sufficient to find contacts. > >> See 3NWH – a homo-4-mer in P2 (4 x 2 chains per unit cell). Here > >> it in > >> its unit cell, colored by the chain id: > >> https://gemmi.readthedocs.io/en/latest/_images/3nwh.png > >> Or 5XG2 – a monomer in P21. Two copies of the chain are > >> rainbow-colored here: > >> https://gemmi.readthedocs.io/en/latest/_images/5xg2.png > >> These chains span over more than 4 unit cells in one direction. One > >> could use big enough supercell, but it'd be slow. I suppose that > >> even > >> using a 3x3x3 supercell is slow. The alternative is to do the > >> distance > >> calculation in fractional coordinates modulo 1. > >> > >> Then you needs to consider atoms on special positions. If you apply > >> symmetry operations to an atom on a 4-fold symmetry axis you get 4 > >> atoms in the same place. So this needs to be handled. The atom may > >> not > >> be exactly on the axis, because the refinement program may not > >> constrain its position. So the symmetry operations should produce, I > >> think, 4 alternative locations of the same atom. But you could also > >> have an atom near the symmetry axis bonded to its symmetry mate - > >> then > >> the symmetry operations should produce different atoms. So the > >> procedure requires a cut-off distance or a heuristics to distinguish > >> the two cases. > >> > >> Then, if you'd like to expand non-crystallographic symmetry from the > >> MTRIX records - this is another complication. And so on... > >> > >> So I'd recommend using one of many available programs for finding > >> contacts or interactions. If none of them is suitable - then try > >> crystallographic libraries. > >> I didn't document yet how to find the contacts using gemmi, but I'll > >> do it in the coming weeks (or months). Cctbx and clipper are other > >> (more mature) libraries worth checking. > >> > >> Best wishes, > >> Marcin > >> > >> On Sat, 11 Jan 2020 at 02:11, Zhijie Li <[email protected]> > >> wrote: > >>> > >>> Hi Orly, > >>> > >>> REMARK 290 should be the easiest way for generating symmetry > >> mates. Other routes are just going to give you the same results. As > >> Jonathan already pointed out, the symm ops do not garantee that the > >> symm copies are close to each other. The most simple-minded > >> solution to this problem would be simply generating 3x3x3 unit cells > >> so that the unit cell in center will be complete. An upgrade to this > >> is to compute the center of mass of the symmetry copies in each of > >> the 3x3c3 cells and find which one is closest to the orignal 1555 > >> copy. Just for fun, I wrote a little python script that does this > >> (attached). In this script for unit cell translation and calculating > >> center-center distances, I converted the Cartesian coordinates to > >> fractional coords first. Then after the translation,I used the > >> inverse of the SCALE1 matrix to get the shifted Cartesian coords. > >> This way I don't need to read wikipedia on geometry . But as noted > >> in the script the distances should better be calculated in > >> Cartesian. > >>> > >>> Zhijie > >>> > >>> ________________________________ > >>> From: CCP4 bulletin board <[email protected]> on behalf of > >> orly avraham <[email protected]> > >>> Sent: Friday, January 10, 2020 3:30 PM > >>> To: [email protected] <[email protected]> > >>> Subject: [ccp4bb] Generating symmetry mates using python > >>> > >>> Hi all, > >>> > >>> I am a crystallographer currently employing computational methods > >> as well as experimental crystallography. > >>> I am trying to generate symmetry mates in python (working with > >> pandas dataframes), in order to analyze inter-sub-unit interactions. > >> To do so I am trying to use the info in "REMARK 290 CRYSTALLOGRAPHIC > >> SYMMETRY" and manually (using numpy) perform a matrix multiplication > >> with the relevant translation (xyz*rotation + translation). > >>> For some reason this doesn't work consistently and I feel I need > >> to use the info in CRYST1 to obtain the unit cell and multiplication > >> matrix. Here I ran into trouble with extracting the correct symmetry > >> operations based on each space group. I found spglib but it doesn't > >> quite solve the problem. > >>> I also tried opening PyMol through the command and generating > >> symmetry mates this way. It worked on a few files but failed quite > >> quickly (segmentation fault) and was also very slow. > >>> Can anyone suggest a useful solution, preferably clear to use > >> and/or well documented? Or even have a python script/code they can > >> share for this? > >>> > >>> Best regards, > >>> Orly > >>> > >>> -- > >>> > >>> Orly Avraham, Ph.D. > >>> Postdoctoral fellow > >>> The lab of Prof. Oded Livnah > >>> and the lab of Prof. Ora Schueler-Furman > >>> The Hebrew University of Jerusalem > >>> Israel > >>> > >>> > >>> ________________________________ > >>> > >>> To unsubscribe from the CCP4BB list, click the following link: > >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >>> > >>> > >>> ________________________________ > >>> > >>> To unsubscribe from the CCP4BB list, click the following link: > >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> > > ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> -- > >> > >> Orly Avraham, Ph.D. > >> Postdoctoral fellow > >> The lab of Prof. Oded Livnah > >> and the lab of Prof. Ora Schueler-Furman > >> The Hebrew University of Jerusalem > >> Israel > >> > >> ------------------------- > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > -- > > > > Orly Avraham, Ph.D. > > Postdoctoral fellow > > The lab of Prof. Oded Livnah > > and the lab of Prof. Ora Schueler-Furman > > The Hebrew University of Jerusalem > > Israel > -- Orly Avraham, Ph.D. Postdoctoral fellow The lab of Prof. Oded Livnah and the lab of Prof. Ora Schueler-Furman The Hebrew University of Jerusalem Israel ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
