Hi, Thank you all for your help! Of course coot works perfectly and also PISA is useful, not I am not sure both can be employed in a high-throuput manner for hundreds of structures. I looked at gemmi but am not familiar with python-mmdb, so I will take a look at that. Thank you Zhijie for the script and the explanation! I will take a look at it when I'm back in the lab.
Thanks again everyone for your help and have a great weekend, Orly On Sat, Jan 11, 2020, 03:11 Zhijie Li <zhijie...@utoronto.ca> 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of orly > avraham <orly.levin...@mail.huji.ac.il> > *Sent:* Friday, January 10, 2020 3:30 PM > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *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
