I am experiencing a strange problem with generating symmetry mates in PyMOL for the coordinate file 1WAP: specifically, the generated molecules clash with each other. I tried using either the menus Action > generate > symmetry mates \u2026. , or using the symexp command; same result<\/p>\n
Coot is able to reconstruct the proper arrangements (see attached image).<\/p>\n
The behavior you are describing is due to PyMOL ignoring SCALE matrix translation. Unfortunately, this bug was accidentally introduced into recent versions of PyMOL. Our developers are aware of it and it will be fixed in the next release. Thank you for bringing it to our attention and apologies for the inconvenience.<\/p>\n
In the meantime, you can use a work-around by explicitly applying ORIGX1 translation (the value is taken from the PDB header). This needs to be done before generating symmetry mates. I.e.:<\/p>\n
fetch 1wap
\nas cartoon
\nalter_state 1, 1wap, x += 38.97750
\nsymexp sym, 1wap, (1wap), 10<\/p>\n
Give it a try and let us know if it doesn’t work for you or if you have additional questions and would like further assistance.<\/p>\n
Best regards,<\/p>\n
Pavel Golubkov<\/p>\n
Yep Chimera does not get the correct crystal symmetry for 1WAP. The problem is Chimera is assuming that the fractional crystal unit cell coordinates origin is 0,0,0 in physical Angstrom coordinates. But the PDB format allows them to be different, and for 1WAP there is a shift by 0.25 along the x axis in fractional coordinates. This is seen in the SCALE1, SCALE2, SCALE3 records in the PDB format file and in the _atom_sites.fract_transf_vector table in the mmCIF format file. I didn’t know the PDB allowed this. A quick search of 900 random PDB files showed 2 with this problem: 1HHO from 1983 and 2DHB from 1972. 1WAP is from 1995. I guess this unfortunate coordinate system irregularity only effects very
\nold PDB entries.<\/p>\n
Let me think about whether it is worth fixing this. We are putting all our effort into our next generation ChimeraX right now.<\/p>\n
You can work around the bug by shifting the 1WAP coordinates 0.25 unit cells along x. Use menu Tools \/ Movement \/ Transform Coordinates, enter shift 38.9775 0 0, press Apply, then the Unit Cell tool and others that use space group symmetry will work correctly.<\/p>\n
Goddard<\/p>\n","protected":false},"excerpt":{"rendered":"
Problem: I am experiencing a strange problem with generating symmetry mates in PyMOL for the coordinate file 1WAP: specifically, the generated molecules clash with each other. I tried using either the menus Action > generate > symmetry mates \u2026. ,<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-1163","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p7sxod-iL","jetpack-related-posts":[{"id":1350,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2017\/08\/01\/nmrpipe-processing-tips-from-alex-hansen\/","url_meta":{"origin":1163,"position":0},"title":"NMRPipe Processing Tips from Alex Hansen","author":"Mark Foster","date":"August 1, 2017","format":false,"excerpt":"Hello, I've noticed a few common 'annoyances' that everyone tends to deal with when processing nmr data in one way or another and I thought I'd offer a few solutions: 1) Getting started with nmrPipe\/nmrDraw: Converting data in Topspin Learning nmrPipe can be a hassle, especially if you're not horribly\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1094,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2016\/06\/15\/pepsi-presents-her-work-at-the-asms\/","url_meta":{"origin":1163,"position":1},"title":"Pepsi presents her work at the ASMS","author":"Mark Foster","date":"June 15, 2016","format":false,"excerpt":"Pepsi (Melody) Holquist presented her poster, \"Using Native MS to Inform Statistical Thermodynamic Models of Cooperativity,\" at the 2016 American Society for Mass Spectrometry conference in San Antonio,TX","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"20160607_125019","src":"https:\/\/i0.wp.com\/research.cbc.osu.edu\/foster.281\/wp-content\/uploads\/2016\/06\/20160607_125019-e1466011932360-300x202.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":952,"url":"https:\/\/research.cbc.osu.edu\/foster.281\/2016\/04\/29\/mark-foster-receives-dick-maxwell-award-from-the-office-of-disability-services\/","url_meta":{"origin":1163,"position":2},"title":"Mark Foster Receives Dick Maxwell Award from the Office of Disability Services","author":"Mark Foster","date":"April 29, 2016","format":false,"excerpt":"Dick Maxwell Award Nomination Statement Nominee: Dr. Mark Foster Nominators: The Interpreting Team Dr. Foster has worked with a student who is deaf that is registered with our office in various capacities since August of 2014. 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