Re: [ccp4bb] Presence of negative density in Sim Omit map

Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE contoured at quite a high level? As Edward suggests - if you omit a well ordered feature the resultant difference maps often show high positive density and a surrounding complementary "sag

Re: [ccp4bb] Presence of negative density in Sim Omit map

Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps are constructed by Fourier transform without the 0 0 0 reflection, they have mean of zero (because the mean of a sinusoid over one period is zero). That means that any time you add positive (difference) density, which

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Renu, you may try using a Polder omit map for the region rather than a simulated annealing map. You may also check if the red density is due to a symmetry related molecule that is not modeled well. Hope it helps. JP On Tuesday, July 23, 2024 at 04:50:00 PM CDT, Renuka Kadirvelraj

Re: [ccp4bb] Off topic: Nobel prize stats

Thank you all for useful links, slides and thoughtful comments. I completely agree with Mark's comment that it is difficult to quote a single number. Precisely for the reasons he mentioned. The link to PDB, https://pdb101.rcsb.org/learn/other-resources/structural-biology-and-nobel-prizes seems the

[ccp4bb] Reminder: CBMS Lecture Series - July 24, 2024 @13:30 - Thomas van de Kamp (KIT)

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. REMINDER Thomas van de Kamp Karlsruhe Institute of Technology (KIT) Institute for Photon Science and Synchrotron Radiation of KIT WEDNESDAY, July 24, 13:30 (EDT) "Digitizing insect morphology: recen

Re: [ccp4bb] Ccp4i2 execution problem

Dear Maria, Could you please try deleting the file /home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml ? I think that this file is corrupted (empty) and that this is causing the problems. Best wishes, Stuart McNicholas On Wed, 24 Jul 2024 at 12:22, Marian Oliva wrote: > > Dear all, > > Since

[ccp4bb] Ccp4i2 execution problem

Dear all, Since yesterday I’m having some issues for running of ccp4i2. At the begging I though it was a disk space memory problem but it wasn´t. I have re-install ccp4 (indeed, I have tried with ccp4-8 and ccp4-9 installations) with the same result. I can run all other programs (ccp4, ccp4clou

Re: [ccp4bb] Question about micro RNA structures

Hi Careina, This recent publication evaluate several methods, might be a useful resource. https://doi.org/10.1093/nar/gkae541 And a webtool: https://doi.org/10.1093/nar/gkae356 Best regards, Tales On Tue, Jul 23, 2024 at 10:02 AM careinaedgo...@yahoo.com < 02531c126adf-dmarc-requ...@jiscmai