Re: [ccp4bb] quantifying electron density

Dear Sriram, dear Jon, The sum of values of a map (always calculated at some finite resolution) is not the same as a sum of density values. In such maps, a contribution of each atom is a function oscillating with the distance to the atomic center. Even when the height of these ripples is

Re: [ccp4bb] quantifying electron density

Dear Pavel, I came across an example of calculating "electron_sums_around_atom" in cctbx . If we don't zero the F000 or if we normalize the density of the real-space map by the unit cell

Re: [ccp4bb] quantifying electron density

Hi Jon, not really the answer to your question but.. This may be very tricky to do because what you look at is not an electron density map but its Fourier image of finite resolution phased by crystal model (that has errors), plus experimental errors, and missing F000 (which is not measured as part

[ccp4bb] Two postdoctoral openings in structural biochemistry of fertilization at Karolinska Institutet

Our research group at Karolinska Institutet (http://jovinelab.org) is looking for two ambitious postdoctoral fellows who would like to spearhead our future steps towards unveiling the molecular basis of gamete recognition and fusion through the evolutionary tree. For more information and to

[ccp4bb] REMINDER: CBMS Lecture Series - Dominique Bourgeois - June 28, 13:30

You are cordially invited to join …….. Dominique Bourgeois Institut de Biologie Structurale J-P. Ebel, GRENOBLE Wednesday, June 28, 2023, 13:30 EDT (New York time) STRUCTURAL PHOTOPHYSICS OF FLUORESCENT PROTEINS USED IN SUPER RESOLUTION MICROSCOPY

[ccp4bb] CCP4 Summer School 2023: deadline approaching!

Dear CCP4bb subscribers, As you may know, the CCP4 Summer School is returning to York after a 4-year hiatus – this is a continuation of the excellent work done by our colleagues at St. Andrews pre-2019. We've got an exciting programme prepared for the students, including lectures not just on

[ccp4bb] quantifying electron density

hello everyone, is there software that can use an electron density map to quantify the number of electrons in a selected volume somewhere in a protein? cheers jon -- Professor Jon Hughes, BSc, PhD Department of Physics Free University of Berlin Arnimallee 14 14195 Berlin Germany mobile: 

Re: [ccp4bb] Binding affinity in AutoDock Vina

Are you doing self-docking or are you analysing the models as-is? Not all binding poses in the PDB are realistic and things like atomic clashes have a massive energy penalty.Have you looked at the model in the electron density? You can also try the pdb-redo version op the same pdb entry to see if

[ccp4bb] Binding affinity in AutoDock Vina

I am performing docking studies for some of the protein structures from PDB using AutoDock Vina. Some of the ligands are giving binding energy as positive integers (eg. 435 kcal/mol). I tried rectifying the issue best to my knowledge. I would be grateful if someone could explain to me the reason

Re: [ccp4bb] Peculiar issue with C2 datasets

C2 Cell : Average unit cell: 119.05 84.31 107.99 90.00 91.50 90.00 Space group: C 1 2 1 C2 shift ( if I have read your image correctly..) 60.32 2.137. 0.088 In fractions 60.32/119.05 2.137/84.31 0.00. = 0.504 0.023 0.00 See this site C121 has alt origin 1/2, ?,0 so your

[ccp4bb] LINXS Structure-Based Drug Discovery Symposium and course on Fragment Based Lead Discovery!

Dear all, I would like to draw your attention to the upcoming symposium on Structure-Based Drug Discovery followed by a course for young researchers with focus on Fragment-Based Lead Discovery, that will take place in September in Lund, Sweden. Hope it can be of interest! Welcome to register

Re: [ccp4bb] Win 10 DHCP-Server to assign fixed IP-address

Hi Tim, Why do you need a DHCP server? Can't you configure a fixed IP address on the Oxford Cryo 800? Check out this site for a possible alternative: https://www.dhcpserver.de/cms/ But if you can connect via USB instead, it's probably better to buy a cable. We have an older 700 and it is

Re: [ccp4bb] Need suggestion

Dear Afsan, Based on the information you provided, it's possible that the crashing issue in COOT when attempting to merge the monomers could be due to several reasons. Here are a few suggestions and potential workarounds you can try: Either Update COOT or Import monomers as coordinates: Instead

[ccp4bb] Win 10 DHCP-Server to assign fixed IP-address

Hello everyone, we connected an Oxford Cryo 800 with the windows PC of our Bruker Diffractometer via network cable (as I didn't have a USB-cable at hand). The Oxford Cryo 800 runs a dhcp-client. Is it possible to set up a local dhcp-server with Win 10 in order to assign a local IP-address to the