Hi Reza, Since nobody answered your question so far, I will do it now: In our hands, ArpWARP autoligand is still the best program to automatically dock ligands into electron density maps. Alternatively, on could also try Rhofit from Global Phasing or some other docking program.
However, the results of even the best docking program are still inferior to the results an experienced crystallographer can achieve. As others said, here you will need all the information you can get hold of: 1. Superimpose homologous structures and look if the ATP position correlates with your electron density. 2. Fit the ATP in every possible pose, refine each one and look which one is the best. 3. Look if the binding mode makes sense, e.g. no highly charged phosphates in hydrophobic pockets. 4. Look if the bad electron density makes structurally sense, e.g. density disappearing after a freely rotatable bond, but not in rigid parts etc. 5. Use your scroll-wheel to scroll up and down the contour level of your electron density map: scrolling up may reveal the phosphate positions, since they should have the highest electron density; scrolling down may reveal parts of the molecule with low electron density due to low occupancy. 6. Keep in mind that you may have a mixture of ATP and ADP bound, causing disordered maps. Good luck! Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Reza Khayat Gesendet: Donnerstag, 23. Juli 2020 18:53 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Modeling ATP/ADP EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk<mailto:owner-ccp...@jiscmail.ac.uk> Hi, Can folks suggest programs for objectively docking ATP/ADP molecules into density? Our density is not so good, probably because of occupancy, and we'd like a less subjecting approach for modeling. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFAw&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=N5ZE4qGmXzt6ID9MVdXb8ZSn8Yxj5ukuqN3itdNLWoE&s=gXgc6YOvt5iwa492yweK5ou1A1Ix-ZfFI5gnlUxeXgw&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
