Re: [ccp4bb] Shortest distance between side chains
Dear Misha,
There is a program in ccp4 called contacts that will give you this information.
You can alter entry parameters to show you the relevant information.
I think you can also try PISA server from EMBL-EBI.
I reckon both these programs show you all distances and you may have to
manually pick out the shortest ones.
Regards
Hari
On Wednesday, May 19, 2021, 16:54, Isupov, Michail
wrote:
#yiv2028539353 P {margin-top:0;margin-bottom:0;}
Hi
I am wondering if there is a simple program that would convert a pdb file into
a matrix that
shows the smallest distance between all pairs of amino-acid side chains?
Thanks,
Misha
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[ccp4bb] Omit maps in phenix and ccp4
Dear All, I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have tried phenix for this purpose but get this error message consistently. "Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary." This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to work. 1. Is there something I have missed out that can solve this issue?2. Is there a program in CCP4i that can be used to generate the required omit maps? 3. In general, how do I omit 3.5 ang of the space around the ligand during this map calculations? Thank you so much for your time. Hari To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Ligand building
Hi all, I want to build a ligand that does not exist in reality (or be able to modify an existing ligand as per choice). 1. JLigand in the ccp4 suite seems to work only on java and gives me an “configuration problem” as an error message on my Windows. I am new to this and unaware of how to solve this issue. Could I get some suggestions on how to start this? 2. Alternatively, I was trying to use eLBOW from phenix but it seems to only build ligands but unable to delete atoms. Is there another program or option for me to delete sections of the ligand and geometrical optimise them in phenix? ThanksHari To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=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/
