Re: [ccp4bb] why does Coot ignore CONECT?
Hi Pavel I work with peptide-scaffold chimeras on a daily basis. Initially, I tried to include the scaffolds as HETATM and use JLigand to create the links between the scaffolds and the natural amino acids. This procedure however is rather fussy and by now I build the chimera in silico, using natural amino acids provided by the program. Subsequently, I run the energy minimization on my own to have a rough control over the conformation. I then feed the coordinates into PRODRG without any further minimization and use the pdb and the restraints as they come from the server. Of course, such a ligand will not make use of the cif libraries of the natural amino acids during refinement. But if you imported the natural amino acids while building the chimera, your minimization used the proper restraints. I have the impression that this procedure is more efficient than trying to maintain the LINK in the pdb header (which, in my case, oftern got lost after running a refinement, so I had to copy-paste it anew after every cycle). Best, Matthias Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Robert-Rössle-Strasse 10 13125 Berlin Germany Phone: +49 (0)30 94793-284 From: CCP4 bulletin board on behalf of Pavel Mader Sent: Monday, November 4, 2019 6:06:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] why does Coot ignore CONECT? Hi Paul, thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids, the side chains of which are linked by click chemistry... I know how to make modified amino acids that will make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain). I was trying to solve the issue by making a CONECT record in the pdb file, but Coot ignored it. LINK "sort of" worked, but it was not possible to control the geometry (bond length and angles), often the real space refinement simply "explodes" probably in a attempt to avoid clashes. My current workaround is to make a cif file for the whole 15 AA long polypeptide (the bonds and angles now behave more or less as expected), but I don't consider this as a good general practice for building long polypeptide chains... Thanks in advance for any hints guiding me in the right direction. Pavel -- Původní e-mail -- Od: Paul Emsley Komu: CCP4BB@JISCMAIL.AC.UK Datum: 1. 11. 2019 21:16:11 Předmět: Re: [ccp4bb] why does Coot ignore CONECT? On 01/11/2019 20:17, Pavel Mader wrote: > Hello, Hello. > > I have a question, can anyone explain, why does Coot not display a covalent > bond manually specified by > CONECT line in a pdb file? Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to cover the bases for which CONECT would be used. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] why does Coot ignore CONECT?
On 04/11/2019 17:06, Pavel Mader wrote: Hi Paul, thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids, the side chains of which are linked by click chemistry... I know how to make modified amino acids that will make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain). OK... I was trying to solve the issue by making a CONECT record in the pdb file, That's not the way to do it. but Coot ignored it. Indeed. LINK "sort of" worked, But not really, right? but it was not possible to control the geometry (bond length and angles), often the real space refinement simply "explodes" probably in a attempt to avoid clashes. Yeah... My current workaround is to make a cif file for the whole 15 AA long polypeptide Blimey! (the bonds and angles now behave more or less as expected), but I don't consider this as a good general practice for building long polypeptide chains... Hmm! Your scepticism is well placed, I feel. The way to do it is to use the Coot (Modules -> CCP4 -> Acedrg Link) or CCP4i2 interface (Ligands -> Make a Link (?)) so that Acedrg is used to make a link between the specified atoms of the specified residue types (monomers). Note: to self: make a YouTube vid to explain how to do this... Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] why does Coot ignore CONECT?
Hello Eleanor, We tried to follow your suggestion. The atoms to be linked were 1.46A apart in the input pdb model and we ran 10 cycles of refinement in Refmac with the "make link between" option chosen in either "defined in the file or residues are close". After the refinement we saw the linkage as dotted line and the distance between the atoms was 2.2A (in other words they moved apart instead of forming a covalent bond). Thanks in advance for any further suggestions, Pavel -- Původní e-mail -- Od: Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Komu: CCP4BB@JISCMAIL.AC.UK Datum: 4. 11. 2019 12:16:38 Předmět: Re: [ccp4bb] why does Coot ignore CONECT? " What does refmac do if you feed it the coordinates with side chains close enough to bond? In some cases it makes a full link dictionary with bonds angles planes etc. But can coot read such a dictionary entry? On Mon, 4 Nov 2019 at 17:06, Pavel Mader mailto:mader.pa...@seznam.cz)> wrote: " Hi Paul, thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids, the side chains of which are linked by click chemistry... I know how to make modified amino acids that will make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain). I was trying to solve the issue by making a CONECT record in the pdb file, but Coot ignored it. LINK "sort of" worked, but it was not possible to control the geometry (bond length and angles), often the real space refinement simply "explodes" probably in a attempt to avoid clashes. My current workaround is to make a cif file for the whole 15 AA long polypeptide (the bonds and angles now behave more or less as expected), but I don't consider this as a good general practice for building long polypeptide chains... Thanks in advance for any hints guiding me in the right direction. Pavel -- Původní e-mail -- Od: Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk) > Komu: CCP4BB@JISCMAIL.AC.UK(mailto:CCP4BB@jiscmail.ac.uk) Datum: 1. 11. 2019 21:16:11 Předmět: Re: [ccp4bb] why does Coot ignore CONECT? "On 01/11/2019 20:17, Pavel Mader wrote: > Hello, Hello. > > I have a question, can anyone explain, why does Coot not display a covalent bond manually specified by > CONECT line in a pdb file? Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to cover the bases for which CONECT would be used. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1) " To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1) " To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 (https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1) " To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] why does Coot ignore CONECT?
What does refmac do if you feed it the coordinates with side chains close enough to bond? In some cases it makes a full link dictionary with bonds angles planes etc. But can coot read such a dictionary entry? On Mon, 4 Nov 2019 at 17:06, Pavel Mader wrote: > Hi Paul, > > thank you for your answer. My problem is that I am building a cyclic > peptide with non-standard amino acids, the side chains of which are linked > by click chemistry... I know how to make modified amino acids that will > make peptide bonds with their neighbors in the polypeptide chain, but I > don't know how to make a covalent link between side chains of amino acids > say No. 3 and 12 for example (of a 15 AA long chain). I was trying to solve > the issue by making a CONECT record in the pdb file, but Coot ignored it. > LINK "sort of" worked, but it was not possible to control the geometry > (bond length and angles), often the real space refinement simply "explodes" > probably in a attempt to avoid clashes. My current workaround is to make a > cif file for the whole 15 AA long polypeptide (the bonds and angles now > behave more or less as expected), but I don't consider this as a good > general practice for building long polypeptide chains... > > Thanks in advance for any hints guiding me in the right direction. > > Pavel > -- Původní e-mail -- > Od: Paul Emsley > Komu: CCP4BB@JISCMAIL.AC.UK > Datum: 1. 11. 2019 21:16:11 > Předmět: Re: [ccp4bb] why does Coot ignore CONECT? > > On 01/11/2019 20:17, Pavel Mader wrote: > > Hello, > > Hello. > > > > > I have a question, can anyone explain, why does Coot not display a > covalent bond manually specified by > > CONECT line in a pdb file? > > Because I have never thought them necessary. Using SSBOND, LINK and > residue dictionaries seemed to me to > cover the bases for which CONECT would be used. > > Paul. > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] why does Coot ignore CONECT?
Hi Paul, thank you for your answer. My problem is that I am building a cyclic peptide with non-standard amino acids, the side chains of which are linked by click chemistry... I know how to make modified amino acids that will make peptide bonds with their neighbors in the polypeptide chain, but I don't know how to make a covalent link between side chains of amino acids say No. 3 and 12 for example (of a 15 AA long chain). I was trying to solve the issue by making a CONECT record in the pdb file, but Coot ignored it. LINK "sort of" worked, but it was not possible to control the geometry (bond length and angles), often the real space refinement simply "explodes" probably in a attempt to avoid clashes. My current workaround is to make a cif file for the whole 15 AA long polypeptide (the bonds and angles now behave more or less as expected), but I don't consider this as a good general practice for building long polypeptide chains... Thanks in advance for any hints guiding me in the right direction. Pavel -- Původní e-mail -- Od: Paul Emsley Komu: CCP4BB@JISCMAIL.AC.UK Datum: 1. 11. 2019 21:16:11 Předmět: Re: [ccp4bb] why does Coot ignore CONECT? "On 01/11/2019 20:17, Pavel Mader wrote: > Hello, Hello. > > I have a question, can anyone explain, why does Coot not display a covalent bond manually specified by > CONECT line in a pdb file? Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to cover the bases for which CONECT would be used. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 " To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] why does Coot ignore CONECT?
Hi Paul, I think this is a very good call as CONECT records are notoriously unreliable. Many PDB files don't have them and many programs don't update them when you change atom numbers. Even in annotated PDB entries there are many problems with those. It's better to forget about them altogether and focus on the mmCIF format. Cheers, Robbie On 2 Nov 2019 02:15, Paul Emsley wrote: On 01/11/2019 20:17, Pavel Mader wrote: > Hello, Hello. > > I have a question, can anyone explain, why does Coot not display a covalent > bond manually specified by > CONECT line in a pdb file? Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to cover the bases for which CONECT would be used. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] why does Coot ignore CONECT?
On 01/11/2019 20:17, Pavel Mader wrote: Hello, Hello. I have a question, can anyone explain, why does Coot not display a covalent bond manually specified by CONECT line in a pdb file? Because I have never thought them necessary. Using SSBOND, LINK and residue dictionaries seemed to me to cover the bases for which CONECT would be used. Paul. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] why does Coot ignore CONECT?
Hello, I have a question, can anyone explain, why does Coot not display a covalent bond manually specified by CONECT line in a pdb file? The same file shows the covalent bond if displayed in Pymol. Thank you in advance, Pavel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
