Re: [ccp4bb] Rigaku CrystalTrak Web not working
Hi Johannes, just making sure that there is no misunderstanding. I am currently working in Dr. Frank Sicheri lab at Mount Sinai Hospital in Toronto, ON, Canada. Is this the local installation you are talking about? I am just using my Czech email account, since I have the CCP4BB already set up on this account... Thanks, Pavel -- Původní e-mail -- Od: Johannes Cramer Komu: Pavel Mader Datum: 19. 2. 2021 7:04:48 Předmět: Re: [ccp4bb] Rigaku CrystalTrak Web not working " Hey Pavel, afaik our local installation of the software still works. So if going there physically is an option for you, you can try that. Cheers, Johannes Am Do., 18. Feb. 2021 um 18:21 Uhr schrieb Pavel Mader mailto:mader.pa...@seznam.cz)>: " Hello everyone, is there anyone else, who is using Rigaku CrystalTrak Web system (in our case version 2.3.4) for checking images of crystallization experiments? Recently (on January 14, 2021) the Adobe has stopped supporting the Flash support needed for the CrystalTrak web version from being fully functional. Is there anyone else, who has been facing this problem? Is there any good solution? Thanks, Pavel Mader To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 (https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1) " " 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] Rigaku CrystalTrak Web not working
Hello everyone, is there anyone else, who is using Rigaku CrystalTrak Web system (in our case version 2.3.4) for checking images of crystallization experiments? Recently (on January 14, 2021) the Adobe has stopped supporting the Flash support needed for the CrystalTrak web version from being fully functional. Is there anyone else, who has been facing this problem? Is there any good solution? Thanks, Pavel Mader 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/
Re: [ccp4bb] Any guesses? - What is this feature modelled (wrongly) as 3 waters
Hello Can you provide the list of all the components in the crystallization experiment? Except the protein of course. What is the resolution of the structure? Have the B-factors been refined anisotropically? At what sigma level is the 2Fo-Fc map and Fo-Fc map (doesn't seem to be shown)? If I were to take a wild guess - the size might accommodate ethanol (glycerol and ethylene glycol would be too big already and the geometry doesn't look right for metal ion complex either). Pavel -- Původní e-mail -- Od: Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Komu: CCP4BB@JISCMAIL.AC.UK Datum: 7. 11. 2019 8:12:51 Předmět: [ccp4bb] Any guesses? - What is this feature modelled (wrongly) as 3 waters " seen in a high resolution map? There is at least one other similar feature??? Eleanor 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?
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?
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
[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
[ccp4bb] D amino acids in Coot
Hi everyone, if I load D-Ala (Get monomer DAL) in Coot and superpose (LSQ) it with regular L-Ala (ALA), the two amino acids look identical to me (not mirror images of each other), see attached image. I have the same problem with D- His. Is this normal, or am I missing something? Thanks, Pavel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
