Re: [ccp4bb] refmac - use weighting term - pdb to mmcif
I deleted a line in the keyword file which was "pdbout format mmcif". It was my first try to convert the pdb file to an mmcif file, but it did not work! Best Marina Zitat von "Krieger, James M" : It could be good to say how you solved it for future users. Best wishes James On Aug 6, 2021, at 09:27, Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk> wrote: Hi, as it is often the case, the mail is out and you are able to solve the problem on your own. Thanks anyway! Best Marina Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>: Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to refine occupancies and tls in Refmac. I also found out that you can use pdb-extract to convert the pdb file to an mmcif file so that you can validate the structure using the validation server. However, during validation, it came out that the bond lengths and angles are hugely different from the expected values. I had used the automatic weighting until then. If I do the weighting by hand (I tried different weighting terms), I cannot convert the pdb file into an mmcif file anymore, because the pdb file has a different structure and pdb-extract does not recognize the pdb file as such. Does anyone know the problem and can help me? Best Marina -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.agklebe.de%2Fdata=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575981454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=oLpz7kaDDGV4UF6wD%2B7mpvkZEmzuA4Bg0aoR0JtLkxk%3Dreserved=0 To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575981454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=S1GsquQVrGdXfvMBRITumN2jFzt2bUH%2BKmJnyzTTiR0%3Dreserved=0 This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BBdata=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575981454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=uA0xW5K99cxQ6vQOms6GBCwVtMiWDRhjyuVa6KTXh4c%3Dreserved=0, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2Fdata=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575981454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=t5jtV0M334AFxiAZPnPB%2FyxsXN95FaYDWXMe42oAi0o%3Dreserved=0, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2Fdata=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575991448%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=kJoNQnDRei5VuJzIzZL4XBNfe3AB3sx%2F8Ef6Sn%2BONmw%3Dreserved=0 -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.agklebe.de%2Fdata=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575991448%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=Gaa%2FEEryWtXD%2BvT9UNHXP6G69JzTQKuz6lqa4mhagSU%3Dreserved=0 To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1data=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575991448%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%
Re: [ccp4bb] refmac - use weighting term - pdb to mmcif
Hi, as it is often the case, the mail is out and you are able to solve the problem on your own. Thanks anyway! Best Marina Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>: Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to refine occupancies and tls in Refmac. I also found out that you can use pdb-extract to convert the pdb file to an mmcif file so that you can validate the structure using the validation server. However, during validation, it came out that the bond lengths and angles are hugely different from the expected values. I had used the automatic weighting until then. If I do the weighting by hand (I tried different weighting terms), I cannot convert the pdb file into an mmcif file anymore, because the pdb file has a different structure and pdb-extract does not recognize the pdb file as such. Does anyone know the problem and can help me? Best Marina -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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/ -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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] refmac - use weighting term - pdb to mmcif
Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to refine occupancies and tls in Refmac. I also found out that you can use pdb-extract to convert the pdb file to an mmcif file so that you can validate the structure using the validation server. However, during validation, it came out that the bond lengths and angles are hugely different from the expected values. I had used the automatic weighting until then. If I do the weighting by hand (I tried different weighting terms), I cannot convert the pdb file into an mmcif file anymore, because the pdb file has a different structure and pdb-extract does not recognize the pdb file as such. Does anyone know the problem and can help me? Best Marina -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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] How can I refine the occupancy with Refmac?
Hi, I didn't know that I can also enter keywords without a file! That is a good note, thank you!! Best regards, Marina Zitat von Jon Cooper : Hello, the keywords can be entered in refmac gui (in one of the dropdown things), so you don't need a file, as such, but it's useful to keep a record. Sent from ProtonMail mobile Original Message On 5 Jun 2021, 16:39, Marina Gárdonyi wrote: Hello everyone, I am trying to refine structures with Refmac. The problem is that nobody from my working group is familiar with this programm. They are using Phenix exclusively. That's why I need your help. I would like to refine the occupancy. I know that I need a keyword file for this, but I have no idea how to create such a keyword file. Can someone maybe send me a sample file? I think that would help me. I have found essential keywords, but I don't know how to build up such a file. Thank you very much in advance! Best regards, Marina -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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/ -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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] How can I refine the occupancy with Refmac?
Hello everyone, I am trying to refine structures with Refmac. The problem is that nobody from my working group is familiar with this programm. They are using Phenix exclusively. That's why I need your help. I would like to refine the occupancy. I know that I need a keyword file for this, but I have no idea how to create such a keyword file. Can someone maybe send me a sample file? I think that would help me. I have found essential keywords, but I don't know how to build up such a file. Thank you very much in advance! Best regards, Marina -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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] Can twinning be seen in the diffraction pattern?
Dear all, thanks to all who helped me solving the question. You sent me a lot of comments and information I have not taken into account. After reading all the answers, I have come to the conclusion that the spots that are very close to each other come from the long cell axis (57-57-160) and that twinning can probably not be seen in my case. I should have mentioned that the diffraction images came from an in-house x-ray machine, recorded with a 0.5 degree rotation range. Thank you all again! Kind regards, Marina -- Marina Gárdonyi PhD Student, Research Group Professor Dr. Klebe Department of Pharmaceutical Chemistry Philipps-University Marburg Marbacher Weg 6, 35032 Marburg, Germany Phone: +49 6421 28 21392 E-Mail: marina@pharmazie.uni-marburg.de http://www.agklebe.de/ 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/
