Re: [ccp4bb] mutate Methionine to Norleucine in Coot.
Hi Xavier, Thank you for your suggestion. Bestt, Jiang On Wed, Oct 26, 2022 at 12:10 AM Xavier Brazzolotto wrote: > You can only link a residue (L-peptide) N to another residue (L-peptide) > N+1 or N-1 > In your case you try to link VAL10 to NLE101… > Just change NLE101 to NLE11, then it should work. > > Le 26 oct. 2022 à 03:37, Jiang Xu a écrit : > > Hi Garib, >Thank you for your reply. I edited the NLE.cif file in the CCP4 monomer > library. You can see I successfully changed the group to L-peptide, as > shown below: > /Applications/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif | awk /NLE/ > NLE NLE NORLEUCINE L-peptide22 9 . > NLE-DNLE PEPT-D D-NORLEUCINE D-peptide > > cat cat /Applications/ccp4-7.1/lib/data/monomers/n/NLE.cif | awk > /L-peptide/ > NLE NLE NORLEUCINE L-peptide22 9 . >As shown in the following graph, I delete MET11 and then use the "Get > monomer" method of Coot using NLE. I then align the NLE to the local > electron density. But I couldn't change the linkage type that Coot still > regard it not as an a.a. residue but as a small molecule ligand. > I also tried to use the "Simple Mutate" tab in Coot to mutate MET11 to > NLE, but there's no NLE option there, even after I edited the NLE.cif in > the monomer library. > So, now the question is how to add the NLE to the Coot "Simple Mutate" > list? Do you have any suggestions? > Sincerely, > Jiang > > On Tue, Oct 25, 2022 at 4:29 PM Garib Murshadov > wrote: > >> It looks like that it is from ccp4 version 7 series. There, our programs >> may have changed HN2 with H2. >> However, you should check if the group name for this entry is L-peptide. >> If it is not L-peptide then coot will not recognise it as L-peptide (as far >> as I know) >> >> Regards >> Garib >> >> On 26 Oct 2022, at 00:18, Jiang Xu wrote: >> >> Hi Garib, >>Thank you for your help. I looked for NLE in the coot monomer library >> and found a file named NLE.cif at >> '/Applications/ccp4-7.1/lib/data/monomers/n'. I then searched this file for >> 'HN2' but didn't find any line that contains this string. So is it a typo >> or I was looking at the wrong file? >> Sincerely >> Jiang >> >> On Thu, Oct 20, 2022 at 12:36 AM Garib Murshadov >> wrote: >> >>> If you import cif dictionary then in coot mutate residue should work. At >>> least it worked n one of our problematic cases. If it does not work then >>> Paul Emsley may be able to help. >>> >>> Regards >>> Garib >>> >>> On 20 Oct 2022, at 02:06, Jiang Xu wrote: >>> >>> Hi Garib, >>>I deleted the Met residue and imported the nle.cif file into the >>> dictionary and checked the "create a molecule" box.I then used "real >>> space refinement" to align it correctly with the electron density. I then >>> save the merged molecule as a new pdb file but when I reopened the new >>> file, I found the NLE molecule's position was not aligned with the electron >>> density and couldn't be corrected with "real space refinement" in Coot. So >>> any suggestions? >>> Thank you, >>> Best, >>> Jiang >>> >>> On Wed, Oct 19, 2022 at 12:44 PM Garib Murshadov < >>> ga...@mrc-lmb.cam.ac.uk> wrote: >>> >>>> NLE is in the monomer library. However, it is marked as non-polymer. >>>> The reason why it is non-polymer is that one of the hydrogen atoms on N is >>>> called HN2 (in peptides they are H, H2 and H3). >>>> One easy way would be replace HN2 with H and save in a cif file. Then >>>> read it in coot using “import cif dictionary" and hope that coot will >>>> recognise it as peptide. I attach nle.cif just in case >>>> >>>> Regards >>>> Garib >>>> >>>> >>>> On 19 Oct 2022, at 20:34, Jiang Xu wrote: >>>> >>>> Hello Guys, >>>>I have a question regarding how to change the standard amino acid in >>>> my structure to Norleucine. It turned out that the one Methionine should be >>>> Norleucine. I tried to use the coot's mutation method but didn't find >>>> NLE(Norleucine) there. Any suggestions? >>>> Thank you, >>>> Best, >>>> Jiang >>>> Lin Chen Lab >>>> University of Southern California >>>> >>>> >>>> --
Re: [ccp4bb] mutate Methionine to Norleucine in Coot.
Hi Paul, Thank you very much for your suggestions. It works. Sincerely, Jiang On Wed, Oct 26, 2022 at 3:22 AM Paul Emsley wrote: > > On 20/10/2022 02:06, Jiang Xu wrote: > > Hi Garib, > >I deleted the Met residue and imported the nle.cif file > > > Import the dictionary for NLE, make sure that the group is L-peptide, > then centre on your Met and Calculate -> Modelling -> Replace Residue -> > NLE > > > Paul. > > > > 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] mutate Methionine to Norleucine in Coot.
Hi Garib, Thank you for your reply. I edited the NLE.cif file in the CCP4 monomer library. You can see I successfully changed the group to L-peptide, as shown below: /Applications/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif | awk /NLE/ NLE NLE NORLEUCINE L-peptide22 9 . NLE-DNLE PEPT-D D-NORLEUCINE D-peptide cat cat /Applications/ccp4-7.1/lib/data/monomers/n/NLE.cif | awk /L-peptide/ NLE NLE NORLEUCINE L-peptide22 9 . As shown in the following graph, I delete MET11 and then use the "Get monomer" method of Coot using NLE. I then align the NLE to the local electron density. But I couldn't change the linkage type that Coot still regard it not as an a.a. residue but as a small molecule ligand. I also tried to use the "Simple Mutate" tab in Coot to mutate MET11 to NLE, but there's no NLE option there, even after I edited the NLE.cif in the monomer library. So, now the question is how to add the NLE to the Coot "Simple Mutate" list? Do you have any suggestions? Sincerely, Jiang On Tue, Oct 25, 2022 at 4:29 PM Garib Murshadov wrote: > It looks like that it is from ccp4 version 7 series. There, our programs > may have changed HN2 with H2. > However, you should check if the group name for this entry is L-peptide. > If it is not L-peptide then coot will not recognise it as L-peptide (as far > as I know) > > Regards > Garib > > On 26 Oct 2022, at 00:18, Jiang Xu wrote: > > Hi Garib, >Thank you for your help. I looked for NLE in the coot monomer library > and found a file named NLE.cif at > '/Applications/ccp4-7.1/lib/data/monomers/n'. I then searched this file for > 'HN2' but didn't find any line that contains this string. So is it a typo > or I was looking at the wrong file? > Sincerely > Jiang > > On Thu, Oct 20, 2022 at 12:36 AM Garib Murshadov > wrote: > >> If you import cif dictionary then in coot mutate residue should work. At >> least it worked n one of our problematic cases. If it does not work then >> Paul Emsley may be able to help. >> >> Regards >> Garib >> >> On 20 Oct 2022, at 02:06, Jiang Xu wrote: >> >> Hi Garib, >>I deleted the Met residue and imported the nle.cif file into the >> dictionary and checked the "create a molecule" box.I then used "real >> space refinement" to align it correctly with the electron density. I then >> save the merged molecule as a new pdb file but when I reopened the new >> file, I found the NLE molecule's position was not aligned with the electron >> density and couldn't be corrected with "real space refinement" in Coot. So >> any suggestions? >> Thank you, >> Best, >> Jiang >> >> On Wed, Oct 19, 2022 at 12:44 PM Garib Murshadov >> wrote: >> >>> NLE is in the monomer library. However, it is marked as non-polymer. The >>> reason why it is non-polymer is that one of the hydrogen atoms on N is >>> called HN2 (in peptides they are H, H2 and H3). >>> One easy way would be replace HN2 with H and save in a cif file. Then >>> read it in coot using “import cif dictionary" and hope that coot will >>> recognise it as peptide. I attach nle.cif just in case >>> >>> Regards >>> Garib >>> >>> >>> On 19 Oct 2022, at 20:34, Jiang Xu wrote: >>> >>> Hello Guys, >>>I have a question regarding how to change the standard amino acid in >>> my structure to Norleucine. It turned out that the one Methionine should be >>> Norleucine. I tried to use the coot's mutation method but didn't find >>> NLE(Norleucine) there. Any suggestions? >>> Thank you, >>> Best, >>> Jiang >>> Lin Chen Lab >>> University of Southern California >>> >>> >>> -- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> 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 >> >> >> > 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] mutate Methionine to Norleucine in Coot.
Hi Garib, Thank you for your help. I looked for NLE in the coot monomer library and found a file named NLE.cif at '/Applications/ccp4-7.1/lib/data/monomers/n'. I then searched this file for 'HN2' but didn't find any line that contains this string. So is it a typo or I was looking at the wrong file? Sincerely Jiang On Thu, Oct 20, 2022 at 12:36 AM Garib Murshadov wrote: > If you import cif dictionary then in coot mutate residue should work. At > least it worked n one of our problematic cases. If it does not work then > Paul Emsley may be able to help. > > Regards > Garib > > On 20 Oct 2022, at 02:06, Jiang Xu wrote: > > Hi Garib, >I deleted the Met residue and imported the nle.cif file into the > dictionary and checked the "create a molecule" box.I then used "real > space refinement" to align it correctly with the electron density. I then > save the merged molecule as a new pdb file but when I reopened the new > file, I found the NLE molecule's position was not aligned with the electron > density and couldn't be corrected with "real space refinement" in Coot. So > any suggestions? > Thank you, > Best, > Jiang > > On Wed, Oct 19, 2022 at 12:44 PM Garib Murshadov > wrote: > >> NLE is in the monomer library. However, it is marked as non-polymer. The >> reason why it is non-polymer is that one of the hydrogen atoms on N is >> called HN2 (in peptides they are H, H2 and H3). >> One easy way would be replace HN2 with H and save in a cif file. Then >> read it in coot using “import cif dictionary" and hope that coot will >> recognise it as peptide. I attach nle.cif just in case >> >> Regards >> Garib >> >> >> On 19 Oct 2022, at 20:34, Jiang Xu wrote: >> >> Hello Guys, >>I have a question regarding how to change the standard amino acid in >> my structure to Norleucine. It turned out that the one Methionine should be >> Norleucine. I tried to use the coot's mutation method but didn't find >> NLE(Norleucine) there. Any suggestions? >> Thank you, >> Best, >> Jiang >> Lin Chen Lab >> University of Southern California >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> 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 > > > 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] mutate Methionine to Norleucine in Coot.
Hi Garib, I deleted the Met residue and imported the nle.cif file into the dictionary and checked the "create a molecule" box.I then used "real space refinement" to align it correctly with the electron density. I then save the merged molecule as a new pdb file but when I reopened the new file, I found the NLE molecule's position was not aligned with the electron density and couldn't be corrected with "real space refinement" in Coot. So any suggestions? Thank you, Best, Jiang On Wed, Oct 19, 2022 at 12:44 PM Garib Murshadov wrote: > NLE is in the monomer library. However, it is marked as non-polymer. The > reason why it is non-polymer is that one of the hydrogen atoms on N is > called HN2 (in peptides they are H, H2 and H3). > One easy way would be replace HN2 with H and save in a cif file. Then read > it in coot using “import cif dictionary" and hope that coot will recognise > it as peptide. I attach nle.cif just in case > > Regards > Garib > > > On 19 Oct 2022, at 20:34, Jiang Xu wrote: > > Hello Guys, >I have a question regarding how to change the standard amino acid in my > structure to Norleucine. It turned out that the one Methionine should be > Norleucine. I tried to use the coot's mutation method but didn't find > NLE(Norleucine) there. Any suggestions? > Thank you, > Best, > Jiang > Lin Chen Lab > University of Southern California > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > 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] mutate Methionine to Norleucine in Coot.
Hello Guys, I have a question regarding how to change the standard amino acid in my structure to Norleucine. It turned out that the one Methionine should be Norleucine. I tried to use the coot's mutation method but didn't find NLE(Norleucine) there. Any suggestions? Thank you, Best, Jiang Lin Chen Lab University of Southern California 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] circular peptide structure refinement
Hi Joel, Thank you for your reply. I just got time to refine the circular peptide structure 1 month later. I use MR to solve the structure. I made the link(Calculate-->Modeling-->Make Link) as the guy who replied to my question suggested. The link generated is a dashed line but disappeared after refinement with Phenix. It seemed that the program didn't consider the link made in coot as a valid bond and intentionally avoided forming a bond between the C atom and the N atom. I still don't know how to fix the problem. Thank you, Best regards, Jiang Lin Chen Lab University of Southern California P.S. coot manually made link between the C and N terminal [image: unnamed.jpg] After refinement [image: unnamed (1).jpg] On Wed, Jul 6, 2022 at 3:29 PM Joel Tyndall wrote: > You will need to add the “link” line to the PDB file so the software > recognises the covalent bond. > > > See the pdb file for 6U6K > > > > Hope this helps > > > > J > > > > *From:* CCP4 bulletin board *On Behalf Of *Jiang > Xu > *Sent:* Thursday, 7 July 2022 10:15 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] circular peptide structure refinement > > > > Hello everyone, > >I have a peptide that forms a peptide bond between the N terminal and C > terminal. I used X-ray crystallography to solve the structure and found > the N and C terminals are pretty close to each other with extra electron > densities clearly showing that they form a peptide bond. However in Coot I > could not make the peptide bond, the two terminals seem to repel each other > when I do real space refinement in coot and, couldn't form the peptide > bond. Any suggestions on how to do it? > > Thank you, > > Best, > > Jiang Xu > > Lin Chen Research Group > > Molecular and Computational Biology > > Department of Biological Sciences > > University of Southern California > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8e27251437384d075b9808da5f9d22ca%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C637927427557539545%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=xUCZ%2BQsYKRSrHmAM%2F0qDFoK2p1T%2BwalD1GErObuAwWU%3D=0> > 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] circular peptide structure refinement
Hello everyone, I have a peptide that forms a peptide bond between the N terminal and C terminal. I used X-ray crystallography to solve the structure and found the N and C terminals are pretty close to each other with extra electron densities clearly showing that they form a peptide bond. However in Coot I could not make the peptide bond, the two terminals seem to repel each other when I do real space refinement in coot and, couldn't form the peptide bond. Any suggestions on how to do it? Thank you, Best, Jiang Xu Lin Chen Research Group Molecular and Computational Biology Department of Biological Sciences University of Southern California 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] missing covalent bond between asparagine and N-acetylglucosamine using coot carbohydrate module and phenix.refine
Hello guys, I have a problem building and refining an xtal structure. My protein has a N-glycosylation site and I want to add N-acetylglucosamine and manose to my protein structure. I used Coot's carbohydrate module and let Coot automatically build the sugar chain to the electron density. It worked pretty well, but I noticed that the bond between the amine group of asparagine and the C1 of N-acetylglucosamine is depicted as a dashed line, rather than a solid line in Coot. After refinement of the structure using Phenix.refine, I found the bond just disappeared, and the amine group still has two hydrogen atoms, which should contain one hydrogen atom. So, how to solve this problem? [image: image.png] Thank you, Best, Jiang Xu Lin Chen's Research Group University of Southern California 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] aimless scale without merging data running Fail
Hello Phil, I just read my email and found I may not ask the question clearly. So my question is, should I use the integrated data from Imosflm, or should I use the output from Pointless as the input of Aimless to do scale without merging the data? Thank you, Best, Jiang Lin Chen Research Group University of Southern California On Wed, Jun 16, 2021 at 2:51 PM Jiang Xu wrote: > Hello Phil, >Thank you for the comments. I noticed that the ccp4 package I used was > 7.0. After upgrading to the latest version, the problem was solved. >I also have another question about Aimless. I want to use aimless to > scale without merging the data for generating the "table1" of my data. I > noticed that in your original publication, one way of doing the scale is to > use the "Quick Scale" button in Imosflm, in which the output from Pointless > will be the input of Aimless. However, I also noticed that some posts claim > that the input of Aimless could also be from the integrated data file from > Imosflm. I tried both ways and found no problem. So which way is the > correct way for my purpose? >Thank you, > Best, > Jiang > Lin Chen Research Group > University of Southern California > > On Wed, Jun 16, 2021 at 12:10 PM Phil Evans wrote: > >> I think it’s trying to write a file TILEIMAGE.img to a directory where >> you aren’t allowed to write. I can’t remember what is done in ccp4i - I >> believe it should work ok in ccp4i2, which produces better reports, and is >> generally recommended as a replacement for ccp4i >> >> As a workaround, you might be able to assign the file to somewhere you >> are allowed to write. Before running ccp4i, type something like (for tosh / >> cash, not sure about bash) >> >> setenv TILEIMAGE /some/suitable/directory/TILEIMAGE.img >> >> This file is an image of the correction factors for a tiled ccd detector >> >> I can look at this next week, to see if I can work out what is happening >> >> Phil >> >> Sent from my iPad >> >> On 16 Jun 2021, at 18:52, Jiang Xu wrote: >> >> >> Hello guys, >>I am having some problems running Aimless from the CCP4i packages. I >> want to scale without merging the data. The input mtz file for aimless was >> either the mtz file directly from Imosflm integration, or from Pointless >> from a previous run on Imosflm. I ran both pointless and aimless >> successfully on the Imosflm UI, after integration. However I just couldn't >> do it from the CCP4i. From the log it seems there's always an error >> message: "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file >> TILEIMAGE.img" >>I googled this line and found no hit. So does anyone know what's >> happening and how to solve this problem? >> Thank you, >> Best, >> Jiang Xu >> Lin Chen Research Group >> University of Southern California >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> 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/
Re: [ccp4bb] aimless scale without merging data running Fail
Hello Phil, Thank you for the comments. I noticed that the ccp4 package I used was 7.0. After upgrading to the latest version, the problem was solved. I also have another question about Aimless. I want to use aimless to scale without merging the data for generating the "table1" of my data. I noticed that in your original publication, one way of doing the scale is to use the "Quick Scale" button in Imosflm, in which the output from Pointless will be the input of Aimless. However, I also noticed that some posts claim that the input of Aimless could also be from the integrated data file from Imosflm. I tried both ways and found no problem. So which way is the correct way for my purpose? Thank you, Best, Jiang Lin Chen Research Group University of Southern California On Wed, Jun 16, 2021 at 12:10 PM Phil Evans wrote: > I think it’s trying to write a file TILEIMAGE.img to a directory where you > aren’t allowed to write. I can’t remember what is done in ccp4i - I believe > it should work ok in ccp4i2, which produces better reports, and is > generally recommended as a replacement for ccp4i > > As a workaround, you might be able to assign the file to somewhere you are > allowed to write. Before running ccp4i, type something like (for tosh / > cash, not sure about bash) > > setenv TILEIMAGE /some/suitable/directory/TILEIMAGE.img > > This file is an image of the correction factors for a tiled ccd detector > > I can look at this next week, to see if I can work out what is happening > > Phil > > Sent from my iPad > > On 16 Jun 2021, at 18:52, Jiang Xu wrote: > > > Hello guys, >I am having some problems running Aimless from the CCP4i packages. I > want to scale without merging the data. The input mtz file for aimless was > either the mtz file directly from Imosflm integration, or from Pointless > from a previous run on Imosflm. I ran both pointless and aimless > successfully on the Imosflm UI, after integration. However I just couldn't > do it from the CCP4i. From the log it seems there's always an error > message: "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file > TILEIMAGE.img" >I googled this line and found no hit. So does anyone know what's > happening and how to solve this problem? > Thank you, > Best, > Jiang Xu > Lin Chen Research Group > University of Southern California > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > 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] aimless scale without merging data running Fail
Hello guys, I am having some problems running Aimless from the CCP4i packages. I want to scale without merging the data. The input mtz file for aimless was either the mtz file directly from Imosflm integration, or from Pointless from a previous run on Imosflm. I ran both pointless and aimless successfully on the Imosflm UI, after integration. However I just couldn't do it from the CCP4i. From the log it seems there's always an error message: "#CCP4I TERMINATION STATUS 0 "OpenFile: cannot open file TILEIMAGE.img" I googled this line and found no hit. So does anyone know what's happening and how to solve this problem? Thank you, Best, Jiang Xu Lin Chen Research Group University of Southern California 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/ #CCP4I VERSION CCP4Interface 7.0.078 #CCP4I SCRIPT LOG aimless #CCP4I DATE 16 Jun 2021 10:32:41 #CCP4I USER linchenlab #CCP4I PROJECT alpha1actx #CCP4I JOB_ID 17 #CCP4I SCRATCH /tmp/linchenlab #CCP4I HOSTNAME linchenlab #CCP4I PID 10938 ### ### ### ### CCP4 7.0.078: POINTLESSversion 1.11.21 : 10/05/19## ### User: unknown Run date: 16/ 6/2021 Run time: 10:32:41 Please reference: Collaborative Computational Project, Number 4. 2011. "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242. as well as any specific reference in the program write-up. Command line arguments HKLOUT /tmp/linchenlab/alpha1actx_17_2_mtz.tmp XMLOUT /home/linchenlab/ccp4/jiangxu/alpha1actx/alpha1actx_17_pointless.xml Release Date: 10th May 2019 Input command lines HKLIN /home/linchenlab/ccp4/jiangxu/alpha1actx/pointless_run_11_1.mtz ## This script run with the command ## # /usr/bin/CCP4/ccp4-7.0/bin/pointless HKLOUT "/tmp/linchenlab/alpha1actx_17_2_mtz.tmp" XMLOUT & "/home/linchenlab/ccp4/jiangxu/alpha1actx/alpha1actx_17_pointless.xml" End of input ** ** * POINTLESS * * 1.11.21 * ** * Determine Laue group from unmerged intensities * * Phil Evans MRC LMB, Cambridge * * Uses cctbx routines by Ralf Grosse-Kunstleve et al.* ** ** Reflection list generated from file: /home/linchenlab/ccp4/jiangxu/alpha1actx/pointless_run_11_1.mtz Title: Untitled Space group from HKLIN file : P 21 21 21 Cell:45.59 46.91 149.84 90.00 90.00 90.00 Resolution range in file: 74.922.26 Time for reading file(s):0.393 secs === >*> Summary of test data read in: Resolution range accepted:74.922.26 Number of reflections = 15828 Number of observations =157818 Number of parts=324574 Number of batches in file = 269 Number of datasets = 1 Project: New Crystal: New Dataset: New Run number: 1 consists of batches 1 - 269 Resolution range for run:74.922.26 Phi range:90.51 to 359.51 Time range:90.51 to 359.51 Closest reciprocal axis to spindle: b* (angle 16.7 degrees) Unit cell for dataset:45.59 46.91 149.84 90.00 90.00 90.00 Wavelength: 0.3 Numbers of observations marked in the FLAG column By default all flagged observations are rejected Observations may be counted in more than one category Flagged Accepted Maximum MaxAccepted BGratio too large 0 0 1.800 0.000 PKratio too large 53 0 5.100 0.000 Negative < 5sigma 1 0 Gradient too large 3 0 0.047 0.000 Profile-fitted overloads 1 1 Spots on edge 3324 0 XDS misfits (outliers) 0 0 =
Re: [ccp4bb] CCP4BB Digest - 18 Jan 2017 to 19 Jan 2017 (#2017-20)
Hi, everyone, I think I found the cause and solution. It was due to the project folder of CCP4i,which was set by me to E:/***/** p reviously, based on which imosflm automatically set its processing folder also as E:/***/. Because disk E: used to be the flash disk on my computer, when I unplug the flash disk, the software cannot find the disk then it will report the error. When I change the project folder in CCP4i to D:/***/**, which was present on my computer, the problem was solved. Best! Jiang On Thu, Jan 19, 2017 at 4:00 PM, CCP4BB automatic digest system < lists...@jiscmail.ac.uk> wrote: > There are 23 messages totaling 6640 lines in this issue. > > Topics of the day: > > 1. on space group (2) > 2. error in startup script > 3. AW: [ccp4bb] on space group > 4. *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error in > startup > script > 5. Call for MX beamtime proposals at HZB, BESSY II, deadline March 01, > 2017 > 6. Off-topic, protein in dye-front (ion front?) on native-PAGE (5) > 7. 6th Edition of the ISBC2017 > 8. Cryosystems series 600 > 9. Unique postdoctoral research opportunity in Tromsø, Norway > 10. PhD fellowships in Spain > 11. Anisotropy and temperature (4) > 12. CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15) (3) > 13. Joint Postdoctoral Position in the Grishin and Chook Labs at UT > Southwestern > > -- > > Date:Thu, 19 Jan 2017 02:33:14 + > From:Smith Lee <smith_lee...@yahoo.com> > Subject: on space group > > > Dear All, > In the literature, somebody call space group P65 crystal as "six fold > screw axis crystal packing", then I would not make any mistake if I call > P64 space group crystal also as "six fold screw axis crystal packing",am I > right? > I am looking forward to getting a reply from you. > > -- > > Date:Wed, 18 Jan 2017 19:40:30 -0800 > From:Jiang Xu <foxj...@gmail.com> > Subject: error in startup script > > Hi, Mr/Ms, >I am a user of CCP4i. I recently discovered that imosflm cannot be used > on my win7. the error message is shown below. >[image: Inline image 1] > However, when I go to 'bin' folder and double click the imosflm.bat, the > program can be start up successfully. I don't know what's the problem. > Thank you! > Best! > Jiang Xu > Department of Molecular and Computational Biology > University of Southern California > > -- > > Date:Thu, 19 Jan 2017 05:22:24 + > From:Smith Lee <smith_lee...@yahoo.com> > Subject: Re: on space group > > Dear All, > Here may I make my question much clear? For the space group P 65 crystal, > it seems we can call it "6-fold packing of subunits around a screw axis in > the crystal". Then for the space group P 64 crystal, can it also be called > "6-fold packing of subunits around a screw axis in the crystal"? > Smith > > On Thursday, January 19, 2017 11:50 AM, Ethan Merritt < > merr...@u.washington.edu> wrote: > > > On Thursday, 19 January 2017 02:33:14 AM you wrote: > > > > Dear All, > > In the literature, somebody call space group P65 crystal as "six fold > screw axis crystal packing", then I would not make any mistake if I call > P64 space group crystal also as "six fold screw axis crystal packing",am I > right? > > I am looking forward to getting a reply from you. > > Smith > > "six-fold screw axis" refers to the symmetry. > > "crystal packing" refers to the molecule-to-molecule contacts regardless > of symmetry. > > So no, I don't think "six fold screw axis crystal packing" makes any sense. > > -- > Ethan A Merritt, Dept of Biochemistry > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > > -- > > Date:Thu, 19 Jan 2017 08:47:52 + > From:herman.schreu...@sanofi.com > Subject: AW: [ccp4bb] on space group > > Dear Smith, > > I think your question was clear, and the answer you got was clear as well. > > However, I think the question you asked was not the right question. You > want to use a particular phrase to describe your crystal packing and you > want the CCP4BB to endorse this. When the answer was negative, you asked > again the same question. > > The real question, in my eyes, is “What is the best way to describe my P65 > crystal packing” since I guess you want to use this in your paper. Here I > would use something like “in the crystal
[ccp4bb] error in startup script
Hi, Mr/Ms, I am a user of CCP4i. I recently discovered that imosflm cannot be used on my win7. the error message is shown below. [image: Inline image 1] However, when I go to 'bin' folder and double click the imosflm.bat, the program can be start up successfully. I don't know what's the problem. Thank you! Best! Jiang Xu Department of Molecular and Computational Biology University of Southern California
