Re: [ccp4bb] How to fix: residues with missing atoms
Dear Paul - your tip seems like a life-saver. I gave it a quick try but failed, not in that it didn't filled up the side chains well, but in that the patched-up residues are now broken apart from its original polypeptide chains. Extensions -> All Molecule -> [Post MR] Fill Partial Residues... I'm using WinCoot 0.8.9.2 EL. Sorry if I have missed anything obvious. Thanks for your helps, -yong On Sat, May 23, 2020 at 9:30 PM Paul Emsley wrote: > On 23/05/2020 20:18, Yong Tang wrote: > > Dear all, is there a way to "automatically" patch up the missing atoms > > in the residues that otherwise are properly defined in a PDB entry. > > For example, an Arginine is defined as Arginine but only has the beta > > carbon on the side chain. > > > > In Coot I could use the Extensions/Modeling/Residues with Missing > > Atoms to identify these residues and then go down the list to "mutate" > > them one by one by hand. Is there anything more efficient? > > > Calculate -> All Molecule -> [Post MR] Fill Partial Residues... > > > > I could also use the Calculate/Mutate Residue Range but this > > inevitably changes the "good" residue side chains also. > > > Yeah... don't do that. > > > Paul. > > > > 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/ > 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/
Re: [ccp4bb] How to fix: residues with missing atoms
On 23/05/2020 20:18, Yong Tang wrote: Dear all, is there a way to "automatically" patch up the missing atoms in the residues that otherwise are properly defined in a PDB entry. For example, an Arginine is defined as Arginine but only has the beta carbon on the side chain. In Coot I could use the Extensions/Modeling/Residues with Missing Atoms to identify these residues and then go down the list to "mutate" them one by one by hand. Is there anything more efficient? Calculate -> All Molecule -> [Post MR] Fill Partial Residues... I could also use the Calculate/Mutate Residue Range but this inevitably changes the "good" residue side chains also. Yeah... don't do that. Paul. 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/
Re: [ccp4bb] How to fix: residues with missing atoms
Try SWISS-MODEL. Sent from Jack's iPhone On May 23, 2020, at 6:24 PM, Eugene Osipov wrote: Dear Yong, you could use freely available Chimera.Use Tools->Structure Editing-> Dock prep. in order to add missing side chains to your protein. Another option - Protein preparation tool from Schrodinger Suite. However, it is non-free. сб, 23 мая 2020 г. в 21:19, Yong Tang mailto:liutan...@gmail.com>>: Dear all, is there a way to "automatically" patch up the missing atoms in the residues that otherwise are properly defined in a PDB entry. For example, an Arginine is defined as Arginine but only has the beta carbon on the side chain. In Coot I could use the Extensions/Modeling/Residues with Missing Atoms to identify these residues and then go down the list to "mutate" them one by one by hand. Is there anything more efficient? I could also use the Calculate/Mutate Residue Range but this inevitably changes the "good" residue side chains also. Any tip is much appreciated, -yong To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O 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 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 to fix: residues with missing atoms
Dear Yong, you could use freely available Chimera.Use Tools->Structure Editing-> Dock prep. in order to add missing side chains to your protein. Another option - Protein preparation tool from Schrodinger Suite. However, it is non-free. сб, 23 мая 2020 г. в 21:19, Yong Tang : > Dear all, is there a way to "automatically" patch up the missing atoms in > the residues that otherwise are properly defined in a PDB entry. For > example, an Arginine is defined as Arginine but only has the beta carbon on > the side chain. > > In Coot I could use the Extensions/Modeling/Residues with Missing Atoms to > identify these residues and then go down the list to "mutate" them one by > one by hand. Is there anything more efficient? I could also use the > Calculate/Mutate Residue Range but this inevitably changes the "good" > residue side chains also. > > Any tip is much appreciated, -yong > >> > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > -- Evgenii Osipov Laboratory for Biocrystallography, Department of Pharmaceutical Sciences, KU Leuven O 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/
Re: [ccp4bb] Space group/Unit cell
Dear Maria - Lipid diffraction resembles powder diffraction rather than discrete spots - you can see examples in Cherezov's 2002 Biophys J article, for example - so you wouldn't mistake them for protein diffraction. If not a case of overlooked predictions as Kay suggests, you have probably crystallized either a small molecule, a protein contaminant, or a proteolytic fragment of your protein. I have accidentally crystallized a contaminating enzyme at low enough concentration that it wasn't visible on SDS PAGE; I could only track it by activity. If Contaminer doesn't reveal anything and you don't believe you have salt crystals, you probably need to do some mass spec to figure out what species in your drop. Best of luck Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Fri, May 22, 2020 at 3:10 AM Demou, Maria wrote: > Dear all, > I have a question that may have a straight forward answer, and was > wondering if this is a common issue. We have a protein crystallised in I222 > space group. This is CRP, but the monomer/pentamer is not predicted to fit > in this space group. Is there a possibility of the lipid cubic phase being > crystallised on it's own, or is there any other obvious reason? > > Thank you, > Maria > > > -- > > 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 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 to fix: residues with missing atoms
Dear all, is there a way to "automatically" patch up the missing atoms in the residues that otherwise are properly defined in a PDB entry. For example, an Arginine is defined as Arginine but only has the beta carbon on the side chain. In Coot I could use the Extensions/Modeling/Residues with Missing Atoms to identify these residues and then go down the list to "mutate" them one by one by hand. Is there anything more efficient? I could also use the Calculate/Mutate Residue Range but this inevitably changes the "good" residue side chains also. Any tip is much appreciated, -yong > 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/
Re: [ccp4bb] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL
> > I thought that some of the list members may be interested in the paper, > titled "DSSR-enabled innovative schematics of 3D nucleic acid structures > with PyMOL", recently published in _Nucleic Acids Research_ ( > https://doi.org/10.1093/nar/gkz1222). *Sorry* about the wrong link to nar/gkz1222 -- I was reading that interesting paper on U•A-U-rich RNA triple helix. The correct URL to the DSSR-PyMOL NAR paper is: https://doi.org/10.1093/nar/gkaa426 Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ On Sat, May 23, 2020 at 1:32 PM Xiang-Jun Lu <3dna...@gmail.com> wrote: > I thought that some of the list members may be interested in the paper, > titled "DSSR-enabled innovative schematics of 3D nucleic acid structures > with PyMOL", recently published in _Nucleic Acids Research_ ( > https://doi.org/10.1093/nar/gkz1222). Among other things, DSSR can > dramatically simplify the depiction of G-quadruplexes by automatically > detecting G-tetrads and treating them as large square blocks. > > The web application interface (http://skmatic.x3dna.org/) also provides > pre-calculated schematics and meta information of nucleic-acid-containing > structures in the PDB. Here are some examples: > > * http://skmatic.x3dna.org/pdb/2lx1 > * http://skmatic.x3dna.org/pdb/2grb > * http://skmatic.x3dna.org/pdb/6vu1 > * http://skmatic.x3dna.org/pdb_entries # 12 random entries > * http://skmatic.x3dna.org/pdb_entries/recent-week > * http://skmatic.x3dna.org/pdb_entries/recent-month > > The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been > written to serve as a practical guide, with complete and reproducible > examples. > > Best regards, > > Xiang-Jun > > -- > Xiang-Jun Lu (Ph.D.) > Email: xiang...@x3dna.org > Web: http://x3dna.org/ > Forum: http://forum.x3dna.org/ > 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/
[ccp4bb] DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL
I thought that some of the list members may be interested in the paper, titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL", recently published in _Nucleic Acids Research_ ( https://doi.org/10.1093/nar/gkz1222). Among other things, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The web application interface (http://skmatic.x3dna.org/) also provides pre-calculated schematics and meta information of nucleic-acid-containing structures in the PDB. Here are some examples: * http://skmatic.x3dna.org/pdb/2lx1 * http://skmatic.x3dna.org/pdb/2grb * http://skmatic.x3dna.org/pdb/6vu1 * http://skmatic.x3dna.org/pdb_entries # 12 random entries * http://skmatic.x3dna.org/pdb_entries/recent-week * http://skmatic.x3dna.org/pdb_entries/recent-month The supplemental PDF (http://skmatic.x3dna.org/gkaa426-supp.pdf) has been written to serve as a practical guide, with complete and reproducible examples. Best regards, Xiang-Jun -- Xiang-Jun Lu (Ph.D.) Email: xiang...@x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ 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/
Re: [ccp4bb] Space group/Unit cell
Dear Maria, maybe a case of underpredicted/overlooked reflections? It could then be P2x2x2x instead of I222/I212121. Have you checked the predictions? best, Kay On Fri, 22 May 2020 10:08:40 +, Demou, Maria wrote: >Dear all, >I have a question that may have a straight forward answer, and was wondering >if this is a common issue. We have a protein crystallised in I222 space group. >This is CRP, but the monomer/pentamer is not predicted to fit in this space >group. Is there a possibility of the lipid cubic phase being crystallised on >it's own, or is there any other obvious reason? > >Thank you, >Maria > > > > >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/ > 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/
