Re: [PyMOL] fix cartoon backbone
Thank you. Interestingly… These alter commands do work on the DNA in my original working .pse file, the file that contains all of the structures. They do work on the “save molecule” as a cif file that I shared with you, if I open it into PyMOL by itself. They also work if I open the chain F.cif into my original working .pse file. This will fix the new chain F but not the old chain F. Something about saving the chain out as a cif file and bringing it back in alters something besides just the atom naming. > On Mar 22, 2019, at 1:43 PM, Thomas Holder > wrote: > > Hi Adam, > > The atom naming is nonstandard. If you fix that, the cartoon will be complete. > > alter name P01, name="P" > alter name O01, name="O5'" > alter name O02, name="OP1" > alter name O03, name="OP2" > unbond name OP1, name O3'+O5' > unbond name OP2, name O3'+O5' > > PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately > the mmCIF spec doesn't make this straight forward). You could save to MMTF > instead, it stores all bonds. > > Cheers, > Thomas > > >> On Mar 22, 2019, at 5:42 PM, h. adam steinberg >> wrote: >> >> Thank you, that certainly brought the chains together, but sill no completed >> cartoon even after a rebuild. >> >> Attached is chain F, can you see anything wrong with this file that won’t >> let it display a complete chain? It must be with how I joined the missing >> atoms? >> >> I also notice that every time I open this object in PyMOL I get odd bonding >> happening. Even when I unbond those odd connections and resave the file, it >> puts them right back in when I reopen the file. >> >> I could simply fake the connection using photoshop, but I’m trying to learn >> to do it correctly! :) I appreciate your help! >> >> >> >>> On Mar 22, 2019, at 11:31 AM, Jared Sampson >>> wrote: >>> >>> Hi Adam - >>> >>> The characters between the object names and the chain IDs are the segment >>> IDs. You can remove them by setting them to the empty string using `alter`: >>> >>> alter all, segi="" >>> >>> Hope that helps. >>> >>> Cheers, >>> Jared >>> >>> >>> On March 22, 2019 at 12:14:46 PM, h. adam steinberg >>> (h.adam.steinb...@gmail.com) wrote: >>> > On Mar 21, 2019, at 1:41 AM, Kevin Jude wrote: > > The DNA in 1CGP is made up of two annealed half sites, so there are four > chain assignments for the two strands. If you want to display it as > intact DNA, after adding the linking phosphate you can use the alter > command to make the chains continuous. HTH. > > -- > 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 Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg > wrote: > Hi All, > > I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. > After I fixed those two breaks (add in the correct atoms and join them) > how do I get the cartoon of the DNA to be complete? PyMOL still creates > the cartoon with the breaks. > > Thanks! > > Adam > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] fix cartoon backbone
Hi Adam, The atom naming is nonstandard. If you fix that, the cartoon will be complete. alter name P01, name="P" alter name O01, name="O5'" alter name O02, name="OP1" alter name O03, name="OP2" unbond name OP1, name O3'+O5' unbond name OP2, name O3'+O5' PyMOL doesn't yet write bonds to mmCIF (it's on our TODO list, unfortunately the mmCIF spec doesn't make this straight forward). You could save to MMTF instead, it stores all bonds. Cheers, Thomas > On Mar 22, 2019, at 5:42 PM, h. adam steinberg > wrote: > > Thank you, that certainly brought the chains together, but sill no completed > cartoon even after a rebuild. > > Attached is chain F, can you see anything wrong with this file that won’t let > it display a complete chain? It must be with how I joined the missing atoms? > > I also notice that every time I open this object in PyMOL I get odd bonding > happening. Even when I unbond those odd connections and resave the file, it > puts them right back in when I reopen the file. > > I could simply fake the connection using photoshop, but I’m trying to learn > to do it correctly! :) I appreciate your help! > > > >> On Mar 22, 2019, at 11:31 AM, Jared Sampson >> wrote: >> >> Hi Adam - >> >> The characters between the object names and the chain IDs are the segment >> IDs. You can remove them by setting them to the empty string using `alter`: >> >> alter all, segi="" >> >> Hope that helps. >> >> Cheers, >> Jared >> >> >> On March 22, 2019 at 12:14:46 PM, h. adam steinberg >> (h.adam.steinb...@gmail.com) wrote: >> >>> >>> On Mar 21, 2019, at 1:41 AM, Kevin Jude wrote: The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH. -- 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 Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg wrote: Hi All, I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks. Thanks! Adam -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] fix cartoon backbone
Thank you, that certainly brought the chains together, but sill no completed cartoon even after a rebuild.Attached is chain F, can you see anything wrong with this file that won’t let it display a complete chain? It must be with how I joined the missing atoms?I also notice that every time I open this object in PyMOL I get odd bonding happening. Even when I unbond those odd connections and resave the file, it puts them right back in when I reopen the file.I could simply fake the connection using photoshop, but I’m trying to learn to do it correctly! :) I appreciate your help! chain F.cif Description: Binary data On Mar 22, 2019, at 11:31 AM, Jared Sampsonwrote:Hi Adam -The characters between the object names and the chain IDs are the segment IDs. You can remove them by setting them to the empty string using `alter`:alter all, segi=""Hope that helps.Cheers,JaredOn March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.adam.steinb...@gmail.com) wrote:On Mar 21, 2019, at 1:41 AM, Kevin Jude wrote:The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH.--Kevin Jude, PhDStructural Biology Research Specialist, Garcia LabHoward Hughes Medical InstituteStanford University School of MedicineBeckman B177, 279 Campus Drive, Stanford CA 94305Phone: (650) 723-6431On Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg wrote:Hi All,I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks.Thanks!Adam___PyMOL-users mailing listArchives: http://www.mail-archive.com/pymol-users@lists.sourceforge.netUnsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] fix cartoon backbone
Hi Adam - The characters between the object names and the chain IDs are the segment IDs. You can remove them by setting them to the empty string using `alter`: alter all, segi="" Hope that helps. Cheers, Jared On March 22, 2019 at 12:14:46 PM, h. adam steinberg (h.adam.steinb...@gmail.com) wrote: On Mar 21, 2019, at 1:41 AM, Kevin Jude wrote: The DNA in 1CGP is made up of two annealed half sites, so there are four chain assignments for the two strands. If you want to display it as intact DNA, after adding the linking phosphate you can use the alter command to make the chains continuous. HTH. -- 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 Wed, Mar 20, 2019 at 12:18 PM h. adam steinberg wrote: Hi All, I opened 1cgp and the DNA has two breaks in the nucleic acid backbone. After I fixed those two breaks (add in the correct atoms and join them) how do I get the cartoon of the DNA to be complete? PyMOL still creates the cartoon with the breaks. Thanks! Adam ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Pymol recolour B factors
Hi Mark, In that data2bfactor.py script (which I wrote) you need to provide the molecular object name, not a file name. In other words in your example you should load the 1d3z.pdb file as an object (defaults to 1d3z as object name). Then after using the run command to load the script into your pymol session then you can type: data2b_res 1d3z, shift_to_b.txt The other script you mention works the same way. The pdb file needs to be loaded into PyMOL as a molecular object first. Cheers, Rob On Fri, 2019-03-22 11:36 +, Dr Mark Bostock wrote: > Hello, > > I'm trying to recolour the B factors in a pymol file with chemical > shift differences (from NMR data). There's a nice script here for > this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ > (data2bfactor.py) and also a simpler one here > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffigshare.com%2Farticles%2FPymol_script_loadBfacts_py%2F1176991&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468&sdata=jDmJ4NSc%2F%2BXy5IG%2BRCCsQOmqh1Xj9l4j6gTMEmJB6Zc%3D&reserved=0. > > In both cases after loading the script with the run command, when I > execute the script I get the following error > > data2b_res 1d3z.pdb, shift_to_b.txt > Selector-Error: Invalid selection name "1d3z.pdb". > ( 1d3z.pdb )<-- > > The pdb file and list of new b-factor values are in the same > directory and can be filled in with tab-completion. I've also tried > using the full file path but get a similar error. I've tried with a > couple of different pdb files as well so it's not just a problem with > that particular pdb file. > > I'd be grateful if anyone has any experience with this or suggestions > as to what is going wrong. > > Thanks in advance, > > Mark > > > > ___ > PyMOL-users mailing list > Archives: > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158871468&sdata=rhUIX1kYhGF0ax1YHrbOBvO5agrVsRdkuUKYJA9A26w%3D&reserved=0 > Unsubscribe: > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&data=02%7C01%7Crobert.campbell%40queensu.ca%7C664f1bfa0c934c52f40108d6aebdf161%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C1%7C636888528158881482&sdata=rsNyC33RqUJbXDKsWpMVagHLOXVUH4bM8vo3cdmTtlE%3D&reserved=0 -- Robert L. Campbell, Ph.D. Adjunct Assistant Professor Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644 Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 http://pldserver1.biochem.queensu.ca/~rlc ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Pymol recolour B factors
Hello, I'm trying to recolour the B factors in a pymol file with chemical shift differences (from NMR data). There's a nice script here for this http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ (data2bfactor.py) and also a simpler one here https://figshare.com/articles/Pymol_script_loadBfacts_py/1176991. In both cases after loading the script with the run command, when I execute the script I get the following error data2b_res 1d3z.pdb, shift_to_b.txt Selector-Error: Invalid selection name "1d3z.pdb". ( 1d3z.pdb )<-- The pdb file and list of new b-factor values are in the same directory and can be filled in with tab-completion. I've also tried using the full file path but get a similar error. I've tried with a couple of different pdb files as well so it's not just a problem with that particular pdb file. I'd be grateful if anyone has any experience with this or suggestions as to what is going wrong. Thanks in advance, Mark ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe