Re: [COOT] stereochemical violations in real space refinement?
Yes (indeed), the CG of a LEU is not a chiral centre - and thus is not refined/optimised. If the the CDx atoms are misassigned, then that is what we call a "nomenclature error" (I think I got the terminology from Refmac). The last chi angle of residues types TYR, PHE, ASP and GLU used to be checked against for IUPAC convention and thus we used to see a nomenclature error for those residues as an outlier in the rotamer graph [1]. VALs and LEUs are not checked in this way for the rotamer graph. However, there is a tool to fix nomenclature errors, and VALs and LEUs are checked there. Have a look in the manual about this: http://www.ysbl.york.ac.uk/~emsley/coot/doc/user-manual.html#SEC146 In the terminal, it will tell you all the nomenclature errors that it found and fixed - i.e. there is no tool in Coot that will just tell you about nomenclature errors without fixing them too. This tool is not available in the GUI - it should be trivial to add an extension. I will make a note to do so. Thanks, Paul. [1] that was before we moved to the Richardson rotamer probability library, that has yet to be rationalised. Dale Tronrud wrote: Yes, real space refinement takes into account stereochemical restraints, that is what all the traffic lights are about. What, exactly, is the PDB complaining about? If it is the chirality of atom CG, then you should realize that this is not a real chiral center. CG becomes chiral when the two CD atoms are given numbers. There are two ways to do it but a convention has been adopted to make all Leu CG atoms look the same. If your residue is being flagged as backwards, simply edit the PDB file and swap the numbers on the two CD atoms. Some programs monitor fake chiral centers but others do not. The PDB certainly does, at least for amino acids. Check the labeling of oxygen atoms in phosphates if you want a scare. If this isn't your problem please add details. Ha! Have you been talking to Gert Vriend :) Dale Tronrud Francis E Reyes wrote: Actually i just checked my structure with the Validate -> Incorrect Chiral Volumes. It seems to check out OK, but the PDB doesn't like it? Anyone? thanks FR On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: Hi all, Just tried to submit a PDB and it seems that LEU is not correctly positioned (CG/CD1,CD2). I real space refined this residue, does the real space refinement take into account stereochemical considerations? Thanks FR
Re: [COOT] stereochemical violations in real space refinement?
Francis: When I had a similar issue, Paul told me that one had to mutate a residue to be sure that the stereochemistry is correct. Moreover, as of the last time I checked with Paul, COOT does look at the chiral volumes for pseudo-chiral centers such as Leu and Val, so it is no surprise that COOT doesn't catch it. Try either Simple Mutate or Mutate & Auto Fit ... Steven >-Original Message- >From: Mailing list for users of COOT Crystallographic Software >[mailto:c...@jiscmail.ac.uk] On Behalf Of Francis E Reyes >Sent: Thursday, March 05, 2009 6:36 PM >To: COOT@JISCMAIL.AC.UK >Subject: Re: stereochemical violations in real space refinement? > >Actually i just checked my structure with the Validate -> Incorrect >Chiral Volumes. It seems to check out OK, but the PDB doesn't like it? >Anyone? > >thanks >FR >On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: > >> Hi all, >> >> Just tried to submit a PDB and it seems that LEU is not correctly >> positioned (CG/CD1,CD2). I real space refined this residue, does the >> real space refinement take into account stereochemical considerations? >> >> Thanks >> FR >> >> - >> Francis Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > >- >Francis Reyes M.Sc. >215 UCB >University of Colorado at Boulder > >gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > >8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [COOT] stereochemical violations in real space refinement?
Yes, real space refinement takes into account stereochemical restraints, that is what all the traffic lights are about. What, exactly, is the PDB complaining about? If it is the chirality of atom CG, then you should realize that this is not a real chiral center. CG becomes chiral when the two CD atoms are given numbers. There are two ways to do it but a convention has been adopted to make all Leu CG atoms look the same. If your residue is being flagged as backwards, simply edit the PDB file and swap the numbers on the two CD atoms. Some programs monitor fake chiral centers but others do not. The PDB certainly does, at least for amino acids. Check the labeling of oxygen atoms in phosphates if you want a scare. If this isn't your problem please add details. Dale Tronrud Francis E Reyes wrote: > Actually i just checked my structure with the Validate -> Incorrect > Chiral Volumes. It seems to check out OK, but the PDB doesn't like it? > Anyone? > > thanks > FR > On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: > >> Hi all, >> >> Just tried to submit a PDB and it seems that LEU is not correctly >> positioned (CG/CD1,CD2). I real space refined this residue, does the >> real space refinement take into account stereochemical considerations? >> >> Thanks >> FR >> >> - >> Francis Reyes M.Sc. >> 215 UCB >> University of Colorado at Boulder >> >> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> >> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > > - > Francis Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [COOT] stereochemical violations in real space refinement?
Actually i just checked my structure with the Validate -> Incorrect Chiral Volumes. It seems to check out OK, but the PDB doesn't like it? Anyone? thanks FR On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: Hi all, Just tried to submit a PDB and it seems that LEU is not correctly positioned (CG/CD1,CD2). I real space refined this residue, does the real space refinement take into account stereochemical considerations? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [COOT] stereochemical violations in real space refinement?
On Mar 5, 2009, at 4:25 PM, Francis E Reyes wrote: Hi all, Just tried to submit a PDB and it seems that LEU is not correctly positioned (CG/CD1,CD2). I real space refined this residue, does the real space refinement take into account stereochemical considerations? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[COOT] stereochemical violations in real space refinement?
Hi all, Just tried to submit a PDB and it seems that LEU is not correctly positioned (CG/CD1,CD2). I real space refined this residue, does the real space refinement take into account stereochemical considerations? Thanks FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [COOT] Bring all windows to front?
Thanks a lot, Bill. This xwit looks promising, I will explore it. I keep procrastinating my immersion in zsh... Ars magna, vita brevis! Miguel Le 5 mars 09 à 18:19, William G. Scott a écrit : Yo Miguel: I wrote a little helper zsh function/shell script called xtwit. http://zsh-templates-osx.googlecode.com/svn-history/r53/trunk/Library/init/zsh/local-functions/darwin/xtwit It wraps the command xwit (available via fink, for example) and gives you a gui that allows you to select a window to pop to the foreground: -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. My guess is xwit itself could be tailored to do exactly as you want, and called from a python or scheme script. eg: xwit version 3.4 usage: xwit -display -sync -pop -iconify -unmap -resize w h -rows r -columns c -[r]move x y -[r]warp x y -colormap -[no]save -name -iconname -bitmap -mask -[r]iconmove x y -[no]backingstore -[no]saveunder -[no]keyrepeat keycode ... keycode - keycode -id -root -current -select -names ... [must be last] HTH, Bill On Mar 5, 2009, at 8:30 AM, Miguel Ortiz Lombardia wrote: Dear all, I have looked in the manuals but haven't found anything concerning the possibility of bringing all coot windows to foreground. In Mac versions there is an annoying feature/bug consisting in some windows going behind the main graphic windows and being invisible in Apple's "Exposé", unless you happen to move your mouse over where they actually are. The ghost windows I call them. In this context, a "Bring all windows to front" or something similar would be helpful. If it would exist it would instantly become a button in my Menu bar... BTW, has anyone else noticed that "Sort by Date" is not working? (again, in Mack fink coot) Best, Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [COOT] problems with ssDNA chi angles
Thank you! That's exactly what I needed. I guess the randomness I was experiencing previously was just me randomly clicking on different atoms in the residue. Scott On Mar 5, 2009, at 10:45 AM, Paul Emsley wrote: Scott Classen wrote: Hi All, I am trying to manually fit ssDNA. Sometime I want the base to remain fixed and rotate the ribose and phosphate (N1-C1*), while other times I want to keep the backbone fixed and rotate only the base. Is there some way to indicate my desire to coot? It seems to work the way I want every once and awhile, but it's random. Hi Scott, The bug I mentioned this morning may be biting you. If not that, then the atom tree root is the atom you click on and the sub-trees are built up from that atom. i.e. when picking the residue for chi angle manipulation, click on a atom that you wish to remain stationary. See section 5.11 of the User Manual http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC111 (if not that, more info is required). Regards, Paul.
Re: [COOT] problems with ssDNA chi angles
Scott Classen wrote: Hi All, I am trying to manually fit ssDNA. Sometime I want the base to remain fixed and rotate the ribose and phosphate (N1-C1*), while other times I want to keep the backbone fixed and rotate only the base. Is there some way to indicate my desire to coot? It seems to work the way I want every once and awhile, but it's random. Hi Scott, The bug I mentioned this morning may be biting you. If not that, then the atom tree root is the atom you click on and the sub-trees are built up from that atom. i.e. when picking the residue for chi angle manipulation, click on a atom that you wish to remain stationary. See section 5.11 of the User Manual http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC111 (if not that, more info is required). Regards, Paul.
[COOT] problems with ssDNA chi angles
Hi All, I am trying to manually fit ssDNA. Sometime I want the base to remain fixed and rotate the ribose and phosphate (N1-C1*), while other times I want to keep the backbone fixed and rotate only the base. Is there some way to indicate my desire to coot? It seems to work the way I want every once and awhile, but it's random. Thanks, Scott ~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~
Re: [COOT] Bring all windows to front?
Yo Miguel: I wrote a little helper zsh function/shell script called xtwit. http://zsh-templates-osx.googlecode.com/svn-history/r53/trunk/Library/init/zsh/local-functions/darwin/xtwit It wraps the command xwit (available via fink, for example) and gives you a gui that allows you to select a window to pop to the foreground: <> My guess is xwit itself could be tailored to do exactly as you want, and called from a python or scheme script. eg: xwit version 3.4 usage: xwit -display -sync -pop -iconify -unmap -resize w h -rows r -columns c -[r]move x y -[r]warp x y -colormap -[no]save -name -iconname -bitmap -mask -[r]iconmove x y -[no]backingstore -[no]saveunder -[no]keyrepeat keycode ... keycode - keycode -id -root -current -select -names ... [must be last] HTH, Bill On Mar 5, 2009, at 8:30 AM, Miguel Ortiz Lombardia wrote: Dear all, I have looked in the manuals but haven't found anything concerning the possibility of bringing all coot windows to foreground. In Mac versions there is an annoying feature/bug consisting in some windows going behind the main graphic windows and being invisible in Apple's "Exposé", unless you happen to move your mouse over where they actually are. The ghost windows I call them. In this context, a "Bring all windows to front" or something similar would be helpful. If it would exist it would instantly become a button in my Menu bar... BTW, has anyone else noticed that "Sort by Date" is not working? (again, in Mack fink coot) Best, Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
[COOT] Bring all windows to front?
Dear all, I have looked in the manuals but haven't found anything concerning the possibility of bringing all coot windows to foreground. In Mac versions there is an annoying feature/bug consisting in some windows going behind the main graphic windows and being invisible in Apple's "Exposé", unless you happen to move your mouse over where they actually are. The ghost windows I call them. In this context, a "Bring all windows to front" or something similar would be helpful. If it would exist it would instantly become a button in my Menu bar... BTW, has anyone else noticed that "Sort by Date" is not working? (again, in Mack fink coot) Best, Miguel -- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [COOT] torsion general
Cathy Lawson wrote: Thanks Paul. I thought it would be something like that. Now I've tested again, I see that torsion general works fine for side chain bonds, but it doesn't seem to work for main-chain, does this sound right? It works for only a single residue/monomer. In some earlier vintage crystallography graphics programs it was possible to "tor" main chain bonds and make a large chunk of structure twirl around on the screen along with the rotating bond Frank von Delft asked for this too. I would guess that he uses the same "vintage crystallography graphics programs" as you do/did. :-). I'll make a note. Thanks, Paul.
[COOT] chi angles recently
I recently found that for 2 weeks or so the chi angles code was broken. Sorry about that (I'd been trying to get conformation sampling to work better). As of rev 1920, things are back to how they used to be. Thanks to Joel Bard for pointing out the problem. Paul.
