Re: [ccp4bb] ALMN
Yes - the RMS for the map is weighted by sin beta Here is the comment: C Mean & RMS need to be weighted by sin beta, to allow for distortions c in Eulerian space. c On the last section, if beta = 90, the weight is 1/2 because of c symmetry. Here we only need to test for last section, because c (a) if last section = 180deg, the weight is zero anyway c (b) if the last section is not 90 or 180, the rms is not valid anyway Eleanor On 09/09/2011 05:42 PM, Ian Tickle wrote: Rex, sorry, addendum to my last post: the grid points in the Eulerian space of the cross-RF (which is what I assume you're talking about) do not occupy equal volumes in angular space as they would do in a Euclidean space (e.g. a normal electron density map). For example the volume of any grid point on the beta=0& 180 sections is zero (these sections actually each consist of a line of points, and a line of course occupies no volume). Therefore it's necessary to weight the values in both the mean and the RMSD by the volume of each grid point (= sin(beta)). Whether ALMN actually does this or not would require an examination of the source code, though it's probably quicker to ask Eleanor! Cheers -- Ian On Fri, Sep 9, 2011 at 5:26 PM, Ian Tickle wrote: Hi Rex I would assume it's the RMS deviation of the rotation function value from the mean. If so then it's defined in the same way as the "population standard deviation" as given here: http://en.wikipedia.org/wiki/Standard_deviation Cheers -- Ian On Fri, Sep 9, 2011 at 4:20 PM, REX PALMERwrote: Dear CCP4'ers In the input instructions for ALMN it says: FIND peak maxpek [RMS] [OUTPUT filename] Read peak threshold and maximum number of peaks. MAXPEK is the maximum number of peaks to find (default = 20). Up to MAXPEK peaks above PEAK will be found, and all symmetry related peaks generated. If the keyword RMS is present, then the peak threshold is PEAK * RMS density, otherwise PEAK is the absolute threshold in the scaled map. Question: RMS density of what and what is the formula used? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] refmac and DNA (and now RNA)
Is ' U ' now the standard vs ' U' ? I'm used to right justified letters for RNA residues in the residue field. This is with a recent refinement with refmac 5.6.0117 . And of course this switch in naming convention breaks compatibility with molprobity (which requires right justified letters in the residue field) F On Sep 8, 2011, at 7:35 AM, Ed Pozharski wrote: > After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I > have found a problem working with DNA that I have not seen with > 6.1.13/5.5.0109. Namely, > > - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to > output DNA as Ad/Td/Gd/Cd no matter what the input names were, refmac > fails with the warning that it found a new monomer. It appears that it > stumbles upon the very first thymidine, but in a strange twist it > reports the problematic residue having the name "DY"! > > - if I use the pdb file previously produced by refmac, which has the > A/T/G/C as residue names, it fails too but now complains about the "new" > monomer named "T". > > - the workaround I found is to rename all the thymidines to "DT". It is > a bit annoying since coot keeps renaming them (well, not refmac/ccp4 > problem per se) and I have to rename back (easily scripted task, of > course). What is peculiar is that Ad/Gd/Cd don't need to be renamed > (does this have anything to do with thymidine being the only one that > changes residue name in RNA?). > > Has anyone else seen this or it's something specific to my setup? > > Cheers, > > Ed. > > -- > After much deep and profound brain things inside my head, > I have decided to thank you for bringing peace to our home. >Julian, King of Lemurs - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] refmac and DNA (and now RNA)
Is there finally, at long last, one convention for nucleic acids? I wonder how many cumulative person-years of exasperation this @#$% issue has caused? And please note, even Mother Nature herself, let alone synthetic chemists, occassionally attaches U to deoxyribose or T to plain ribose. = Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message >Date: Mon, 12 Sep 2011 12:23:17 -0600 >From: CCP4 bulletin board (on behalf of Francis E >Reyes ) >Subject: Re: [ccp4bb] refmac and DNA (and now RNA) >To: CCP4BB@JISCMAIL.AC.UK > >Is ' U ' now the standard vs ' U' ? I'm used to right justified letters for >RNA residues in the residue field. > >This is with a recent refinement with refmac 5.6.0117 . > >And of course this switch in naming convention breaks compatibility with >molprobity (which requires right justified letters in the residue field) > > >F > > >On Sep 8, 2011, at 7:35 AM, Ed Pozharski wrote: > >> After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I >> have found a problem working with DNA that I have not seen with >> 6.1.13/5.5.0109. Namely, >> >> - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to >> output DNA as Ad/Td/Gd/Cd no matter what the input names were, refmac >> fails with the warning that it found a new monomer. It appears that it >> stumbles upon the very first thymidine, but in a strange twist it >> reports the problematic residue having the name "DY"! >> >> - if I use the pdb file previously produced by refmac, which has the >> A/T/G/C as residue names, it fails too but now complains about the "new" >> monomer named "T". >> >> - the workaround I found is to rename all the thymidines to "DT". It is >> a bit annoying since coot keeps renaming them (well, not refmac/ccp4 >> problem per se) and I have to rename back (easily scripted task, of >> course). What is peculiar is that Ad/Gd/Cd don't need to be renamed >> (does this have anything to do with thymidine being the only one that >> changes residue name in RNA?). >> >> Has anyone else seen this or it's something specific to my setup? >> >> Cheers, >> >> Ed. >> >> -- >> After much deep and profound brain things inside my head, >> I have decided to thank you for bringing peace to our home. >>Julian, King of Lemurs > > > >- >Francis E. Reyes M.Sc. >215 UCB >University of Colorado at Boulder
Re: [ccp4bb] refmac and DNA (and now RNA)
Hi Garib Thanks for the quick reply! Refmac however is writing my pdb's as with the residue letter in the centered position. Is the newest pdb requiring centered residue letters for RNA? F On Sep 12, 2011, at 1:05 PM, Garib N Murshudov wrote: > Refmac will read right or left justified residue names, however pdb may use > only one of them. - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] refmac and DNA (and now RNA)
Yes, new version of the dictionary uses U. Refmac will read right or left justified residue names, however pdb may use only one of them. There are some backward compatibility code/dictionary elements. For example Ad/Ar are also accepted. However it is encouraged to use new pdb v2.3 residue/atom names. It will make sure that all software use same naming convention and moving between them is smooth. Hopefully we all will have one naming conventions. regards Garib On 12 Sep 2011, at 19:23, Francis E Reyes wrote: > Is ' U ' now the standard vs ' U' ? I'm used to right justified letters for > RNA residues in the residue field. > > This is with a recent refinement with refmac 5.6.0117 . > > And of course this switch in naming convention breaks compatibility with > molprobity (which requires right justified letters in the residue field) > > > F > > > On Sep 8, 2011, at 7:35 AM, Ed Pozharski wrote: > >> After switching (finally) to 6.2.0 and therefore to Refmac 5.6.0117 I >> have found a problem working with DNA that I have not seen with >> 6.1.13/5.5.0109. Namely, >> >> - if I use the pdb file produced by Coot (0.7.pre-1.3470) that seems to >> output DNA as Ad/Td/Gd/Cd no matter what the input names were, refmac >> fails with the warning that it found a new monomer. It appears that it >> stumbles upon the very first thymidine, but in a strange twist it >> reports the problematic residue having the name "DY"! >> >> - if I use the pdb file previously produced by refmac, which has the >> A/T/G/C as residue names, it fails too but now complains about the "new" >> monomer named "T". >> >> - the workaround I found is to rename all the thymidines to "DT". It is >> a bit annoying since coot keeps renaming them (well, not refmac/ccp4 >> problem per se) and I have to rename back (easily scripted task, of >> course). What is peculiar is that Ad/Gd/Cd don't need to be renamed >> (does this have anything to do with thymidine being the only one that >> changes residue name in RNA?). >> >> Has anyone else seen this or it's something specific to my setup? >> >> Cheers, >> >> Ed. >> >> -- >> After much deep and profound brain things inside my head, >> I have decided to thank you for bringing peace to our home. >> Julian, King of Lemurs > > > > - > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] refmac and DNA (and now RNA)
Hi Francis Is that newer version of refmac? regards Garib On 12 Sep 2011, at 20:09, Francis E Reyes wrote: > Hi Garib > > Thanks for the quick reply! > > Refmac however is writing my pdb's as with the residue letter in the > centered position. > > Is the newest pdb requiring centered residue letters for RNA? > > F > On Sep 12, 2011, at 1:05 PM, Garib N Murshudov wrote: > >> Refmac will read right or left justified residue names, however pdb may use >> only one of them. > > > > - > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > > > > Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] COOT on CentOS 6 (x86_64)
Hi Paul, I am running the centos5 build. After a couple of yum installs it seems to be happy... Except I cannot maximize the window for some reason. Thanks for the reply. Yuri
