[Chimera-users] Contact Maps (RRdistance Maps) questions:

Wed May 3 11:43:01 PDT 2017

Hi Again!
So sorry to bother you again, do you by any chance know if there is a
command line similar to

findclash #0 at ca test self overlap -2.3 log true

but instead of finding Ca-Ca distances that are less than 6 angstrom to
use all of the atoms in a residue and look for other atoms/residues that
come within 4 angstroms?

Thanks so much!!

Sincerely,
Nicky

On Thu, Mar 23, 2017 at 6:24 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Nicky,
> Great!  I worried that my reply included too many words before the actual
> solution.  :-)
>
> There is an Export button near the bottom of the RR Distance Maps dialog,
> as shown in the image:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> rrdistmaps/rrdistmaps.html>
>
> If you don’t see this button in your Chimera, it must be an older version…
> according to the release notes, export was added sometime before the
> version 1.11 release.  Either get the Chimera 1.11.2 production release or
> a 1.12 daily build to obtain this feature.
>
> Download: <http://www.rbvi.ucsf.edu/chimera/download.html>
> Best,
> Elaine
>
> > On Mar 23, 2017, at 2:31 PM, Nicole Persky <persky at broadinstitute.org>
> wrote:
> >
> > Oh Wow! Thanks so much Elaine! That command line was super helpful.
> > I should definitely be able to work with this. Thank you so much!
> > One quick followup question, you mentioned in (C) that there is an
> export button for giving value matrices for all pairs, where is that
> located? I wasn't able to locate it.
> > Again, thank you so much for your help! It totally helped me get started.
> > Sincerely,
> > Nicky
> >
> > On Wed, Mar 22, 2017 at 10:05 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Nicky,
> > Unfortunately the RR Dist Maps tool is limited in just the ways you
> describe, so not that useful for what you want to do.  A better way is with
> “findclash”  but that would entail some postprocessing, see the last part
> of this message.
> >
> > (A) Coloring applies across the whole value range, not just the unmasked
> part… e.g. even if you have masked everything above 6 A with some solid
> color (let’s say dark blue) and specified showing short-long distances with
> a white-black gradient, white is 0 angstroms and black is longest
> residue-residue distance in the protein, typically >50 A.  So the unmasked
> part of 0-6 A is only white to very light gray and you can’t really see any
> color differences…not that helpful if you are only interested in smaller
> differences between these shorter-range contacts.  (I realize you
> understand this problem, I’m just laying it out in case anybody else is
> following along.)  This problem is mentioned in the technical notes at the
> bottom of the help page for this tool:
> > <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/
> rrdistmaps/rrdistmaps.html>
> >
> > (B) Cannot show two RR Dist Maps dialogs at the same time.  So to see
> two maps side by side, you’d have to either run two Chimera sessions
> concurrently or within a single session, do one calculation, save image, do
> another, save image again or compare current dialog with previously saved
> image.
> >
> > One way to compare the below-6-angstrom contacts only is to show
> side-by-side images of the distance map calculated for each protein
> separately with the distances >6 A masked out.  However, this will only
> show differences of where there is a contact <6A in one protein and not the
> other, but because of the coloring issue, subtleties in different distances
> within that range will not be perceptible.
> >
> > Another way is to compare the individual distance maps (or a single map
> of average distance) with a difference map.  However, it would be difficult
> to tell exactly where the unmasked parts of the distance maps would be on
> the difference map and only look at those latter areas of the difference
> map.
> >
> > (C) the Export button gives all the values of RR distance, and (if a
> comparison) standard deviation in RR distance and difference in RR
> distance.  There isn’t an option to give only the residue IDs for contact
> pairs within some distance; it only gives value matrices for all pairs.
> >
> > (D) RR DIst Maps visualization is also focused on those 3 quantities,
> not attribute values.  Chimera attributes are assigned to individual atoms,
> residues, or models, not a pair of residues. The RR distance map shows
> residue-pair values with color.
> >
> > If you want to use Chimera, for your purposes I think the best approach
> would be to use "Find Clashes/Contacts” or the “findclash” command to
> measure (intraprotein) CA-CA distances, and then filter to list only the
> pairs within 6 A.  Then you could do that for the other protein as well,
> then compare the two lists.  For example, if you had one of your proteins
> already open as #0, command:
> >
> > findclash #0 at ca test self overlap -2.3 save ~/Desktop/protein1.txt
> >
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
> >
> > … would save a text file listing all CA-CA pairs with VDW surfaces
> within 2.3 angstroms.  The distance from atom center to atom center will be
> larger, but the output file will also give that distance and you can delete
> the pairs for which it is >6 angstroms.  I chose -2.3 because that should
> give you all the pairs within 6 angstroms and only a few with larger
> distances, using the VDW radii of CA atoms in structures without hydrogen
> atoms.  You may need to use a larger distance to get them all if your
> protein has hydrogens, but in any case, you will be able to tell by looking
> at the center-center distances included in the output.  The list is sorted
> by decreasing overlap so that longer distances willl be near the end.  This
> example command will automatically exclude residues that are adjacent in
> sequence (separated by no more than 4 bonds), but you could add the
> findclash command option “bondsep 2” to include those as well.
> >
> > You can use “log true” instead of (or in addition to) the “save” option
> to show the output in the Reply Log.  For example, if I have PDB 2gbp open
> as model #0, command:
> >
> > findclash #0 at ca test self overlap -2.3 log true
> >
> > … sends the following stuff to the Reply Log, primarily a list of the
> two atoms’ identifiers, atom-atom VDW overlap (negative value = separation
> between VDW surfaces of the two atoms), and atom-atom center-to-center
> distance:
> > -------------------
> > Allowed overlap: -2.3
> > H-bond overlap reduction: 0.4
> > Ignore contacts between atoms separated by 4 bonds or less
> > Detect intra-residue contacts: False
> > Detect intra-molecule contacts: True
> >
> > 620 contacts
> > atom1  atom2  overlap  distance
> > ARG 158.A CA  GLY 116.A CA  -0.203  3.963
> > LYS 189.A CA  GLY 217.A CA  -0.321  4.081
> > ARG 292.A CA  THR 110.A CA  -0.372  4.132
> > GLY 297.A CA  VAL 254.A CA  -0.453  4.213
> > THR 180.A CA  LYS 147.A CA  -0.460  4.220
> > VAL 235.A CA  ASN 211.A CA  -0.480  4.240
> > GLY 120.A CA  VAL 162.A CA  -0.493  4.253
> > LEU 196.A CA  ALA 201.A CA  -0.572  4.332
> > GLY 116.A CA  VAL 162.A CA  -0.663  4.423
> > MET 182.A CA  GLY 148.A CA  -0.668  4.428
> > THR 185.A CA  GLY 217.A CA  -0.697  4.457
> > ASN 256.A CA  ASP 236.A CA  -0.732  4.492
> > MET 182.A CA  GLU 149.A CA  -0.748  4.508
> > GLY 234.A CA  ASP 212.A CA  -0.794  4.554
> > […. many lines …]
> > PHE 266.A CA  LYS 270.A CA  -2.269  6.029
> > ALA 155.A CA  THR 159.A CA  -2.274  6.034
> > ASN 302.A CA  GLU 305.A CA  -2.277  6.037
> > ILE 9.A CA    SER 41.A CA   -2.283  6.043
> > VAL 206.A CA  ILE 204.A CA  -2.285  6.045
> > LYS 92.A CA   LEU 67.A CA   -2.286  6.046
> > ALA 264.A CA  LEU 268.A CA  -2.286  6.046
> > LYS 270.A CA  ASP 274.A CA  -2.288  6.048
> > PRO 86.A CA   ALA 105.A CA  -2.289  6.049
> > ASN 130.A CA  HIS 126.A CA  -2.292  6.052
> > PHE 89.A CA   TYR 106.A CA  -2.293  6.053
> > ALA 251.A CA  VAL 245.A CA  -2.298  6.058
> > 620 contacts
> > ---------------
> > So, you would need to do some minor postprocessing to remove pairs with
> distances >6 angstroms and probably the harder part would be figuring out
> how to compare the two lists. Sorry I couldn’t give a more convenient
> solution.
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Mar 22, 2017, at 12:44 PM, Nicole Persky <persky at broadinstitute.org>
> wrote:
> > >
> > > Hi All,
> > > I've just found the RRdistance Map function on Chimera and
> > > would like to compare between structures.
> > > I would like to:
> > > 1- make contact map of protein 1 to protein 1 with a cutoff of about 6
> angstroms
> > > 2- make a contact map of protein 2 to protein 2 with a cutoff of about
> 6 angstroms
> > > 3- compare these two contact maps using the colors available for the
> whole contact map.
> > >
> > > I can only seem to compare the ENTIRE contact map of protein 1 to the
> ENTIRE map of protein 2, whereas I'd like to mask any contacts over 6
> angstroms.
> > >
> > > Alternatively, if anyone knows of a way to export residue lists of
> contacts from the contact map site I could just compare them that way.
> > >
> > > ALSO:
> > > Anyone know of a way to map defined attributes onto a contact map?
> > >
> > > Thanks so much!
> > > Sincerely,
> > > Nicky
> >
>
>
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