Francis, do you have CCP4 installed on this machine as well? What
version is it? Also, what's the naming on the newly created ideal RNA.
Is it using * or ' for prime?
If your installation of CCP4 isn't the newest version (6.2), that may
be causing your problem. Starting with rev 3489, Coot switched from
PDB2-style naming of RNA (O1P, O2P, C1*, C2*, etc) to PDB3-style naming
(OP1, OP2, C1', C2', etc). However, if Coot finds CCP4 installed on the
computer, it defaults to using CCP4's monomer libraries. If CCP4 is 6.1
(or older), than the monomer libraries will contain the old-style names
and Coot will have problems.
When Coot launches, you should see a bunch of messages along the
lines of:
There are 125 data in
C:\Programs\WinCoot\0.6.2\share\coot\lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
C:\Programs\WinCoot\0.6.2\share\coot\lib/data/monomers/a/ALA.cif
There are 2 data in
C:\Programs\WinCoot\0.6.2\share\coot\lib/data/monomers/a/ASP.cif
If those messages point to Coot's directory, then your problem is
different from what I'm describing and you can safely ignore the rest of
the e-mail. If those messages point to CCP4 6.1's directory, then this
is probably causing your issues.
There are two solutions for fixing the issue. You can either update
CCP4 to 6.2, or force Coot to use it's own monomer libraries. To force
Coot, run
export COOT_REFMAC_LIB_DIR=//path/to/coot//share/coot/lib
on the command line before launching Coot. Coot should then use it's
own PDB3-based monomer libraries. Also, note that I've had some issues
when I've included a slash after the final "lib". I'm not sure if
that's was just something weird going on with my system, but if you run
into problems, make sure you have "/lib" at the end and not "/lib/".
Also note that if the Coot binary is in your path, then you can
copy and paste the command
export COOT_REFMAC_LIB_DIR=`dirname \`which coot\``/../share/coot/lib
and save yourself some typing. It'll do the same thing as the above
command.
This command will change Coot over to using PDB3-style naming
exclusively, so you won't be able to minimize any PDB2-named files. If
you want to convert your existing PDB files, you can use the Richardson
lab's Remediator
(http://kinemage.biochem.duke.edu/software/remediator.php), although
their web page appears to be down at the moment.
Hopefully that will fix your problem.
- Kevin
On 8/15/2011 2:13 PM, Francis E Reyes wrote:
What's a bug report without the affected coot version :
Coot 0.6.2 rev 3562
F
On Aug 15, 2011, at 12:12 PM, Francis E Reyes wrote:
When using the Build ideal RNA dialog in Other Modeling tools the generated RNA
has incorrect atom labels and o-phosphate labels. They're inconsistent with
coot's internal CIFs such that usage of any real space refine tool complains of
exploding atoms b/c the atom labels can't be interpreted.
F
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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
