phenix.refine use_experimental_phases vs target=mlhl
Are these settings redundant? i.e. what happens when you have target=mlhl, use_experimental_phases=False? Thanks! F --------------------------------------------- Francis E. 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
Hi Francis, there are some automatic decisions/adjustments done based on the combination of these two parameters. For example, even if the default setting for target is ml, but if your input data file contains HL coefficients then the target name will automatically switch to mlhl (if use_experimental_phases=True, otherwise it will remain ml). Something of this sort. You can quickly find out by trying representative combinations of these parameters. Pavel. On 12/9/10 9:47 AM, Francis E Reyes wrote:
Are these settings redundant? i.e. what happens when you have target=mlhl, use_experimental_phases=False?
Hi Francis,
Are these settings redundant? i.e. what happens when you have target=mlhl, use_experimental_phases=False?
Good question. Yes, currently these two are strictly speaking redundant. The thinking was that we may have more than one target using experimental phases in the future. So this part of phenix.refine is future proof! Ralf
Hi All, I am trying to see if I can save myself some time by using the loop fitting tools in Phenix. I think I am stalling out because of a trivial problem, but cursory googling, etc, has not helped. Sorry if I should have tried harder. I appreciate any help. I am using the gui, dev-601. My fasta sequence gets read fine because the output reports the sequence of the missing residues. Whether I use the loop library or not, I get the following error: Unable to find suitable gap to fill Then it appears to try to build the loop using sequence from a different chain (I have three chains in my structure). What am I doing wrong? Luke -- Luke M. Rice Assistant Professor and Thomas O. Hicks Scholar in Medical Research Department of Biochemistry, ND10.300 UT Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-8816 phone: (214) 645-5931 email: [email protected]
Hi Luke,
How big is your loop. I normally try to built it one molecule at a time from
both ends of the loop in COOT, refine and re-try loop building. Some times,
if the electron density is ok you can build the whole loop one amino-acid at
a time by iterative COOT, refinement and loop building.
Ivan
On Fri, Dec 10, 2010 at 11:40 AM, Luke Rice
Hi All,
I am trying to see if I can save myself some time by using the loop fitting tools in Phenix. I think I am stalling out because of a trivial problem, but cursory googling, etc, has not helped. Sorry if I should have tried harder. I appreciate any help.
I am using the gui, dev-601. My fasta sequence gets read fine because the output reports the sequence of the missing residues. Whether I use the loop library or not, I get the following error:
Unable to find suitable gap to fill
Then it appears to try to build the loop using sequence from a different chain (I have three chains in my structure).
What am I doing wrong?
Luke
-- Luke M. Rice Assistant Professor and Thomas O. Hicks Scholar in Medical Research Department of Biochemistry, ND10.300 UT Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-8816 phone: (214) 645-5931 email: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Luke, Just reporting to the list what we found out... There were two problems that your case helped me fix: 1. Resolve was reading sequences only up to 132 characters on a line. That is now changed to be unlimited. (The other sequence interpretation tools always read any number of characters on a line, including autobuild/autosol/automr etc). 2. At the end of loop fitting, a check was done to make sure that the new loop does not overlap with anything in the rest of the model. That check was done by reassembling the chains in the model with resolve. It had the side-effect of losing the sequence assignment if the density was poor. The default is now to skip that check (skip_trim=True) in fit_loops, but to carry out the check in autobuilding, reasoning that a user is not likely to try to build a loop where something is already present. These changes are now checked in so versions starting with tomorrow should have the behavior that you were looking for. Thanks for letting me know of the problems! All the best, Tom T
Hi All,
I am trying to see if I can save myself some time by using the loop fitting tools in Phenix. I think I am stalling out because of a trivial problem, but cursory googling, etc, has not helped. Sorry if I should have tried harder. I appreciate any help.
I am using the gui, dev-601. My fasta sequence gets read fine because the output reports the sequence of the missing residues. Whether I use the loop library or not, I get the following error:
Unable to find suitable gap to fill
Then it appears to try to build the loop using sequence from a different chain (I have three chains in my structure).
What am I doing wrong?
Luke
-- Luke M. Rice Assistant Professor and Thomas O. Hicks Scholar in Medical Research Department of Biochemistry, ND10.300 UT Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75390-8816 phone: (214) 645-5931 email: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (6)
-
Francis E Reyes -
Luke Rice -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Thomas C. Terwilliger -
xaravich ivan