Hi again, I upgraded my phenix to the prerelease and I didn't see major improvement with the clashes (ranking 13%). If I take the phenix refined coordinates, keep the aniso records from TLS and run some refmac cycles, my structure is better than average with regards to the clash scores (69 %). I do not know how valid refinement strategy this is. (Rfree-R = 5.4 %) Only way I have found so far to fix it in phenix is:

phenix.reduce -build -flips mymodel.pdb > hydrogens.pdb phenix.refine remove_hydrogens=False hydrogens.pdb mydata.mtz params_july29.txt ncs=true hydrogens.mode=riding

This results in higher Rfree (Rfree-R = 6.4 %) but the clashscores are ok (66%) I still feel that I'm missing some keyword to prevent the clashes. ~L~ _______________________________________ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________ ----- Original Message ----- From: Paul Adams Date: Sunday, July 29, 2007 7:27 pm Subject: Re: [phenixbb] problems with clashes To: PHENIX user mailing list

Hi Lari,

are you using the latest (d7) prerelease of phenix? We have made some changes to the way the vdw interactions are dealt with that I would expect to improve the clash scores. Note that the rmsds are likely to be smaller for a lower resolution structure (there is less data available to support differences in the model from ideality). However, you can of course try a few different values of wxc_scale to see what happens to r-factors etc.

Cheers, Paul

...

Hi,

I nowadays use phenix.refine almost always in the first stages of

Lari Lehtio wrote: the> refinement and later usually move to refmac. Now I have two modest> resolution structures which behave much better in phenix than in refmac.

...

In addition to the more tedious deposition (I guess), I have a

problem> with clashes. When I analyse the structures with molprobity, I get much

...

better clashscores with refmac refined files. Is there a way to increase> the restraint for these contacts or should I just keep decreasing the wxc_scale (from the default)? Rmsds reported by refmac (0 cycles) for> bonds and angles are already lower than what I'm used to. B- factors on the other hand seem to be less restrained in phenix.

~Lari~

_______________________________________

Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________

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-- Paul Adams Senior Staff Scientist, Physical Biosciences Division Head, Berkeley Center for Structural Biology Deputy Principal Investigator, Berkeley Structural Genomics Center

Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/

Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. -- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Hi Pavel,

In upcoming version of PHENIX there will be more detailed manual for phenix.refine. Until recently phenix.refine was not using H atoms by default. We changed this behavior very recently. In newer version, if you have an input PDB file with H atoms (generated for example, with phenix.reduce), then phenix.refine will use these hydrogens by default. You don't need to do anything special for this.

OK. So I did the right thing by generating these hydrogens. If phenix does not use hydrogens at all e.g. generated riding hydrogens on the fly like refmac, it seems to me like the most likely cause of difference in clash scores. I don't like to see those hydrogens in the coordinate file though as they are mocking my resolution.

Analogously to wxc_scale in coordinates refinement, to play with B-factors restraints use wxu_scale.

I tried reducing it but I didn't see major improvements in Rfree-R difference.

Please look another post on phenixbb (Subject: "Re: [phenixbb] R- factor problem !!!") regarding how tricky and error prone could be to jump between different programs.

I haven't found it that tricky. I have to grep away the ANISOU records and perhaps reset B-factors before TLS refinement. In my limited experience however the TLS refinent seems more stable in phenix. With refmac I tend to get negative Us quite easily. Especially when changing the model. I understand that for comparing statistics or R-factors, but if you refine the structure, it is just a bunch of coordinates. Scaling is another issue. I've had cases with ice rings and xtriage tells me there is no problem. Refinement in phenix goes okish, but to get decent results with refmac, I had to cut away those resolution shells. I guess I'm going off topic now. Time to do more test runs, ~L~

Sorry, It was just an attempt to be sarcastic about my 2.8 Å data. In refmac you do not see riding hydrogens although it uses them. I'll try to be more serious (might be difficult) or use smileys from now on, ~L~ _______________________________________ Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________ ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" Date: Monday, July 30, 2007 5:32 pm Subject: Re: [phenixbb] problems with clashes To: [email protected]

Hi Lari,

...

I don't like to see those hydrogens in the coordinate file though as they are mocking my resolution.

Sorry, I don't understand what this means. Could you please explain?

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb