I just realized that you could do it even without using truncate_to_polyala: phenix.pdbtools model.pdb keep="backbone" or, equivalently: phenix.pdbtools model.pdb remove="sidechain" and it works for both: proteins and RNA/DNA. Pavel. On 5/13/09 12:43 PM, Francis E Reyes wrote:

Though the original question was for protein, is there a mutate to poly C for RNA as well? :)

It just came to mind right now.

FR

On May 13, 2009, at 1:42 PM, Pavel Afonine wrote:

...

Hi,

the next nightly build of PHENIX will have this option available from phenix.pdbtools.

Example:

phenix.pdbtools model.pdb truncate_to_polyala=true

As always, any feedback will be very appreciated.

Pavel.

On 5/7/09 7:01 AM, Francis E Reyes wrote:

...

Is there an option or a phenix.* utility to mutate a MR model to poly ALA before the MR is done?

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--------------------------------------------- Francis 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

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On May 14, 2009, at 4:48 AM, Schubert, Carsten [PRDUS] wrote:

Sometimes truncation/mutation to poly-gly or poly-Ser is desirable. If not already present could this be another option? Another interesting option would be to be able to change OR keep the residue names of the template to be mutated. Sometimes it is useful to chop the sidechains, but still be able to tell what residue this is supposed to be via the residue name. Again some of this may already be present, haven’t had a chance to play around with this.

None of this actually changes the atom names - I just looked at the pdbtools source code and it only deletes atoms after Cbeta. Specifying an atom selection to keep can also be used for poly-Gly or poly-Ser:

phenix.pdbtools model.pdb keep="backbone" phenix.pdbtools model.pdb remove="sidechain"

. . . these will actually get rid of Cbeta too, so poly-Gly, and phenix.pdbtools model.pdb keep="backbone or name cb or name cg or name cg1 or name og1 or name sg1" will chop off everything but the beta and gamma positions (without branching). Smaller residues will be untouched. I don't think there's a simple way to actually change the identity of every residue in phenix/cctbx, but I've found that this usually just creates problems anyway. I'm working on a graphical frontend to pdbtools - it may take another week or two for it to be usable, but it will make all of this relatively easy, I hope. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

On May 15, 2009, at 10:08 AM, Raja Dey wrote:

Hi Pavel, I was trying to create map file only as follows: phenix.refine 1205A-p21212.mtz may15_1_001.pdb map.params strategy=none output.prefix=may15_2 ,

Add "output.write_maps=True" to the command line. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

Could you try this? refinement.ncs.restraint_group { reference = chain I and not (resid 18 or resid 61 or resid 63 or resid 64 or resid 82)" selection = chain J and not (resid 18 or resid 61 or resid 63 or resid 64 or resid 82)" } Or slightly more compact: refinement.ncs.restraint_group { free_residues = (resid 18 or resid 61 or resid 63 or resid 64 or resid 82) reference = chain I and not $free_residues selection = chain J and not $free_residues } BTW: You can use the command phenix.pdb_atom_selection to try out atom selections (to check if the syntax is correct and to see the list of selected atoms). In recent versions of the phenix.refine GUI, you can check the atom selections visually. Ralf

Also, don't forget to add ncs.find_automatically=false

I have run many runs with NCS defined with proper syntax, just to be overwritten by NCS derived automatically by phenix, until I realized what was happening. I have always thought that if I define the NCS restraints, phenix should follow it, not try to "improve" upon it. What is the reason for this default behavior?

Thanks very much for the feedback. I'm thinking setting up the NCS restraints really should be part of the "ready-set" stage, done once, as an explicit step, strongly suggesting review of the results before continuing. With the new GUI tools Nat is working on, we will be in a better position to re-organize the functionality in and around phenix.refine, to reduce the potential for confusion in the future. Ralf

Hi Pavel, It is very rarely sensible to disagree with automation, definitely in this case. My problem was that the automated NCS was including bits that were clearly violators of NCS (This was with 1.3 final release). I will be looking forward to any improvements in this respect. Here are a couple questions/suggestions: 1. Does automated NCS picking only work based on the input pdb? Should it not consider electron density maps as well for true automation (which may not be easy to implement)? Otherwise, regions that should eventually be excluded from NCS will be initially restrained, and stay that way cycle after cycle by the automated NCS picking, until some person intervenes and remodels the pdb. Automated analysis of model and electron density for violations of NCS would be a god-send for those large structures with many, many (> 10) NCS chains. (How about a phenix.analyse_complex_ncs instead of phenix.simple_ncs_from_pdb :)) 2. Any automation on restraint weights (possibly based on Rfree behaviour, or something even more complicated)? That would be nice. And definitely not excluding NCS restraints on ADPs (It seems to me commonplace to have one or more NCS related groups to be more "flexible", more "fuzzy". It helps to relax NCS-ADP restraints on those chains). Thanks, Engin On 5/25/09 3:41 PM, Pavel Afonine wrote:

Hi Engin,

since the model gets improved during refinement (hopefully), it is a good idea to update NCS restraints based on improved model, so the default behavior.

The use of NCS restraints in phenix.refine is explained in the manual: http://www.phenix-online.org/documentation/refinement.htm#anch24

I admit that the automatic NCS determination has a room for improvement, but once again: ideally it should be done fully automatically and be updated as model gets improved. It is in my list...

As it is now it's always good to check the automatic choice (as Ralf mentioned).

Pavel.

On 5/18/09 3:33 PM, Engin Ozkan wrote:

...

Also, don't forget to add ncs.find_automatically=false

I have run many runs with NCS defined with proper syntax, just to be overwritten by NCS derived automatically by phenix, until I realized what was happening. I have always thought that if I define the NCS restraints, phenix should follow it, not try to "improve" upon it. What is the reason for this default behavior?

Engin

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Dear Ralf, Many thanks. This is now working. Regards... Raja ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" Date: Monday, May 18, 2009 3:14 pm Subject: Re: [phenixbb] ncs restraint To: [email protected]

Could you try this?

refinement.ncs.restraint_group { reference = chain I and not (resid 18 or resid 61 or resid 63 or resid 64 or resid 82)" selection = chain J and not (resid 18 or resid 61 or resid 63 or resid 64 or resid 82)" }

Or slightly more compact:

refinement.ncs.restraint_group { free_residues = (resid 18 or resid 61 or resid 63 or resid 64 or resid 82) reference = chain I and not $free_residues selection = chain J and not $free_residues }

BTW: You can use the command

phenix.pdb_atom_selection

to try out atom selections (to check if the syntax is correct and to see the list of selected atoms).

In recent versions of the phenix.refine GUI, you can check the atom selections visually.

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Dear Friends, I have Zn atoms in my pdb file. So, I think I need to run elbow to create the cif otherwise refinement stops. I did the following and got the error as follows: phenix.elbow generate_easy_r4.pdb --do-all ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3 - Nigel W. Moriarty ([email protected]) ------------------------------------------------------------------------------ Random number seed: 664322001 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P No molecule read Use --all-residues to view residues if this is a PDB file Can anyone suggests at this point, what I should do? Thanking you in advance... Raja

Hi Pavel, I enclosed the line below: ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Z I also tried with ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Zn None worked. Raja ----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 26, 2009 12:40 pm Subject: Re: [phenixbb] creating cif for Zn To: PHENIX user mailing list

Hi Raja,

normally phenix.refine should recognize Zn atoms without any problems and you don't need run elbow for this. If it doesn't, that most likely means your PDB file is ill-formatted (for example, no element type defined in 77(?) column). Could you please send me copy of the ATOM line from your PDB file containing Zn so I can tell what is wrong?

Pavel.

On 5/26/09 12:31 PM, Raja Dey wrote:

...

Dear Friends, I have Zn atoms in my pdb file. So, I think I need to run elbow to create the cif otherwise refinement stops. I did the following and got the error as follows:

phenix.elbow generate_easy_r4.pdb --do-all

-----------------------------------------------------------------

---

...

electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3 - Nigel W. Moriarty ([email protected]) -----------------------------------------------------------------

---

...

Random number seed: 664322001 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing

Parsing Parsing P

...

No molecule read

Use --all-residues to view residues if this is a PDB file

Can anyone suggests at this point, what I should do? Thanking you in advance...

Raja

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Hi Pavel, Thanks for your mail. Sorry, It was my mistake. I fixed that. By the by, one more question. I want to create Fo(native protein)-Fo(native protein + drug) map in phenix using the phase calculated from the refined structure of native protein to see if the density for the drug can pop up. Can you tell me how I can do that? I am now using version phenix-1.4-3. Do I need to install current version? Thanks... Raja ----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 26, 2009 1:58 pm Subject: Re: [phenixbb] creating cif for Zn To: PHENIX user mailing list

Hi Raja,

this should work (the rightmost Zn is shifted one space left as required by PDB format):

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 Zn

let me know if it doesn't.

Pavel.

...

Hi Pavel, I enclosed the line below:

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Z

I also tried with

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 A Zn

None worked.

Raja ----- Original Message ----- From: Pavel Afonine Date: Tuesday, May 26, 2009 12:40 pm Subject: Re: [phenixbb] creating cif for Zn To: PHENIX user mailing list

...

Hi Raja,

normally phenix.refine should recognize Zn atoms without any problems and you don't need run elbow for this. If it doesn't, that most likely means your PDB file is ill-formatted (for example, no element type defined in 77(?) column). Could you please send me copy of the ATOM line from your PDB file containing Zn so I can tell what is wrong?

Pavel.

On 5/26/09 12:31 PM, Raja Dey wrote:

...

Dear Friends, I have Zn atoms in my pdb file. So, I

On 5/26/09 1:52 PM, Raja Dey wrote: think

...

...

...

I need to run elbow to create the cif otherwise refinement stops.

...

I did the following and got the error as follows:

phenix.elbow generate_easy_r4.pdb --do-all

--------------------------------------------------------------- --

-------------

...

electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3 - Nigel W. Moriarty ([email protected]) --------------------------------------------------------------- --

-------------

...

Random number seed: 664322001 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing

Parsing Parsing P

...

No molecule read

Use --all-residues to view residues if this is a PDB file

Can anyone suggests at this point, what I should do? Thanking you in advance...

Raja

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SPASIBO, stuchatx nado po takim idiotam vrode menya ! Ya delal vtoroj file (s occ=1.0) posle nedelxnogo pereryva i SOVSEM ZABYL zamenitx starting occupancy na 0.5 !! V pervom file'e ya eto sdelal srazu, a vo vtorom - zabyl. Eto vedx i po suti nado, i iz opisaniya ya eto vyuchil - a vot klinch v golove. I esche specialxno glazom smotrel na oba file'a , iskal v nih raznicu - I NE VIDEL !! Izvini za glupyj vopros. Sejchas budu probovatx, dolzhno rabotatx. S

Dear Friends, I was running phenix refinement with the following command: phenix.refine YCd4p4_output.mtz p53_2.1.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls rigid_body_selections.params output.write_maps=true output.prefix=may27_1 --overwrite It ran for a while and then got the following error... Does anyone have idea what's going wrong? Traceback (most recent call last): File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 153, in refinement_machine model.show_groups(rigid_body = True, out = log) File "/usr/local/phenix-1.4-3/mmtbx/model.py", line 709, in show_groups start = i_selection[0] IndexError: Index out of range. Thanks... Raja

Hi everyone, I have a native set to 2.3A resolution and mercury MAD data in a different space group to 3.3A resolution (anomalous signal to 4.2A). How I can use autosol with the data I have. There is no such example. (Native +MAD)? What is the best strategy in this case? Maia

Hi Tom, thank you for your reply. How can I build a model at this resolution 3.3A (anomalous signal 4.2A). Actually, that was my major question. Is it possible to build a model at this resolution? Or how else I can use the phases from the low resolution solution (if I get it) with the high resolution native data? I did not see such a combination in the examples. Maia Thomas C. Terwilliger wrote:

Hi Maia,

As your datasets are in 2 different space groups, you pretty much have to solve the structure in one space group, then transfer information about the structure (model) to the other space group.

So...you want to run an autosol run with the MAD data (or as SAD, sometimes that works better if you have a lot of decay) to solve the structure...then you want to build a model if you can in that space group.

Then you have to figure out where that model goes in the high-res crystal...you'll use phenix.automr with your model from the low-res crystal to do that.

Then you can do cross-crystal averaging with phenix.multi_crystal average to improve the phases (optional). You can also just rebuild the model in the high-res crystal form and you may be done.

Good luck! All the best, -Tom T

...

...

Hi everyone,

I have a native set to 2.3A resolution and mercury MAD data in a different space group to 3.3A resolution (anomalous signal to 4.2A).

How I can use autosol with the data I have. There is no such example. (Native +MAD)? What is the best strategy in this case?

Maia

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Thanks Tom, Miguel, for your help. I would like you to know that the older version of phenix (1.4-3) works, but the newer versions 1.4-4 and 1.4-58 don't recognize some key words. The error message is Sorry, unknown file or keyword: peak.data=peak1_p6422.sca Maia Miguel Ortiz Lombardia wrote:

Hi Maia,

If your phases are good enough I think resolve should be able to build at least a good partial model. Otherwise, you can build it manually... Your resolution isn't great, but you may be able to place some secondary structure elements (ARP/wARP 'Quick fold' can also come to help here).

Perhaps another option is to solve your native dataset by molecular replacement using the best map you have from the MAD dataset, then you wouldn't need to build a model in the low resolution MAD data. Molrep and AMoRe can do that, probably Phaser can as well.

Good luck,

Miguel

Le 28 mai 09 à 06:12, Maia Cherney a écrit :

...

Hi Tom, thank you for your reply. How can I build a model at this resolution 3.3A (anomalous signal 4.2A). Actually, that was my major question. Is it possible to build a model at this resolution? Or how else I can use the phases from the low resolution solution (if I get it) with the high resolution native data?

I did not see such a combination in the examples.

Maia

Thomas C. Terwilliger wrote:

...

Hi Maia,

As your datasets are in 2 different space groups, you pretty much have to solve the structure in one space group, then transfer information about the structure (model) to the other space group.

So...you want to run an autosol run with the MAD data (or as SAD, sometimes that works better if you have a lot of decay) to solve the structure...then you want to build a model if you can in that space group.

Then you have to figure out where that model goes in the high-res crystal...you'll use phenix.automr with your model from the low-res crystal to do that.

Then you can do cross-crystal averaging with phenix.multi_crystal average to improve the phases (optional). You can also just rebuild the model in the high-res crystal form and you may be done.

Good luck! All the best, -Tom T

...

...

Hi everyone,

I have a native set to 2.3A resolution and mercury MAD data in a different space group to 3.3A resolution (anomalous signal to 4.2A).

How I can use autosol with the data I have. There is no such example. (Native +MAD)? What is the best strategy in this case?

Maia

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-- Miguel Ortiz Lombardía Architecture et Fonction des Macromolécules Biologiques UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée ) Case 932 163 Avenue de Luminy 13288 Marseille cedex 9 France Tel : +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: [email protected] Web: http://www.pangea.org/mol/spip.php?rubrique2

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Hi Maia, Some keywords have changed between 1.4-3 and the current versions. I think you'll like the current ones much better. To see all the current keywords, say: phenix.doc and select "Automated Structure Solution using AutoSol" and and then click on "List of all AutoSol keywords" The keywords for MAD now are entered as a little parameters file: autosol { seq_file = seq.dat sites = 2 atom_type = Se wavelength { data = peak.sca lambda = .9798 f_prime = -8.0 f_double_prime = 4.5 } wavelength { data = inf.sca lambda = .9792 f_prime = -9.0 f_double_prime = 1.5 } You can do that for SAD too, or just say phenix.autosol data=peak.sca ha_type=Br sites=6 seq_file=seq.dat If you have a heavy atom like Br where you really don't know how many sites there are, you can just guess. For SAD phasing, Phaser will put in however many sites it can find whatever you say. For MAD phasing, SOLVE will put in just the number of sites you ask for. I would guess a number about 1/20 the number of residues in the protein as a starting point. All the best, Tom T

...

Hi Tom,

how do I determine the number of heavy sites? I gave 2 as in your example, but it can be more. Should I try several different numbers?

Maia

Maia Cherney wrote:

...

Thanks Tom, Miguel, for your help.

I would like you to know that the older version of phenix (1.4-3) works, but the newer versions 1.4-4 and 1.4-58 don't recognize some key words. The error message is

Sorry, unknown file or keyword: peak.data=peak1_p6422.sca

Maia

Miguel Ortiz Lombardia wrote:

...

Hi Maia,

If your phases are good enough I think resolve should be able to build at least a good partial model. Otherwise, you can build it manually... Your resolution isn't great, but you may be able to place some secondary structure elements (ARP/wARP 'Quick fold' can also come to help here).

Perhaps another option is to solve your native dataset by molecular replacement using the best map you have from the MAD dataset, then you wouldn't need to build a model in the low resolution MAD data. Molrep and AMoRe can do that, probably Phaser can as well.

Good luck,

Miguel

Le 28 mai 09 à 06:12, Maia Cherney a écrit :

...

Hi Tom, thank you for your reply. How can I build a model at this resolution 3.3A (anomalous signal 4.2A). Actually, that was my major question. Is it possible to build a model at this resolution? Or how else I can use the phases from the low resolution solution (if I get it) with the high resolution native data?

I did not see such a combination in the examples.

Maia

Thomas C. Terwilliger wrote:

...

Hi Maia,

As your datasets are in 2 different space groups, you pretty much have to solve the structure in one space group, then transfer information about the structure (model) to the other space group.

So...you want to run an autosol run with the MAD data (or as SAD, sometimes that works better if you have a lot of decay) to solve the structure...then you want to build a model if you can in that space group.

Then you have to figure out where that model goes in the high-res crystal...you'll use phenix.automr with your model from the low-res crystal to do that.

Then you can do cross-crystal averaging with phenix.multi_crystal average to improve the phases (optional). You can also just rebuild the model in the high-res crystal form and you may be done.

Good luck! All the best, -Tom T

>> Hi everyone, >> >> I have a native set to 2.3A resolution and mercury MAD data in a >> different space group to 3.3A resolution (anomalous signal to >> 4.2A). >> >> How I can use autosol with the data I have. There is no such >> example. >> (Native +MAD)? What is the best strategy in this case? >> >> Maia >> >> >> _______________________________________________ >> phenixbb mailing list >> [email protected] >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> >> >> _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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On May 26, 2009, at 12:31 PM, Raja Dey wrote:

Dear Friends, I have Zn atoms in my pdb file. So, I think I need to run elbow to create the cif otherwise refinement stops.

Like Pavel said, this isn't necessary - however, if you want to define metal coordination geometry restraints, you can just use the commands phenix.metal_coordination or phenix.ready_set (which combines many functions for preparing PDB files). -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]