where is brute rotation output

newer
Problems placing second component...

older
Phaser problem for flexible domain...

Ursula Schulze-Gahmen

30 Jan 2013 30 Jan '13

10:43 p.m.

Hi, Has anybody experience with the output from the brute rotation function. I ran this and it finished without complaints, but there are no output files ***.rlist or ***.sol in the directory. I cannot figure out why and how to continue now with the translation function. From the log file it seemed that there were peaks that could have been written out. Thanks for any help Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

Attachments:

attachment.html (text/html — 561 bytes)

Show replies by date

Nathaniel Echols

30 Jan 30 Jan

11:09 p.m.

On Wed, Jan 30, 2013 at 2:43 PM, Ursula Schulze-Gahmen wrote:

...

Has anybody experience with the output from the brute rotation function. I ran this and it finished without complaints, but there are no output files ***.rlist or ***.sol in the directory. I cannot figure out why and how to continue now with the translation function. From the log file it seemed that there were peaks that could have been written out.

In Phenix, all of this info (regardless of what mode you ran Phaser in) is stored internally in a result object buried in the tracking directory; there are no additional output files because they're not needed here. If you want to continue to the translation function, you simply select the rotation function job from the "Use previous result" menu, set the mode to translation function, and it will extract the angles from there. Since this isn't at all obvious (and not at all like CCP4i), I will see if I can add a note to the results tab to make it clear how to proceed. -Nat

Ursula Schulze-Gahmen

11:18 p.m.

OK. So in my case there was no file created. Is this because there was no good solution or why? Ursula On Wed, Jan 30, 2013 at 3:09 PM, Nathaniel Echols wrote:

...

...
Has anybody experience with the output from the brute rotation function. I ran this and it finished without complaints, but there are no output files ***.rlist or ***.sol in the directory. I cannot figure out why and how to continue now with the translation function. From the log file it seemed

On Wed, Jan 30, 2013 at 2:43 PM, Ursula Schulze-Gahmen wrote: that

...
there were peaks that could have been written out.

In Phenix, all of this info (regardless of what mode you ran Phaser in) is stored internally in a result object buried in the tracking directory; there are no additional output files because they're not needed here. If you want to continue to the translation function, you simply select the rotation function job from the "Use previous result" menu, set the mode to translation function, and it will extract the angles from there.

Since this isn't at all obvious (and not at all like CCP4i), I will see if I can add a note to the results tab to make it clear how to proceed.

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

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

Nathaniel Echols

11:22 p.m.

On Wed, Jan 30, 2013 at 3:18 PM, Ursula Schulze-Gahmen wrote:

...

OK. So in my case there was no file created. Is this because there was no good solution or why?

No, it's just that the result file isn't created where you expect it, i.e. in the Phaser output directory. (Which I admit is also confusing, since I don't think anything else will end up in the output directory in this case.) The file isn't human-readable anyway; extracting the solution object is handled internally. -Nat

Ursula Schulze-Gahmen

11:27 p.m.

But i don't think it is wherever it should be because if I try to run the translation function giving as input the previous job solution I get an error saying that there are no parameters for the ensemble. So the program doesn't seem to be able to read the output from the previously run rotation function. Ursula On Wed, Jan 30, 2013 at 3:22 PM, Nathaniel Echols wrote:

...

On Wed, Jan 30, 2013 at 3:18 PM, Ursula Schulze-Gahmen wrote:

...
OK. So in my case there was no file created. Is this because there was no good solution or why?

No, it's just that the result file isn't created where you expect it, i.e. in the Phaser output directory. (Which I admit is also confusing, since I don't think anything else will end up in the output directory in this case.) The file isn't human-readable anyway; extracting the solution object is handled internally.

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

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

Nathaniel Echols

11:59 p.m.

On Wed, Jan 30, 2013 at 3:27 PM, Ursula Schulze-Gahmen wrote:

...

But i don't think it is wherever it should be because if I try to run the translation function giving as input the previous job solution I get an error saying that there are no parameters for the ensemble. So the program doesn't seem to be able to read the output from the previously run rotation function.

What is the exact error message? I just ran into something similar when I tried it on one of the tutorial datasets ("INPUT ERROR: No solution sets"), and the reason turned out to be that I didn't actually have the previous solution selected. Once I actually selected it it started running and seems to be fine, if very slow. (I did find three or four other bugs in the current code, but I assume if you got this far you're using version 1.8.1.) -Nat

Ursula Schulze-Gahmen

31 Jan 31 Jan

12:06 a.m.

The message is "No orientations to test for Set #1" I am quite sure I selected the previous solution. Ursula On Wed, Jan 30, 2013 at 3:59 PM, Nathaniel Echols wrote:

...

...
But i don't think it is wherever it should be because if I try to run the translation function giving as input the previous job solution I get an error saying that there are no parameters for the ensemble. So the

On Wed, Jan 30, 2013 at 3:27 PM, Ursula Schulze-Gahmen wrote: program

...
doesn't seem to be able to read the output from the previously run rotation function.

What is the exact error message? I just ran into something similar when I tried it on one of the tutorial datasets ("INPUT ERROR: No solution sets"), and the reason turned out to be that I didn't actually have the previous solution selected. Once I actually selected it it started running and seems to be fine, if very slow. (I did find three or four other bugs in the current code, but I assume if you got this far you're using version 1.8.1.)

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

-- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

Nathaniel Echols

12:15 a.m.

On Wed, Jan 30, 2013 at 4:06 PM, Ursula Schulze-Gahmen wrote:

...

The message is "No orientations to test for Set #1"

I am quite sure I selected the previous solution.

My guess would be either it's a bug, or (less likely) it didn't actually find any solutions but didn't make that obvious. I see very different output in the current code versus the log file you sent me, so it's not clear which is the likely explanation. However, if you can dig through the tracking data, you should find a file like this: $PROJECT/.phenix/project_data/phaser_mr_1.pkl with "1" replaced by the job ID for the brute rotation function search; if you can send me this file off-list I will take a look. (Fortunately it does appear to be possible to extract the keywords for specifying the solution, but you'll have to run Phaser in CCP4i to use it.) I'm hoping the problem is magically solved with the new code, although you'll have to wait at least another 20 hours to use it. -Nat

Williams, John Charles

18 Feb 18 Feb

8:37 p.m.

New subject: WCPCW21

Dear All, The West Coast Protein Crystallography Workshop is coming up fast. Consistent with previous WCPCW meetings, there will be ample discussion of methods, structural analyses and new structures. The keynote speaker will be Wayne Hendrickson. He will be presenting some of his recent work on SAD phasing and its application to important biological problems including membrane proteins. Andy Karplus will also give a talk on his and Kay Diederichs' CC1/2. That said, the focus will be on postdoctoral and predoctoral presentations. The meeting will be held at the Monterey Plaza and Spa, March 17th to 20th and the registration is all-inclusive (e.g., meeting fees, room, board and social hours are included). There is still space available for those who are interested in attending. See www.wcpcw.org or contact me directly. For those who have already registered, please send your abstract asap if you have yet to do so. We need to compile the program, assign speaking slots, etc... Best, John John C. Williams, PhD Assoc. Professor, Dept. of Molecular Medicine, Beckman Research Institute; Co-Director, Drug Discovery and Structural Biology Core, NCI Comprehensive Cancer Center; City of Hope 1710 Flower St., Duarte, CA 91016 (626) 256 4673 (x60227) For messages and meetings: Ariadno Bello, Administrative Assistant [email protected] (626) 256 4673 (x60226) --------------------------------------------------------------------- *SECURITY/CONFIDENTIALITY WARNING: This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (fpc5p) ---------------------------------------------------------------------

4330

Age (days ago)

4349

Last active (days ago)

List overview

Download

8 comments

3 participants

participants (3)

Nathaniel Echols
Ursula Schulze-Gahmen
Williams, John Charles