Re: [ccp4bb] Structural Alignment

UCSF chimera or chimeraX versions both could do the alignment of multiple structures that also pop up the sequence alignment with secondary structures highlighted in different colors through Match Maker. Up-to six structures I have aligned. Best regards Rajivgandhi Sundaram. On Wed, Apr 8, 2020

Re: [ccp4bb] Structural Alignment

Thank you all, I have done it with chimera. It does structural alignment and use it as a template. Then, you can add sequences one after the other and align to this template. You can save this alignment in clustalw format and load it to ESPrit3 and do a nice picture. Armando > El 8 abr 202

Re: [ccp4bb] Structural Alignment

Hi Armando, The PyMol version of this would involve the 'align' command: https://pymolwiki.org/index.php/Align Import your two structures into a PyMol session. In the command line of PyMol, run "align NameOfStructure1, NameOfStructure2, object=SomeNameYouMadeUp". Next, run "save SomeNameYouMadeUp

Re: [ccp4bb] Structural Alignment

I used STRAP back in the late 2000s to do structure-based sequence alignments of some TonB Dependent transporters: http://www.bioinformatics.org/strap/ Looks like it is still being updated. Cheers, Jim -- Jim Fairman C: 1-240

Re: [ccp4bb] Structural Alignment

Hi Armando, This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ More specifically, its matchmaker command will align two structures and print the corresponding sequence alignment: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmak

[ccp4bb] Structural Alignment

Dear all, I want to align two structures and then, I want to align several sequences to that structural alignment. How can I do this? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jisc

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC

In addition, REFMAC has tightened your model's geometry which can cause a slight increase in the working R. A one percent increase in while in the upper thirties is slight. Dale Tronrud On 4/8/2020 7:30 AM, Schreuder, Herman /DE wrote: > I guess the molecular replacement model has never been

[ccp4bb] Support and Resources for COVID-19 Related Crystallography Research - MiTeGen

Dear CCP4, We have always been proud to be a part of this incredible community, but are now even more so. Thank you to everyone contributing to the massive efforts to combat this epidemic. Given our unique position of having connections at nearly every MX beamline and with a large number of resea

Re: [ccp4bb] Coot 0.9 Released

At the moment I am struggling a bit to have it to compile under WSL2-ubuntu18.04 But the pre release version included in the ccpem nightly 20200327 is working well, it is a bit laggy when showing maps and you end up having to decrease the map radius a bit. but overall it is perfectly usable. The co

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC

I guess the molecular replacement model has never been refined against this data set, so there is no reason why the Rfree should be better or worse than the Rfactor. The difference is larger than I would expect, but it may just be a statistical fluke. That the Rfree goes up significantly during

Re: [ccp4bb] Increase in R-factor following REFMAC

Well - there is something funny about your first Rfree - it shouldnt be significantly lower than R? I suspect there is some muddle over the assignment of Rfree - one used for Phaser and a different value for REFMAC? And of course at low resolution especiall Rfactors are very sensitive to scaling p

[ccp4bb] Increase in R-factor following REFMAC

Hello, I haven't seen this before but doing a round of refinment with REFMAC, after molecular replacement with phaser, my R factor and R free have increased? Also is it weird that my Rfree is smaller than my R factor? Result: Initial Final R factor0.3621 0.3761 R free 0.3108 0.4733

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Average B factors with TLS

This is a very good point. I never was very happy with calculating the average of all B-factors. E.g. if one adds a lot of high-B water molecules, the average B goes up, but with the structure itself nothing changes. Instead of calculating the average B, it would probably better to calculate the

[ccp4bb] Phd and postdoc positions in Structural biology

Hi The Magnus Wolf-Watz lab in Umeå, Sweden has two openings in structural biology: One PhD position directed at human protein kinases and their linkage to human cancer application deadline May 20 One Postdoc in structural biology of silk and cellulose modifying enzymes, application deadline A